Starting phenix.real_space_refine on Sat Mar 7 04:14:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7et2_31296/03_2026/7et2_31296.cif Found real_map, /net/cci-nas-00/data/ceres_data/7et2_31296/03_2026/7et2_31296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7et2_31296/03_2026/7et2_31296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7et2_31296/03_2026/7et2_31296.map" model { file = "/net/cci-nas-00/data/ceres_data/7et2_31296/03_2026/7et2_31296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7et2_31296/03_2026/7et2_31296.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 24876 2.51 5 N 6972 2.21 5 O 6888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 269 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38880 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "B" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "C" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "D" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "G" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "J" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "E" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "H" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "K" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "F" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "I" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Chain: "L" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3240 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 2 Time building chain proxies: 8.62, per 1000 atoms: 0.22 Number of scatterers: 38880 At special positions: 0 Unit cell: (167.375, 167.375, 144.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 6888 8.00 N 6972 7.00 C 24876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.9 seconds 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9240 Finding SS restraints... Secondary structure from input PDB file: 248 helices and 44 sheets defined 57.5% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 63 through 70 Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 92 through 106 removed outlier: 4.326A pdb=" N THR A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 120 removed outlier: 4.297A pdb=" N VAL A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 164 removed outlier: 4.204A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 179 removed outlier: 4.350A pdb=" N GLY A 172 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 205 removed outlier: 3.951A pdb=" N GLU A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARG A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 removed outlier: 4.291A pdb=" N ARG A 209 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A 211 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 224 removed outlier: 4.477A pdb=" N GLN A 218 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP A 219 " --> pdb=" O PRO A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 235 removed outlier: 3.560A pdb=" N LEU A 228 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG A 234 " --> pdb=" O GLN A 230 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 235 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 311 removed outlier: 3.713A pdb=" N ASP A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS A 304 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.728A pdb=" N TYR A 492 " --> pdb=" O ALA A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 507 removed outlier: 4.129A pdb=" N ARG A 501 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP A 505 " --> pdb=" O ARG A 501 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 551 removed outlier: 4.084A pdb=" N GLN A 541 " --> pdb=" O ARG A 537 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 548 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG A 549 " --> pdb=" O ASN A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 561 No H-bonds generated for 'chain 'A' and resid 559 through 561' Processing helix chain 'A' and resid 571 through 582 removed outlier: 4.167A pdb=" N LEU A 578 " --> pdb=" O GLU A 574 " (cutoff:3.500A) Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 595 through 600 removed outlier: 3.774A pdb=" N GLN A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 600 " --> pdb=" O ALA A 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 595 through 600' Processing helix chain 'A' and resid 604 through 612 removed outlier: 3.662A pdb=" N ASP A 612 " --> pdb=" O ALA A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 630 removed outlier: 3.802A pdb=" N LEU A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS A 627 " --> pdb=" O CYS A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'B' and resid 65 through 70 Processing helix chain 'B' and resid 80 through 83 Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 92 through 106 removed outlier: 4.293A pdb=" N THR B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 120 removed outlier: 4.070A pdb=" N VAL B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU B 117 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 164 removed outlier: 4.268A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B 164 " --> pdb=" O ASP B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 179 removed outlier: 4.274A pdb=" N GLY B 172 " --> pdb=" O ASN B 168 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 179 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 205 removed outlier: 4.000A pdb=" N GLU B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARG B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 211 removed outlier: 4.223A pdb=" N ARG B 209 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 211 " --> pdb=" O GLN B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 224 through 231 Processing helix chain 'B' and resid 291 through 311 removed outlier: 3.829A pdb=" N ASP B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS B 304 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 310 " --> pdb=" O LYS B 306 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU B 311 " --> pdb=" O ILE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 493 removed outlier: 3.815A pdb=" N TYR B 492 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 507 removed outlier: 3.950A pdb=" N ARG B 501 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG B 504 " --> pdb=" O VAL B 500 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP B 505 " --> pdb=" O ARG B 501 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 551 removed outlier: 4.185A pdb=" N GLN B 541 " --> pdb=" O ARG B 537 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN B 545 " --> pdb=" O GLN B 541 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ARG B 549 " --> pdb=" O ASN B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 562 removed outlier: 3.886A pdb=" N ALA B 562 " --> pdb=" O HIS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 584 removed outlier: 4.184A pdb=" N LEU B 578 " --> pdb=" O GLU B 574 " (cutoff:3.500A) Proline residue: B 579 - end of helix Processing helix chain 'B' and resid 595 through 600 removed outlier: 3.598A pdb=" N GLN B 599 " --> pdb=" O GLU B 595 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 600 " --> pdb=" O ALA B 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 595 through 600' Processing helix chain 'B' and resid 604 through 611 Processing helix chain 'B' and resid 615 through 630 removed outlier: 3.900A pdb=" N LEU B 621 " --> pdb=" O ARG B 617 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS B 627 " --> pdb=" O CYS B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 635 Processing helix chain 'C' and resid 63 through 70 Processing helix chain 'C' and resid 80 through 83 Processing helix chain 'C' and resid 84 through 89 Processing helix chain 'C' and resid 92 through 106 removed outlier: 4.311A pdb=" N THR C 104 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 120 removed outlier: 4.154A pdb=" N VAL C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU C 116 " --> pdb=" O ARG C 112 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU C 117 " --> pdb=" O ARG C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 164 removed outlier: 4.174A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 155 " --> pdb=" O GLN C 151 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP C 160 " --> pdb=" O GLY C 156 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE C 161 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN C 164 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 179 removed outlier: 4.302A pdb=" N GLY C 172 " --> pdb=" O ASN C 168 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL C 179 " --> pdb=" O VAL C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 205 removed outlier: 3.930A pdb=" N GLU C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 removed outlier: 4.218A pdb=" N ARG C 209 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.696A pdb=" N LEU C 228 " --> pdb=" O ASN C 224 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 311 removed outlier: 3.841A pdb=" N ASP C 299 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS C 304 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU C 311 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 493 removed outlier: 3.801A pdb=" N TYR C 492 " --> pdb=" O ALA C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 507 removed outlier: 3.920A pdb=" N ARG C 501 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 504 " --> pdb=" O VAL C 500 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP C 505 " --> pdb=" O ARG C 501 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA C 507 " --> pdb=" O ALA C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 551 removed outlier: 3.536A pdb=" N GLU C 536 " --> pdb=" O THR C 532 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG C 537 " --> pdb=" O GLU C 533 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE C 538 " --> pdb=" O SER C 534 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN C 541 " --> pdb=" O ARG C 537 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN C 545 " --> pdb=" O GLN C 541 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ARG C 549 " --> pdb=" O ASN C 545 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE C 551 " --> pdb=" O TYR C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 561 No H-bonds generated for 'chain 'C' and resid 559 through 561' Processing helix chain 'C' and resid 569 through 584 removed outlier: 3.931A pdb=" N VAL C 573 " --> pdb=" O SER C 569 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU C 574 " --> pdb=" O ASN C 570 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU C 578 " --> pdb=" O GLU C 574 " (cutoff:3.500A) Proline residue: C 579 - end of helix removed outlier: 3.511A pdb=" N HIS C 583 " --> pdb=" O PRO C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 600 removed outlier: 3.793A pdb=" N GLN C 599 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 600 " --> pdb=" O ALA C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 613 removed outlier: 4.353A pdb=" N ALA C 607 " --> pdb=" O GLY C 603 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 630 removed outlier: 3.845A pdb=" N LEU C 621 " --> pdb=" O ARG C 617 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS C 627 " --> pdb=" O CYS C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 635 Processing helix chain 'D' and resid 63 through 70 Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 92 through 106 removed outlier: 4.326A pdb=" N THR D 104 " --> pdb=" O GLY D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 120 removed outlier: 4.297A pdb=" N VAL D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU D 116 " --> pdb=" O ARG D 112 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU D 117 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 164 removed outlier: 4.204A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA D 157 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 179 removed outlier: 4.345A pdb=" N GLY D 172 " --> pdb=" O ASN D 168 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR D 174 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL D 179 " --> pdb=" O VAL D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 205 removed outlier: 3.964A pdb=" N GLU D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ARG D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG D 204 " --> pdb=" O ALA D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 211 removed outlier: 4.294A pdb=" N ARG D 209 " --> pdb=" O ALA D 206 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR D 211 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 224 removed outlier: 4.475A pdb=" N GLN D 218 " --> pdb=" O HIS D 214 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP D 219 " --> pdb=" O PRO D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 235 removed outlier: 3.561A pdb=" N LEU D 228 " --> pdb=" O ASN D 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG D 234 " --> pdb=" O GLN D 230 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 311 removed outlier: 3.711A pdb=" N ASP D 299 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N HIS D 304 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D 311 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 493 removed outlier: 3.727A pdb=" N TYR D 492 " --> pdb=" O ALA D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 507 removed outlier: 4.129A pdb=" N ARG D 501 " --> pdb=" O LEU D 497 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG D 504 " --> pdb=" O VAL D 500 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP D 505 " --> pdb=" O ARG D 501 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA D 507 " --> pdb=" O ALA D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 551 removed outlier: 4.085A pdb=" N GLN D 541 " --> pdb=" O ARG D 537 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN D 545 " --> pdb=" O GLN D 541 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE D 548 " --> pdb=" O GLU D 544 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG D 549 " --> pdb=" O ASN D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 561 No H-bonds generated for 'chain 'D' and resid 559 through 561' Processing helix chain 'D' and resid 571 through 582 removed outlier: 4.213A pdb=" N LEU D 578 " --> pdb=" O GLU D 574 " (cutoff:3.500A) Proline residue: D 579 - end of helix Processing helix chain 'D' and resid 595 through 600 removed outlier: 3.704A pdb=" N GLN D 599 " --> pdb=" O GLU D 595 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 600 " --> pdb=" O ALA D 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 595 through 600' Processing helix chain 'D' and resid 604 through 612 removed outlier: 3.661A pdb=" N ASP D 612 " --> pdb=" O ALA D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 630 removed outlier: 3.794A pdb=" N LEU D 621 " --> pdb=" O ARG D 617 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS D 627 " --> pdb=" O CYS D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 635 Processing helix chain 'G' and resid 63 through 70 Processing helix chain 'G' and resid 80 through 83 Processing helix chain 'G' and resid 84 through 89 Processing helix chain 'G' and resid 92 through 106 removed outlier: 4.293A pdb=" N THR G 104 " --> pdb=" O GLY G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 120 removed outlier: 4.069A pdb=" N VAL G 114 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU G 116 " --> pdb=" O ARG G 112 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU G 117 " --> pdb=" O ARG G 113 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP G 118 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 164 removed outlier: 4.268A pdb=" N ALA G 144 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU G 155 " --> pdb=" O GLN G 151 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA G 157 " --> pdb=" O GLY G 153 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP G 160 " --> pdb=" O GLY G 156 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE G 161 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU G 162 " --> pdb=" O LEU G 158 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN G 164 " --> pdb=" O ASP G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 179 removed outlier: 4.274A pdb=" N GLY G 172 " --> pdb=" O ASN G 168 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR G 174 " --> pdb=" O ASP G 170 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL G 179 " --> pdb=" O VAL G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 205 removed outlier: 3.999A pdb=" N GLU G 198 " --> pdb=" O SER G 194 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG G 199 " --> pdb=" O GLU G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 211 removed outlier: 4.223A pdb=" N ARG G 209 " --> pdb=" O ALA G 206 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR G 211 " --> pdb=" O GLN G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 224 Processing helix chain 'G' and resid 224 through 231 Processing helix chain 'G' and resid 291 through 311 removed outlier: 3.833A pdb=" N ASP G 299 " --> pdb=" O ILE G 295 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS G 304 " --> pdb=" O GLY G 300 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU G 310 " --> pdb=" O LYS G 306 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU G 311 " --> pdb=" O ILE G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 489 through 493 removed outlier: 3.815A pdb=" N TYR G 492 " --> pdb=" O ALA G 489 " (cutoff:3.500A) Processing helix chain 'G' and resid 495 through 507 removed outlier: 3.952A pdb=" N ARG G 501 " --> pdb=" O LEU G 497 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG G 504 " --> pdb=" O VAL G 500 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP G 505 " --> pdb=" O ARG G 501 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA G 507 " --> pdb=" O ALA G 503 " (cutoff:3.500A) Processing helix chain 'G' and resid 532 through 551 removed outlier: 3.913A pdb=" N GLU G 536 " --> pdb=" O THR G 532 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG G 537 " --> pdb=" O GLU G 533 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE G 538 " --> pdb=" O SER G 534 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN G 541 " --> pdb=" O ARG G 537 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN G 545 " --> pdb=" O GLN G 541 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ARG G 549 " --> pdb=" O ASN G 545 " (cutoff:3.500A) Processing helix chain 'G' and resid 558 through 562 removed outlier: 3.887A pdb=" N ALA G 562 " --> pdb=" O HIS G 559 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 584 removed outlier: 4.173A pdb=" N LEU G 578 " --> pdb=" O GLU G 574 " (cutoff:3.500A) Proline residue: G 579 - end of helix Processing helix chain 'G' and resid 595 through 600 removed outlier: 3.595A pdb=" N GLN G 599 " --> pdb=" O GLU G 595 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU G 600 " --> pdb=" O ALA G 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 595 through 600' Processing helix chain 'G' and resid 604 through 611 Processing helix chain 'G' and resid 615 through 630 removed outlier: 3.901A pdb=" N LEU G 621 " --> pdb=" O ARG G 617 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS G 627 " --> pdb=" O CYS G 623 " (cutoff:3.500A) Processing helix chain 'G' and resid 631 through 635 Processing helix chain 'J' and resid 63 through 70 Processing helix chain 'J' and resid 80 through 83 Processing helix chain 'J' and resid 84 through 89 Processing helix chain 'J' and resid 92 through 106 removed outlier: 4.313A pdb=" N THR J 104 " --> pdb=" O GLY J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 120 removed outlier: 4.154A pdb=" N VAL J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU J 116 " --> pdb=" O ARG J 112 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU J 117 " --> pdb=" O ARG J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 164 removed outlier: 4.172A pdb=" N ALA J 144 " --> pdb=" O LEU J 140 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER J 149 " --> pdb=" O SER J 145 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU J 155 " --> pdb=" O GLN J 151 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA J 157 " --> pdb=" O GLY J 153 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP J 160 " --> pdb=" O GLY J 156 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE J 161 " --> pdb=" O ALA J 157 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU J 162 " --> pdb=" O LEU J 158 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN J 164 " --> pdb=" O ASP J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 179 removed outlier: 4.298A pdb=" N GLY J 172 " --> pdb=" O ASN J 168 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR J 174 " --> pdb=" O ASP J 170 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL J 179 " --> pdb=" O VAL J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 192 through 205 removed outlier: 3.931A pdb=" N GLU J 198 " --> pdb=" O SER J 194 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG J 199 " --> pdb=" O GLU J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 211 removed outlier: 4.218A pdb=" N ARG J 209 " --> pdb=" O ALA J 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 224 Processing helix chain 'J' and resid 224 through 232 removed outlier: 3.692A pdb=" N LEU J 228 " --> pdb=" O ASN J 224 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA J 232 " --> pdb=" O LEU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 291 through 311 removed outlier: 3.842A pdb=" N ASP J 299 " --> pdb=" O ILE J 295 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N HIS J 304 " --> pdb=" O GLY J 300 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU J 311 " --> pdb=" O ILE J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 489 through 493 removed outlier: 3.801A pdb=" N TYR J 492 " --> pdb=" O ALA J 489 " (cutoff:3.500A) Processing helix chain 'J' and resid 495 through 507 removed outlier: 3.919A pdb=" N ARG J 501 " --> pdb=" O LEU J 497 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG J 504 " --> pdb=" O VAL J 500 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP J 505 " --> pdb=" O ARG J 501 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA J 507 " --> pdb=" O ALA J 503 " (cutoff:3.500A) Processing helix chain 'J' and resid 532 through 551 removed outlier: 3.535A pdb=" N GLU J 536 " --> pdb=" O THR J 532 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG J 537 " --> pdb=" O GLU J 533 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE J 538 " --> pdb=" O SER J 534 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN J 541 " --> pdb=" O ARG J 537 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN J 545 " --> pdb=" O GLN J 541 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ARG J 549 " --> pdb=" O ASN J 545 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE J 551 " --> pdb=" O TYR J 547 " (cutoff:3.500A) Processing helix chain 'J' and resid 559 through 561 No H-bonds generated for 'chain 'J' and resid 559 through 561' Processing helix chain 'J' and resid 569 through 584 removed outlier: 3.899A pdb=" N VAL J 573 " --> pdb=" O SER J 569 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU J 574 " --> pdb=" O ASN J 570 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU J 578 " --> pdb=" O GLU J 574 " (cutoff:3.500A) Proline residue: J 579 - end of helix removed outlier: 3.512A pdb=" N HIS J 583 " --> pdb=" O PRO J 579 " (cutoff:3.500A) Processing helix chain 'J' and resid 594 through 600 removed outlier: 3.797A pdb=" N GLN J 599 " --> pdb=" O GLU J 595 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU J 600 " --> pdb=" O ALA J 596 " (cutoff:3.500A) Processing helix chain 'J' and resid 603 through 613 removed outlier: 4.350A pdb=" N ALA J 607 " --> pdb=" O GLY J 603 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP J 612 " --> pdb=" O ALA J 608 " (cutoff:3.500A) Processing helix chain 'J' and resid 615 through 630 removed outlier: 3.844A pdb=" N LEU J 621 " --> pdb=" O ARG J 617 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS J 627 " --> pdb=" O CYS J 623 " (cutoff:3.500A) Processing helix chain 'J' and resid 631 through 635 Processing helix chain 'E' and resid 63 through 70 Processing helix chain 'E' and resid 84 through 89 Processing helix chain 'E' and resid 92 through 106 removed outlier: 4.326A pdb=" N THR E 104 " --> pdb=" O GLY E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 120 removed outlier: 4.297A pdb=" N VAL E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU E 116 " --> pdb=" O ARG E 112 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU E 117 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 164 removed outlier: 4.204A pdb=" N ALA E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU E 155 " --> pdb=" O GLN E 151 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP E 160 " --> pdb=" O GLY E 156 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE E 161 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 179 removed outlier: 4.348A pdb=" N GLY E 172 " --> pdb=" O ASN E 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR E 174 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL E 179 " --> pdb=" O VAL E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 205 removed outlier: 3.962A pdb=" N GLU E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ARG E 199 " --> pdb=" O GLU E 195 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG E 204 " --> pdb=" O ALA E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 211 removed outlier: 4.294A pdb=" N ARG E 209 " --> pdb=" O ALA E 206 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR E 211 " --> pdb=" O GLN E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 224 removed outlier: 4.475A pdb=" N GLN E 218 " --> pdb=" O HIS E 214 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP E 219 " --> pdb=" O PRO E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 235 removed outlier: 3.561A pdb=" N LEU E 228 " --> pdb=" O ASN E 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA E 232 " --> pdb=" O LEU E 228 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG E 234 " --> pdb=" O GLN E 230 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU E 235 " --> pdb=" O VAL E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 311 removed outlier: 3.714A pdb=" N ASP E 299 " --> pdb=" O ILE E 295 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS E 304 " --> pdb=" O GLY E 300 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU E 311 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 493 removed outlier: 3.728A pdb=" N TYR E 492 " --> pdb=" O ALA E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 507 removed outlier: 4.128A pdb=" N ARG E 501 " --> pdb=" O LEU E 497 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG E 504 " --> pdb=" O VAL E 500 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP E 505 " --> pdb=" O ARG E 501 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA E 507 " --> pdb=" O ALA E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 551 removed outlier: 4.083A pdb=" N GLN E 541 " --> pdb=" O ARG E 537 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN E 545 " --> pdb=" O GLN E 541 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE E 548 " --> pdb=" O GLU E 544 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG E 549 " --> pdb=" O ASN E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 561 No H-bonds generated for 'chain 'E' and resid 559 through 561' Processing helix chain 'E' and resid 571 through 582 removed outlier: 4.210A pdb=" N LEU E 578 " --> pdb=" O GLU E 574 " (cutoff:3.500A) Proline residue: E 579 - end of helix Processing helix chain 'E' and resid 595 through 600 removed outlier: 3.773A pdb=" N GLN E 599 " --> pdb=" O GLU E 595 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU E 600 " --> pdb=" O ALA E 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 595 through 600' Processing helix chain 'E' and resid 604 through 612 removed outlier: 3.662A pdb=" N ASP E 612 " --> pdb=" O ALA E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 630 removed outlier: 3.801A pdb=" N LEU E 621 " --> pdb=" O ARG E 617 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS E 627 " --> pdb=" O CYS E 623 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 635 Processing helix chain 'H' and resid 65 through 70 Processing helix chain 'H' and resid 80 through 83 Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'H' and resid 92 through 106 removed outlier: 4.296A pdb=" N THR H 104 " --> pdb=" O GLY H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 120 removed outlier: 4.069A pdb=" N VAL H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU H 116 " --> pdb=" O ARG H 112 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP H 118 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 164 removed outlier: 4.269A pdb=" N ALA H 144 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU H 155 " --> pdb=" O GLN H 151 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA H 157 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP H 160 " --> pdb=" O GLY H 156 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE H 161 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU H 162 " --> pdb=" O LEU H 158 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN H 164 " --> pdb=" O ASP H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 179 removed outlier: 4.280A pdb=" N GLY H 172 " --> pdb=" O ASN H 168 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR H 174 " --> pdb=" O ASP H 170 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL H 179 " --> pdb=" O VAL H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 205 removed outlier: 4.002A pdb=" N GLU H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG H 199 " --> pdb=" O GLU H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 211 removed outlier: 4.223A pdb=" N ARG H 209 " --> pdb=" O ALA H 206 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 211 " --> pdb=" O GLN H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 224 Processing helix chain 'H' and resid 224 through 231 Processing helix chain 'H' and resid 291 through 311 removed outlier: 3.835A pdb=" N ASP H 299 " --> pdb=" O ILE H 295 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N HIS H 304 " --> pdb=" O GLY H 300 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU H 310 " --> pdb=" O LYS H 306 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU H 311 " --> pdb=" O ILE H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 489 through 493 removed outlier: 3.815A pdb=" N TYR H 492 " --> pdb=" O ALA H 489 " (cutoff:3.500A) Processing helix chain 'H' and resid 495 through 507 removed outlier: 3.952A pdb=" N ARG H 501 " --> pdb=" O LEU H 497 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG H 504 " --> pdb=" O VAL H 500 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP H 505 " --> pdb=" O ARG H 501 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA H 507 " --> pdb=" O ALA H 503 " (cutoff:3.500A) Processing helix chain 'H' and resid 535 through 551 removed outlier: 4.185A pdb=" N GLN H 541 " --> pdb=" O ARG H 537 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN H 545 " --> pdb=" O GLN H 541 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ARG H 549 " --> pdb=" O ASN H 545 " (cutoff:3.500A) Processing helix chain 'H' and resid 558 through 562 removed outlier: 3.892A pdb=" N ALA H 562 " --> pdb=" O HIS H 559 " (cutoff:3.500A) Processing helix chain 'H' and resid 571 through 584 removed outlier: 4.173A pdb=" N LEU H 578 " --> pdb=" O GLU H 574 " (cutoff:3.500A) Proline residue: H 579 - end of helix Processing helix chain 'H' and resid 595 through 600 removed outlier: 3.599A pdb=" N GLN H 599 " --> pdb=" O GLU H 595 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU H 600 " --> pdb=" O ALA H 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 595 through 600' Processing helix chain 'H' and resid 604 through 611 Processing helix chain 'H' and resid 615 through 630 removed outlier: 3.900A pdb=" N LEU H 621 " --> pdb=" O ARG H 617 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS H 627 " --> pdb=" O CYS H 623 " (cutoff:3.500A) Processing helix chain 'H' and resid 631 through 635 Processing helix chain 'K' and resid 63 through 70 Processing helix chain 'K' and resid 80 through 83 Processing helix chain 'K' and resid 84 through 89 Processing helix chain 'K' and resid 92 through 106 removed outlier: 4.295A pdb=" N THR K 104 " --> pdb=" O GLY K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 120 removed outlier: 4.154A pdb=" N VAL K 114 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU K 116 " --> pdb=" O ARG K 112 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU K 117 " --> pdb=" O ARG K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 164 removed outlier: 4.173A pdb=" N ALA K 144 " --> pdb=" O LEU K 140 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER K 149 " --> pdb=" O SER K 145 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU K 155 " --> pdb=" O GLN K 151 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA K 157 " --> pdb=" O GLY K 153 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP K 160 " --> pdb=" O GLY K 156 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE K 161 " --> pdb=" O ALA K 157 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU K 162 " --> pdb=" O LEU K 158 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN K 164 " --> pdb=" O ASP K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 179 removed outlier: 4.301A pdb=" N GLY K 172 " --> pdb=" O ASN K 168 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR K 174 " --> pdb=" O ASP K 170 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL K 179 " --> pdb=" O VAL K 175 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 205 removed outlier: 3.929A pdb=" N GLU K 198 " --> pdb=" O SER K 194 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG K 199 " --> pdb=" O GLU K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 211 removed outlier: 4.218A pdb=" N ARG K 209 " --> pdb=" O ALA K 206 " (cutoff:3.500A) Processing helix chain 'K' and resid 216 through 224 Processing helix chain 'K' and resid 224 through 232 removed outlier: 3.693A pdb=" N LEU K 228 " --> pdb=" O ASN K 224 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA K 232 " --> pdb=" O LEU K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 311 removed outlier: 3.845A pdb=" N ASP K 299 " --> pdb=" O ILE K 295 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N HIS K 304 " --> pdb=" O GLY K 300 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU K 311 " --> pdb=" O ILE K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 489 through 493 removed outlier: 3.800A pdb=" N TYR K 492 " --> pdb=" O ALA K 489 " (cutoff:3.500A) Processing helix chain 'K' and resid 495 through 507 removed outlier: 3.917A pdb=" N ARG K 501 " --> pdb=" O LEU K 497 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG K 504 " --> pdb=" O VAL K 500 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP K 505 " --> pdb=" O ARG K 501 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA K 507 " --> pdb=" O ALA K 503 " (cutoff:3.500A) Processing helix chain 'K' and resid 532 through 551 removed outlier: 3.535A pdb=" N GLU K 536 " --> pdb=" O THR K 532 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG K 537 " --> pdb=" O GLU K 533 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N PHE K 538 " --> pdb=" O SER K 534 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN K 541 " --> pdb=" O ARG K 537 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN K 545 " --> pdb=" O GLN K 541 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ARG K 549 " --> pdb=" O ASN K 545 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE K 551 " --> pdb=" O TYR K 547 " (cutoff:3.500A) Processing helix chain 'K' and resid 559 through 561 No H-bonds generated for 'chain 'K' and resid 559 through 561' Processing helix chain 'K' and resid 569 through 584 removed outlier: 3.933A pdb=" N VAL K 573 " --> pdb=" O SER K 569 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU K 574 " --> pdb=" O ASN K 570 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU K 578 " --> pdb=" O GLU K 574 " (cutoff:3.500A) Proline residue: K 579 - end of helix removed outlier: 3.513A pdb=" N HIS K 583 " --> pdb=" O PRO K 579 " (cutoff:3.500A) Processing helix chain 'K' and resid 594 through 600 removed outlier: 3.797A pdb=" N GLN K 599 " --> pdb=" O GLU K 595 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU K 600 " --> pdb=" O ALA K 596 " (cutoff:3.500A) Processing helix chain 'K' and resid 603 through 613 removed outlier: 4.350A pdb=" N ALA K 607 " --> pdb=" O GLY K 603 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP K 612 " --> pdb=" O ALA K 608 " (cutoff:3.500A) Processing helix chain 'K' and resid 615 through 630 removed outlier: 3.844A pdb=" N LEU K 621 " --> pdb=" O ARG K 617 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS K 627 " --> pdb=" O CYS K 623 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 635 Processing helix chain 'F' and resid 63 through 70 Processing helix chain 'F' and resid 84 through 89 Processing helix chain 'F' and resid 92 through 106 removed outlier: 4.326A pdb=" N THR F 104 " --> pdb=" O GLY F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 120 removed outlier: 4.297A pdb=" N VAL F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU F 116 " --> pdb=" O ARG F 112 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP F 118 " --> pdb=" O VAL F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 164 removed outlier: 4.204A pdb=" N ALA F 144 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 155 " --> pdb=" O GLN F 151 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA F 157 " --> pdb=" O GLY F 153 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP F 160 " --> pdb=" O GLY F 156 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE F 161 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU F 162 " --> pdb=" O LEU F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 179 removed outlier: 4.351A pdb=" N GLY F 172 " --> pdb=" O ASN F 168 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR F 174 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL F 179 " --> pdb=" O VAL F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 205 removed outlier: 3.951A pdb=" N GLU F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARG F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 211 removed outlier: 4.291A pdb=" N ARG F 209 " --> pdb=" O ALA F 206 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR F 211 " --> pdb=" O GLN F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 224 removed outlier: 4.475A pdb=" N GLN F 218 " --> pdb=" O HIS F 214 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP F 219 " --> pdb=" O PRO F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 235 removed outlier: 3.561A pdb=" N LEU F 228 " --> pdb=" O ASN F 224 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU F 233 " --> pdb=" O LEU F 229 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG F 234 " --> pdb=" O GLN F 230 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU F 235 " --> pdb=" O VAL F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 311 removed outlier: 3.710A pdb=" N ASP F 299 " --> pdb=" O ILE F 295 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS F 304 " --> pdb=" O GLY F 300 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU F 311 " --> pdb=" O ILE F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 493 removed outlier: 3.727A pdb=" N TYR F 492 " --> pdb=" O ALA F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 507 removed outlier: 4.129A pdb=" N ARG F 501 " --> pdb=" O LEU F 497 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG F 504 " --> pdb=" O VAL F 500 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP F 505 " --> pdb=" O ARG F 501 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA F 507 " --> pdb=" O ALA F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 551 removed outlier: 4.076A pdb=" N GLN F 541 " --> pdb=" O ARG F 537 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN F 545 " --> pdb=" O GLN F 541 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE F 548 " --> pdb=" O GLU F 544 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ARG F 549 " --> pdb=" O ASN F 545 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE F 551 " --> pdb=" O TYR F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 561 No H-bonds generated for 'chain 'F' and resid 559 through 561' Processing helix chain 'F' and resid 571 through 582 removed outlier: 4.200A pdb=" N LEU F 578 " --> pdb=" O GLU F 574 " (cutoff:3.500A) Proline residue: F 579 - end of helix Processing helix chain 'F' and resid 595 through 600 removed outlier: 3.767A pdb=" N GLN F 599 " --> pdb=" O GLU F 595 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU F 600 " --> pdb=" O ALA F 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 595 through 600' Processing helix chain 'F' and resid 604 through 612 removed outlier: 3.659A pdb=" N ASP F 612 " --> pdb=" O ALA F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 615 through 630 removed outlier: 3.794A pdb=" N LEU F 621 " --> pdb=" O ARG F 617 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS F 627 " --> pdb=" O CYS F 623 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 635 Processing helix chain 'I' and resid 63 through 70 Processing helix chain 'I' and resid 80 through 83 Processing helix chain 'I' and resid 84 through 89 Processing helix chain 'I' and resid 92 through 106 removed outlier: 4.294A pdb=" N THR I 104 " --> pdb=" O GLY I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 120 removed outlier: 4.070A pdb=" N VAL I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU I 116 " --> pdb=" O ARG I 112 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU I 117 " --> pdb=" O ARG I 113 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP I 118 " --> pdb=" O VAL I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 164 removed outlier: 4.268A pdb=" N ALA I 144 " --> pdb=" O LEU I 140 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU I 155 " --> pdb=" O GLN I 151 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA I 157 " --> pdb=" O GLY I 153 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP I 160 " --> pdb=" O GLY I 156 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN I 164 " --> pdb=" O ASP I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 179 removed outlier: 4.275A pdb=" N GLY I 172 " --> pdb=" O ASN I 168 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR I 174 " --> pdb=" O ASP I 170 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL I 179 " --> pdb=" O VAL I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 205 removed outlier: 4.000A pdb=" N GLU I 198 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG I 199 " --> pdb=" O GLU I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 211 removed outlier: 4.223A pdb=" N ARG I 209 " --> pdb=" O ALA I 206 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR I 211 " --> pdb=" O GLN I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 224 Processing helix chain 'I' and resid 224 through 231 Processing helix chain 'I' and resid 291 through 311 removed outlier: 3.836A pdb=" N ASP I 299 " --> pdb=" O ILE I 295 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS I 304 " --> pdb=" O GLY I 300 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU I 310 " --> pdb=" O LYS I 306 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU I 311 " --> pdb=" O ILE I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 489 through 493 removed outlier: 3.815A pdb=" N TYR I 492 " --> pdb=" O ALA I 489 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 507 removed outlier: 3.951A pdb=" N ARG I 501 " --> pdb=" O LEU I 497 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG I 504 " --> pdb=" O VAL I 500 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP I 505 " --> pdb=" O ARG I 501 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA I 507 " --> pdb=" O ALA I 503 " (cutoff:3.500A) Processing helix chain 'I' and resid 532 through 551 removed outlier: 3.915A pdb=" N GLU I 536 " --> pdb=" O THR I 532 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG I 537 " --> pdb=" O GLU I 533 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE I 538 " --> pdb=" O SER I 534 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN I 541 " --> pdb=" O ARG I 537 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN I 545 " --> pdb=" O GLN I 541 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG I 549 " --> pdb=" O ASN I 545 " (cutoff:3.500A) Processing helix chain 'I' and resid 558 through 562 removed outlier: 3.892A pdb=" N ALA I 562 " --> pdb=" O HIS I 559 " (cutoff:3.500A) Processing helix chain 'I' and resid 571 through 584 removed outlier: 4.174A pdb=" N LEU I 578 " --> pdb=" O GLU I 574 " (cutoff:3.500A) Proline residue: I 579 - end of helix Processing helix chain 'I' and resid 595 through 600 removed outlier: 3.598A pdb=" N GLN I 599 " --> pdb=" O GLU I 595 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU I 600 " --> pdb=" O ALA I 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 595 through 600' Processing helix chain 'I' and resid 604 through 611 Processing helix chain 'I' and resid 615 through 630 removed outlier: 3.900A pdb=" N LEU I 621 " --> pdb=" O ARG I 617 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS I 627 " --> pdb=" O CYS I 623 " (cutoff:3.500A) Processing helix chain 'I' and resid 631 through 635 Processing helix chain 'L' and resid 63 through 70 Processing helix chain 'L' and resid 80 through 83 Processing helix chain 'L' and resid 84 through 89 Processing helix chain 'L' and resid 92 through 106 removed outlier: 4.312A pdb=" N THR L 104 " --> pdb=" O GLY L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 120 removed outlier: 4.154A pdb=" N VAL L 114 " --> pdb=" O THR L 110 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU L 116 " --> pdb=" O ARG L 112 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU L 117 " --> pdb=" O ARG L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 164 removed outlier: 4.174A pdb=" N ALA L 144 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER L 149 " --> pdb=" O SER L 145 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU L 155 " --> pdb=" O GLN L 151 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA L 157 " --> pdb=" O GLY L 153 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP L 160 " --> pdb=" O GLY L 156 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE L 161 " --> pdb=" O ALA L 157 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU L 162 " --> pdb=" O LEU L 158 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN L 164 " --> pdb=" O ASP L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 179 removed outlier: 4.295A pdb=" N GLY L 172 " --> pdb=" O ASN L 168 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR L 174 " --> pdb=" O ASP L 170 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL L 179 " --> pdb=" O VAL L 175 " (cutoff:3.500A) Processing helix chain 'L' and resid 192 through 205 removed outlier: 3.928A pdb=" N GLU L 198 " --> pdb=" O SER L 194 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG L 199 " --> pdb=" O GLU L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 211 removed outlier: 4.217A pdb=" N ARG L 209 " --> pdb=" O ALA L 206 " (cutoff:3.500A) Processing helix chain 'L' and resid 216 through 224 Processing helix chain 'L' and resid 224 through 232 removed outlier: 3.690A pdb=" N LEU L 228 " --> pdb=" O ASN L 224 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA L 232 " --> pdb=" O LEU L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 311 removed outlier: 3.840A pdb=" N ASP L 299 " --> pdb=" O ILE L 295 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS L 304 " --> pdb=" O GLY L 300 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU L 311 " --> pdb=" O ILE L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 489 through 493 removed outlier: 3.800A pdb=" N TYR L 492 " --> pdb=" O ALA L 489 " (cutoff:3.500A) Processing helix chain 'L' and resid 495 through 507 removed outlier: 3.920A pdb=" N ARG L 501 " --> pdb=" O LEU L 497 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG L 504 " --> pdb=" O VAL L 500 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP L 505 " --> pdb=" O ARG L 501 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA L 507 " --> pdb=" O ALA L 503 " (cutoff:3.500A) Processing helix chain 'L' and resid 532 through 551 removed outlier: 3.536A pdb=" N GLU L 536 " --> pdb=" O THR L 532 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG L 537 " --> pdb=" O GLU L 533 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE L 538 " --> pdb=" O SER L 534 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN L 541 " --> pdb=" O ARG L 537 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN L 545 " --> pdb=" O GLN L 541 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG L 549 " --> pdb=" O ASN L 545 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE L 551 " --> pdb=" O TYR L 547 " (cutoff:3.500A) Processing helix chain 'L' and resid 559 through 561 No H-bonds generated for 'chain 'L' and resid 559 through 561' Processing helix chain 'L' and resid 569 through 584 removed outlier: 3.930A pdb=" N VAL L 573 " --> pdb=" O SER L 569 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU L 574 " --> pdb=" O ASN L 570 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU L 578 " --> pdb=" O GLU L 574 " (cutoff:3.500A) Proline residue: L 579 - end of helix removed outlier: 3.510A pdb=" N HIS L 583 " --> pdb=" O PRO L 579 " (cutoff:3.500A) Processing helix chain 'L' and resid 594 through 600 removed outlier: 3.795A pdb=" N GLN L 599 " --> pdb=" O GLU L 595 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU L 600 " --> pdb=" O ALA L 596 " (cutoff:3.500A) Processing helix chain 'L' and resid 603 through 613 removed outlier: 4.370A pdb=" N ALA L 607 " --> pdb=" O GLY L 603 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP L 612 " --> pdb=" O ALA L 608 " (cutoff:3.500A) Processing helix chain 'L' and resid 615 through 630 removed outlier: 3.845A pdb=" N LEU L 621 " --> pdb=" O ARG L 617 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS L 627 " --> pdb=" O CYS L 623 " (cutoff:3.500A) Processing helix chain 'L' and resid 631 through 635 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 removed outlier: 3.556A pdb=" N ARG A 247 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 259 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 185 removed outlier: 4.018A pdb=" N VAL A 184 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR A 269 " --> pdb=" O VAL A 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.874A pdb=" N LEU A 512 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 522 through 525 removed outlier: 3.832A pdb=" N LEU L 512 " --> pdb=" O VAL L 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 554 through 557 removed outlier: 4.132A pdb=" N LEU A 556 " --> pdb=" O ALA A 565 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA A 565 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 56 through 57 removed outlier: 3.704A pdb=" N ARG B 247 " --> pdb=" O GLN B 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 183 through 185 removed outlier: 4.087A pdb=" N VAL B 184 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR B 269 " --> pdb=" O VAL B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 512 through 513 removed outlier: 3.846A pdb=" N LEU B 512 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 320 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 317 " --> pdb=" O PHE C 524 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 56 through 57 removed outlier: 3.831A pdb=" N ARG C 247 " --> pdb=" O GLN C 260 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C 259 " --> pdb=" O ILE C 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 183 through 185 removed outlier: 4.132A pdb=" N VAL C 184 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR C 269 " --> pdb=" O VAL C 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 512 through 513 removed outlier: 3.833A pdb=" N LEU C 512 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 554 through 557 removed outlier: 4.125A pdb=" N LEU C 556 " --> pdb=" O ALA C 565 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ALA C 565 " --> pdb=" O LEU C 556 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 56 through 57 removed outlier: 3.560A pdb=" N ARG D 247 " --> pdb=" O GLN D 260 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA D 259 " --> pdb=" O ILE D 266 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 183 through 185 removed outlier: 4.016A pdb=" N VAL D 184 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR D 269 " --> pdb=" O VAL D 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 512 through 513 removed outlier: 3.872A pdb=" N LEU D 512 " --> pdb=" O VAL D 318 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 554 through 557 removed outlier: 4.131A pdb=" N LEU D 556 " --> pdb=" O ALA D 565 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA D 565 " --> pdb=" O LEU D 556 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 56 through 57 removed outlier: 3.696A pdb=" N ARG G 247 " --> pdb=" O GLN G 260 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 183 through 185 removed outlier: 4.088A pdb=" N VAL G 184 " --> pdb=" O TYR G 269 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR G 269 " --> pdb=" O VAL G 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'G' and resid 512 through 513 removed outlier: 3.843A pdb=" N LEU G 512 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR G 320 " --> pdb=" O LEU G 512 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS G 317 " --> pdb=" O PHE J 524 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 56 through 57 removed outlier: 3.831A pdb=" N ARG J 247 " --> pdb=" O GLN J 260 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA J 259 " --> pdb=" O ILE J 266 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 183 through 185 removed outlier: 4.131A pdb=" N VAL J 184 " --> pdb=" O TYR J 269 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR J 269 " --> pdb=" O VAL J 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'J' and resid 512 through 513 removed outlier: 3.834A pdb=" N LEU J 512 " --> pdb=" O VAL J 318 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 554 through 557 removed outlier: 4.124A pdb=" N LEU J 556 " --> pdb=" O ALA J 565 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ALA J 565 " --> pdb=" O LEU J 556 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 56 through 57 removed outlier: 3.559A pdb=" N ARG E 247 " --> pdb=" O GLN E 260 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA E 259 " --> pdb=" O ILE E 266 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 183 through 185 removed outlier: 4.015A pdb=" N VAL E 184 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR E 269 " --> pdb=" O VAL E 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 512 through 513 removed outlier: 3.875A pdb=" N LEU E 512 " --> pdb=" O VAL E 318 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 554 through 557 removed outlier: 4.133A pdb=" N LEU E 556 " --> pdb=" O ALA E 565 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA E 565 " --> pdb=" O LEU E 556 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 56 through 57 removed outlier: 3.699A pdb=" N ARG H 247 " --> pdb=" O GLN H 260 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 183 through 185 removed outlier: 4.087A pdb=" N VAL H 184 " --> pdb=" O TYR H 269 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR H 269 " --> pdb=" O VAL H 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'H' and resid 512 through 513 removed outlier: 3.845A pdb=" N LEU H 512 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR H 320 " --> pdb=" O LEU H 512 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS H 317 " --> pdb=" O PHE K 524 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 56 through 57 removed outlier: 3.832A pdb=" N ARG K 247 " --> pdb=" O GLN K 260 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA K 259 " --> pdb=" O ILE K 266 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 183 through 185 removed outlier: 4.131A pdb=" N VAL K 184 " --> pdb=" O TYR K 269 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR K 269 " --> pdb=" O VAL K 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'K' and resid 512 through 513 removed outlier: 3.832A pdb=" N LEU K 512 " --> pdb=" O VAL K 318 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 554 through 557 removed outlier: 4.127A pdb=" N LEU K 556 " --> pdb=" O ALA K 565 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ALA K 565 " --> pdb=" O LEU K 556 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 56 through 57 removed outlier: 3.559A pdb=" N ARG F 247 " --> pdb=" O GLN F 260 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA F 259 " --> pdb=" O ILE F 266 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 183 through 185 removed outlier: 4.016A pdb=" N VAL F 184 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR F 269 " --> pdb=" O VAL F 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'F' and resid 512 through 513 removed outlier: 3.873A pdb=" N LEU F 512 " --> pdb=" O VAL F 318 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 554 through 557 removed outlier: 3.515A pdb=" N ARG F 554 " --> pdb=" O VAL F 567 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU F 556 " --> pdb=" O ALA F 565 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA F 565 " --> pdb=" O LEU F 556 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 56 through 57 removed outlier: 3.696A pdb=" N ARG I 247 " --> pdb=" O GLN I 260 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 183 through 185 removed outlier: 4.086A pdb=" N VAL I 184 " --> pdb=" O TYR I 269 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR I 269 " --> pdb=" O VAL I 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'I' and resid 512 through 513 removed outlier: 3.845A pdb=" N LEU I 512 " --> pdb=" O VAL I 318 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR I 320 " --> pdb=" O LEU I 512 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS I 317 " --> pdb=" O PHE L 524 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 56 through 57 removed outlier: 3.831A pdb=" N ARG L 247 " --> pdb=" O GLN L 260 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA L 259 " --> pdb=" O ILE L 266 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 183 through 185 removed outlier: 4.129A pdb=" N VAL L 184 " --> pdb=" O TYR L 269 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR L 269 " --> pdb=" O VAL L 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'L' and resid 554 through 557 removed outlier: 4.129A pdb=" N LEU L 556 " --> pdb=" O ALA L 565 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ALA L 565 " --> pdb=" O LEU L 556 " (cutoff:3.500A) 1410 hydrogen bonds defined for protein. 3909 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.10 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12908 1.34 - 1.46: 8259 1.46 - 1.58: 18325 1.58 - 1.70: 0 1.70 - 1.81: 180 Bond restraints: 39672 Sorted by residual: bond pdb=" C PHE D 314 " pdb=" N PRO D 315 " ideal model delta sigma weight residual 1.337 1.314 0.023 1.24e-02 6.50e+03 3.50e+00 bond pdb=" C PHE A 314 " pdb=" N PRO A 315 " ideal model delta sigma weight residual 1.337 1.314 0.023 1.24e-02 6.50e+03 3.50e+00 bond pdb=" C PHE E 314 " pdb=" N PRO E 315 " ideal model delta sigma weight residual 1.337 1.315 0.022 1.24e-02 6.50e+03 3.28e+00 bond pdb=" C PHE F 314 " pdb=" N PRO F 315 " ideal model delta sigma weight residual 1.337 1.315 0.022 1.24e-02 6.50e+03 3.28e+00 bond pdb=" C LEU L 590 " pdb=" N ASP L 591 " ideal model delta sigma weight residual 1.329 1.353 -0.024 1.35e-02 5.49e+03 3.12e+00 ... (remaining 39667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 52512 2.63 - 5.27: 1052 5.27 - 7.90: 144 7.90 - 10.54: 96 10.54 - 13.17: 16 Bond angle restraints: 53820 Sorted by residual: angle pdb=" N VAL L 92 " pdb=" CA VAL L 92 " pdb=" C VAL L 92 " ideal model delta sigma weight residual 112.12 105.21 6.91 8.40e-01 1.42e+00 6.76e+01 angle pdb=" N VAL K 92 " pdb=" CA VAL K 92 " pdb=" C VAL K 92 " ideal model delta sigma weight residual 112.12 105.52 6.60 8.40e-01 1.42e+00 6.18e+01 angle pdb=" N VAL J 92 " pdb=" CA VAL J 92 " pdb=" C VAL J 92 " ideal model delta sigma weight residual 112.12 105.53 6.59 8.40e-01 1.42e+00 6.16e+01 angle pdb=" N VAL C 92 " pdb=" CA VAL C 92 " pdb=" C VAL C 92 " ideal model delta sigma weight residual 112.12 105.54 6.58 8.40e-01 1.42e+00 6.13e+01 angle pdb=" N VAL E 92 " pdb=" CA VAL E 92 " pdb=" C VAL E 92 " ideal model delta sigma weight residual 112.12 105.72 6.40 8.40e-01 1.42e+00 5.80e+01 ... (remaining 53815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 20972 17.98 - 35.97: 2363 35.97 - 53.95: 488 53.95 - 71.94: 105 71.94 - 89.92: 48 Dihedral angle restraints: 23976 sinusoidal: 9756 harmonic: 14220 Sorted by residual: dihedral pdb=" CA LEU B 587 " pdb=" C LEU B 587 " pdb=" N GLY B 588 " pdb=" CA GLY B 588 " ideal model delta harmonic sigma weight residual 180.00 154.21 25.79 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA LEU H 587 " pdb=" C LEU H 587 " pdb=" N GLY H 588 " pdb=" CA GLY H 588 " ideal model delta harmonic sigma weight residual 180.00 154.23 25.77 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA LEU G 587 " pdb=" C LEU G 587 " pdb=" N GLY G 588 " pdb=" CA GLY G 588 " ideal model delta harmonic sigma weight residual 180.00 154.26 25.74 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 23973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4394 0.055 - 0.109: 1342 0.109 - 0.164: 378 0.164 - 0.218: 43 0.218 - 0.273: 11 Chirality restraints: 6168 Sorted by residual: chirality pdb=" CG LEU J 70 " pdb=" CB LEU J 70 " pdb=" CD1 LEU J 70 " pdb=" CD2 LEU J 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CG LEU C 70 " pdb=" CB LEU C 70 " pdb=" CD1 LEU C 70 " pdb=" CD2 LEU C 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CG LEU K 70 " pdb=" CB LEU K 70 " pdb=" CD1 LEU K 70 " pdb=" CD2 LEU K 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 6165 not shown) Planarity restraints: 6888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 286 " -0.054 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO H 287 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO H 287 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO H 287 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 573 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C VAL B 573 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL B 573 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU B 574 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 286 " 0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO B 287 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 287 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 287 " 0.044 5.00e-02 4.00e+02 ... (remaining 6885 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 10697 2.81 - 3.33: 35325 3.33 - 3.85: 62774 3.85 - 4.38: 69906 4.38 - 4.90: 118021 Nonbonded interactions: 296723 Sorted by model distance: nonbonded pdb=" O PRO C 90 " pdb=" OH TYR D 571 " model vdw 2.282 3.040 nonbonded pdb=" OG1 THR A 320 " pdb=" OD2 ASP B 516 " model vdw 2.282 3.040 nonbonded pdb=" OG1 THR D 320 " pdb=" OD2 ASP G 516 " model vdw 2.282 3.040 nonbonded pdb=" OG1 THR F 320 " pdb=" OD2 ASP I 516 " model vdw 2.282 3.040 nonbonded pdb=" O PRO K 90 " pdb=" OH TYR F 571 " model vdw 2.282 3.040 ... (remaining 296718 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.060 Set scattering table: 0.110 Process input model: 34.470 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 39672 Z= 0.249 Angle : 1.043 13.171 53820 Z= 0.562 Chirality : 0.057 0.273 6168 Planarity : 0.008 0.082 6888 Dihedral : 16.252 89.922 14736 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.41 % Allowed : 12.96 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.80 (0.09), residues: 4740 helix: -3.92 (0.06), residues: 2148 sheet: -2.30 (0.41), residues: 120 loop : -2.49 (0.11), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 88 TYR 0.035 0.003 TYR H 568 PHE 0.041 0.003 PHE F 67 TRP 0.019 0.002 TRP I 543 HIS 0.007 0.002 HIS K 304 Details of bonding type rmsd covalent geometry : bond 0.00555 (39672) covalent geometry : angle 1.04260 (53820) hydrogen bonds : bond 0.21873 ( 1410) hydrogen bonds : angle 8.91675 ( 3909) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2310 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 2293 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8472 (tp-100) cc_final: 0.7934 (tp-100) REVERT: A 111 VAL cc_start: 0.8729 (t) cc_final: 0.8454 (t) REVERT: A 220 LEU cc_start: 0.8354 (tt) cc_final: 0.7974 (tt) REVERT: A 256 ARG cc_start: 0.8593 (mmt180) cc_final: 0.8308 (mmm160) REVERT: A 305 GLN cc_start: 0.8662 (tp40) cc_final: 0.7990 (tm-30) REVERT: A 309 GLN cc_start: 0.8655 (mt0) cc_final: 0.8191 (mt0) REVERT: A 315 PRO cc_start: 0.8863 (Cg_endo) cc_final: 0.8659 (Cg_exo) REVERT: A 536 GLU cc_start: 0.6851 (tm-30) cc_final: 0.6598 (tm-30) REVERT: A 548 PHE cc_start: 0.9159 (m-10) cc_final: 0.8909 (m-10) REVERT: A 597 TYR cc_start: 0.8254 (m-10) cc_final: 0.7843 (m-10) REVERT: A 599 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7704 (tm-30) REVERT: B 195 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7922 (mt-10) REVERT: B 264 LYS cc_start: 0.8198 (mmtt) cc_final: 0.7957 (mtpp) REVERT: B 306 LYS cc_start: 0.9009 (tttt) cc_final: 0.8757 (tttt) REVERT: B 512 LEU cc_start: 0.9102 (pt) cc_final: 0.8735 (pt) REVERT: B 538 PHE cc_start: 0.8840 (t80) cc_final: 0.8539 (t80) REVERT: B 548 PHE cc_start: 0.9227 (m-10) cc_final: 0.8914 (m-10) REVERT: B 614 LYS cc_start: 0.8886 (mtpt) cc_final: 0.8672 (mtmm) REVERT: B 633 MET cc_start: 0.3022 (tpt) cc_final: 0.2729 (tpt) REVERT: C 91 CYS cc_start: 0.8402 (m) cc_final: 0.7763 (m) REVERT: C 164 GLN cc_start: 0.7684 (tt0) cc_final: 0.7458 (tt0) REVERT: C 195 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8056 (mt-10) REVERT: C 225 LEU cc_start: 0.9413 (tp) cc_final: 0.9129 (tt) REVERT: C 245 GLU cc_start: 0.7297 (mp0) cc_final: 0.7071 (mp0) REVERT: C 275 LEU cc_start: 0.8556 (mp) cc_final: 0.8254 (mp) REVERT: C 312 ASN cc_start: 0.8448 (p0) cc_final: 0.7820 (p0) REVERT: C 502 LYS cc_start: 0.8676 (ttmt) cc_final: 0.8413 (mtpp) REVERT: C 548 PHE cc_start: 0.9141 (m-10) cc_final: 0.8624 (m-10) REVERT: C 571 TYR cc_start: 0.7991 (t80) cc_final: 0.7696 (t80) REVERT: C 583 HIS cc_start: 0.7961 (m-70) cc_final: 0.7759 (m-70) REVERT: C 591 ASP cc_start: 0.8802 (t70) cc_final: 0.8590 (t0) REVERT: C 599 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7802 (tm-30) REVERT: C 625 ARG cc_start: 0.7179 (ttt-90) cc_final: 0.6720 (tpt90) REVERT: D 85 GLN cc_start: 0.8492 (tp-100) cc_final: 0.7869 (tp-100) REVERT: D 111 VAL cc_start: 0.8710 (t) cc_final: 0.8450 (t) REVERT: D 220 LEU cc_start: 0.8356 (tt) cc_final: 0.7971 (tt) REVERT: D 256 ARG cc_start: 0.8587 (mmt180) cc_final: 0.8275 (mmm160) REVERT: D 315 PRO cc_start: 0.8857 (Cg_endo) cc_final: 0.8645 (Cg_exo) REVERT: D 536 GLU cc_start: 0.6868 (tm-30) cc_final: 0.6570 (tm-30) REVERT: D 597 TYR cc_start: 0.8241 (m-10) cc_final: 0.7857 (m-10) REVERT: D 599 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7700 (tm-30) REVERT: G 195 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7918 (mt-10) REVERT: G 264 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7920 (mtpp) REVERT: G 306 LYS cc_start: 0.9001 (tttt) cc_final: 0.8742 (tttt) REVERT: G 512 LEU cc_start: 0.9098 (pt) cc_final: 0.8739 (pt) REVERT: G 528 PHE cc_start: 0.8629 (t80) cc_final: 0.8354 (t80) REVERT: G 538 PHE cc_start: 0.8813 (t80) cc_final: 0.8512 (t80) REVERT: G 548 PHE cc_start: 0.9243 (m-10) cc_final: 0.8895 (m-10) REVERT: G 614 LYS cc_start: 0.8884 (mtpt) cc_final: 0.8668 (mtmm) REVERT: G 633 MET cc_start: 0.3010 (tpt) cc_final: 0.2700 (tpt) REVERT: J 91 CYS cc_start: 0.8397 (m) cc_final: 0.7741 (m) REVERT: J 164 GLN cc_start: 0.7691 (tt0) cc_final: 0.7460 (tt0) REVERT: J 195 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8065 (mt-10) REVERT: J 225 LEU cc_start: 0.9413 (tp) cc_final: 0.9121 (tt) REVERT: J 245 GLU cc_start: 0.7306 (mp0) cc_final: 0.7078 (mp0) REVERT: J 312 ASN cc_start: 0.8446 (p0) cc_final: 0.7822 (p0) REVERT: J 502 LYS cc_start: 0.8671 (ttmt) cc_final: 0.8419 (mtpp) REVERT: J 548 PHE cc_start: 0.9139 (m-10) cc_final: 0.8631 (m-10) REVERT: J 571 TYR cc_start: 0.7992 (t80) cc_final: 0.7736 (t80) REVERT: J 591 ASP cc_start: 0.8804 (t70) cc_final: 0.8546 (t0) REVERT: J 599 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7817 (tm-30) REVERT: J 625 ARG cc_start: 0.7190 (ttt-90) cc_final: 0.6727 (tpt90) REVERT: E 63 GLN cc_start: 0.7522 (tm-30) cc_final: 0.7199 (tm-30) REVERT: E 85 GLN cc_start: 0.8489 (tp-100) cc_final: 0.7913 (tp-100) REVERT: E 93 LEU cc_start: 0.9141 (tp) cc_final: 0.8935 (tp) REVERT: E 111 VAL cc_start: 0.8714 (t) cc_final: 0.8440 (t) REVERT: E 220 LEU cc_start: 0.8352 (tt) cc_final: 0.7964 (tt) REVERT: E 256 ARG cc_start: 0.8581 (mmt180) cc_final: 0.8268 (mmm160) REVERT: E 315 PRO cc_start: 0.8855 (Cg_endo) cc_final: 0.8655 (Cg_exo) REVERT: E 536 GLU cc_start: 0.6883 (tm-30) cc_final: 0.6551 (tm-30) REVERT: E 548 PHE cc_start: 0.9161 (m-10) cc_final: 0.8956 (m-10) REVERT: E 597 TYR cc_start: 0.8249 (m-10) cc_final: 0.7827 (m-10) REVERT: E 599 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7714 (tm-30) REVERT: E 614 LYS cc_start: 0.8870 (mtpt) cc_final: 0.8619 (mtmm) REVERT: H 195 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7917 (mt-10) REVERT: H 264 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7956 (mtpp) REVERT: H 293 GLU cc_start: 0.8149 (tp30) cc_final: 0.7938 (tp30) REVERT: H 306 LYS cc_start: 0.9018 (tttt) cc_final: 0.8771 (tttt) REVERT: H 512 LEU cc_start: 0.9101 (pt) cc_final: 0.8741 (pt) REVERT: H 528 PHE cc_start: 0.8641 (t80) cc_final: 0.8365 (t80) REVERT: H 538 PHE cc_start: 0.8824 (t80) cc_final: 0.8515 (t80) REVERT: H 548 PHE cc_start: 0.9250 (m-10) cc_final: 0.8898 (m-10) REVERT: H 614 LYS cc_start: 0.8876 (mtpt) cc_final: 0.8639 (mtmm) REVERT: H 633 MET cc_start: 0.3014 (tpt) cc_final: 0.2715 (tpt) REVERT: K 91 CYS cc_start: 0.8435 (m) cc_final: 0.7741 (m) REVERT: K 164 GLN cc_start: 0.7679 (tt0) cc_final: 0.7453 (tt0) REVERT: K 195 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8060 (mt-10) REVERT: K 225 LEU cc_start: 0.9407 (tp) cc_final: 0.9117 (tt) REVERT: K 245 GLU cc_start: 0.7404 (mp0) cc_final: 0.7141 (mp0) REVERT: K 312 ASN cc_start: 0.8439 (p0) cc_final: 0.7815 (p0) REVERT: K 502 LYS cc_start: 0.8663 (ttmt) cc_final: 0.8427 (mtpp) REVERT: K 548 PHE cc_start: 0.9122 (m-10) cc_final: 0.8592 (m-10) REVERT: K 571 TYR cc_start: 0.7994 (t80) cc_final: 0.7725 (t80) REVERT: K 583 HIS cc_start: 0.7968 (m-70) cc_final: 0.7760 (m-70) REVERT: K 591 ASP cc_start: 0.8804 (t70) cc_final: 0.8588 (t0) REVERT: K 599 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7818 (tm-30) REVERT: K 625 ARG cc_start: 0.7193 (ttt-90) cc_final: 0.6730 (tpt90) REVERT: F 63 GLN cc_start: 0.7521 (tm-30) cc_final: 0.7220 (tm-30) REVERT: F 85 GLN cc_start: 0.8463 (tp-100) cc_final: 0.7896 (tp-100) REVERT: F 111 VAL cc_start: 0.8710 (t) cc_final: 0.8438 (t) REVERT: F 220 LEU cc_start: 0.8355 (tt) cc_final: 0.7971 (tt) REVERT: F 256 ARG cc_start: 0.8597 (mmt180) cc_final: 0.8276 (mmm160) REVERT: F 305 GLN cc_start: 0.8667 (tp40) cc_final: 0.7993 (tm-30) REVERT: F 309 GLN cc_start: 0.8648 (mt0) cc_final: 0.8176 (mt0) REVERT: F 536 GLU cc_start: 0.6868 (tm-30) cc_final: 0.6578 (tm-30) REVERT: F 548 PHE cc_start: 0.9140 (m-10) cc_final: 0.8908 (m-10) REVERT: F 597 TYR cc_start: 0.8257 (m-10) cc_final: 0.7844 (m-10) REVERT: F 599 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7696 (tm-30) REVERT: I 195 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7932 (mt-10) REVERT: I 264 LYS cc_start: 0.8198 (mmtt) cc_final: 0.7938 (mtpp) REVERT: I 306 LYS cc_start: 0.9016 (tttt) cc_final: 0.8779 (tttt) REVERT: I 512 LEU cc_start: 0.9097 (pt) cc_final: 0.8744 (pt) REVERT: I 538 PHE cc_start: 0.8850 (t80) cc_final: 0.8527 (t80) REVERT: I 548 PHE cc_start: 0.9207 (m-10) cc_final: 0.8845 (m-10) REVERT: I 614 LYS cc_start: 0.8882 (mtpt) cc_final: 0.8668 (mtmm) REVERT: I 633 MET cc_start: 0.3003 (tpt) cc_final: 0.2715 (tpt) REVERT: L 164 GLN cc_start: 0.7659 (tt0) cc_final: 0.7428 (tt0) REVERT: L 177 TRP cc_start: 0.8346 (m100) cc_final: 0.8136 (m100) REVERT: L 195 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8044 (mt-10) REVERT: L 225 LEU cc_start: 0.9410 (tp) cc_final: 0.9120 (tt) REVERT: L 245 GLU cc_start: 0.7425 (mp0) cc_final: 0.7167 (mp0) REVERT: L 312 ASN cc_start: 0.8446 (p0) cc_final: 0.7800 (p0) REVERT: L 502 LYS cc_start: 0.8658 (ttmt) cc_final: 0.8445 (mtpp) REVERT: L 548 PHE cc_start: 0.9131 (m-10) cc_final: 0.8616 (m-10) REVERT: L 571 TYR cc_start: 0.7999 (t80) cc_final: 0.7688 (t80) REVERT: L 591 ASP cc_start: 0.8808 (t70) cc_final: 0.8602 (t0) REVERT: L 599 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7820 (tm-30) REVERT: L 625 ARG cc_start: 0.7190 (ttt-90) cc_final: 0.6727 (tpt90) outliers start: 17 outliers final: 5 residues processed: 2297 average time/residue: 0.2550 time to fit residues: 932.7937 Evaluate side-chains 2123 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 2118 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 470 optimal weight: 3.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 85 GLN ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS B 72 HIS B 85 GLN B 214 HIS B 260 GLN B 304 HIS B 541 GLN B 545 ASN B 632 GLN C 72 HIS C 81 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 ASN C 304 HIS C 632 GLN D 72 HIS D 85 GLN D 304 HIS D 309 GLN ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 GLN G 304 HIS G 541 GLN G 632 GLN J 72 HIS J 81 GLN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 242 ASN J 304 HIS J 632 GLN E 72 HIS E 85 GLN E 304 HIS E 309 GLN E 632 GLN H 72 HIS H 85 GLN H 260 GLN H 304 HIS H 541 GLN H 632 GLN K 72 HIS K 81 GLN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 242 ASN K 304 HIS K 632 GLN F 72 HIS F 81 GLN F 85 GLN F 304 HIS F 632 GLN I 72 HIS I 85 GLN I 214 HIS I 260 GLN I 304 HIS I 541 GLN I 632 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 242 ASN L 304 HIS L 632 GLN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.158753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.132293 restraints weight = 68191.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.136603 restraints weight = 37435.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.139535 restraints weight = 24054.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.141476 restraints weight = 17238.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.142971 restraints weight = 13477.029| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 39672 Z= 0.146 Angle : 0.672 8.099 53820 Z= 0.344 Chirality : 0.042 0.136 6168 Planarity : 0.006 0.054 6888 Dihedral : 5.747 21.352 5424 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.10 % Allowed : 5.92 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.78 (0.11), residues: 4740 helix: -2.79 (0.08), residues: 2400 sheet: -2.58 (0.37), residues: 120 loop : -2.04 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 617 TYR 0.019 0.002 TYR H 568 PHE 0.023 0.002 PHE D 67 TRP 0.032 0.003 TRP J 118 HIS 0.004 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00324 (39672) covalent geometry : angle 0.67231 (53820) hydrogen bonds : bond 0.04040 ( 1410) hydrogen bonds : angle 5.35986 ( 3909) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2210 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 2206 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8248 (tm-30) REVERT: A 83 MET cc_start: 0.8203 (mmp) cc_final: 0.7782 (mmm) REVERT: A 99 TYR cc_start: 0.8794 (t80) cc_final: 0.8579 (t80) REVERT: A 105 LEU cc_start: 0.9479 (mt) cc_final: 0.9203 (mt) REVERT: A 195 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7732 (mt-10) REVERT: A 219 ASP cc_start: 0.7995 (m-30) cc_final: 0.7557 (p0) REVERT: A 227 LEU cc_start: 0.8861 (tt) cc_final: 0.8609 (tp) REVERT: A 281 LYS cc_start: 0.8561 (tttt) cc_final: 0.8216 (tttt) REVERT: A 297 ARG cc_start: 0.9227 (ttt-90) cc_final: 0.8754 (ttt-90) REVERT: A 305 GLN cc_start: 0.9070 (tp40) cc_final: 0.8619 (tm-30) REVERT: A 306 LYS cc_start: 0.9031 (tttt) cc_final: 0.8797 (ttmm) REVERT: A 309 GLN cc_start: 0.9360 (mt0) cc_final: 0.9055 (mt0) REVERT: A 491 LEU cc_start: 0.9514 (pt) cc_final: 0.9301 (pp) REVERT: A 523 SER cc_start: 0.8759 (p) cc_final: 0.8395 (p) REVERT: A 536 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7578 (tm-30) REVERT: A 548 PHE cc_start: 0.9283 (m-10) cc_final: 0.9012 (m-10) REVERT: A 578 LEU cc_start: 0.9288 (mt) cc_final: 0.8992 (mt) REVERT: A 599 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8398 (tm-30) REVERT: A 600 LEU cc_start: 0.9490 (tt) cc_final: 0.9267 (tt) REVERT: A 618 TYR cc_start: 0.8162 (m-80) cc_final: 0.7958 (m-80) REVERT: B 83 MET cc_start: 0.9226 (tpp) cc_final: 0.8558 (tpp) REVERT: B 91 CYS cc_start: 0.8373 (m) cc_final: 0.7410 (m) REVERT: B 101 VAL cc_start: 0.9184 (p) cc_final: 0.8840 (p) REVERT: B 105 LEU cc_start: 0.9534 (mt) cc_final: 0.9113 (mt) REVERT: B 116 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8151 (tp30) REVERT: B 195 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7658 (mt-10) REVERT: B 234 ARG cc_start: 0.7743 (ttm170) cc_final: 0.7383 (ttp-170) REVERT: B 264 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8176 (mtpp) REVERT: B 317 LYS cc_start: 0.8793 (mtmm) cc_final: 0.8502 (mtmt) REVERT: B 498 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8249 (mm-30) REVERT: B 512 LEU cc_start: 0.9003 (pt) cc_final: 0.8593 (pt) REVERT: B 538 PHE cc_start: 0.9236 (t80) cc_final: 0.8950 (t80) REVERT: B 548 PHE cc_start: 0.9242 (m-10) cc_final: 0.8958 (m-10) REVERT: B 599 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8418 (tm-30) REVERT: B 625 ARG cc_start: 0.7795 (tmt170) cc_final: 0.7171 (tpt90) REVERT: C 63 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8183 (tm-30) REVERT: C 81 GLN cc_start: 0.8368 (tp-100) cc_final: 0.7793 (tp-100) REVERT: C 85 GLN cc_start: 0.9014 (tp-100) cc_final: 0.8593 (tp-100) REVERT: C 88 ARG cc_start: 0.8039 (tmt-80) cc_final: 0.7738 (tpt-90) REVERT: C 101 VAL cc_start: 0.9325 (p) cc_final: 0.8978 (p) REVERT: C 105 LEU cc_start: 0.9415 (mt) cc_final: 0.9193 (mt) REVERT: C 195 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7822 (mt-10) REVERT: C 225 LEU cc_start: 0.9385 (tp) cc_final: 0.9102 (tt) REVERT: C 245 GLU cc_start: 0.8036 (mp0) cc_final: 0.7628 (mp0) REVERT: C 305 GLN cc_start: 0.9251 (tm-30) cc_final: 0.8852 (tt0) REVERT: C 309 GLN cc_start: 0.9352 (mt0) cc_final: 0.9079 (mt0) REVERT: C 491 LEU cc_start: 0.9360 (pt) cc_final: 0.9135 (pt) REVERT: C 502 LYS cc_start: 0.9192 (ttmt) cc_final: 0.8963 (mtpp) REVERT: C 528 PHE cc_start: 0.8927 (t80) cc_final: 0.8624 (t80) REVERT: C 536 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7587 (tm-30) REVERT: C 546 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8429 (tm-30) REVERT: C 548 PHE cc_start: 0.9237 (m-10) cc_final: 0.8988 (m-10) REVERT: C 574 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8495 (tm-30) REVERT: C 583 HIS cc_start: 0.8625 (m-70) cc_final: 0.8302 (m-70) REVERT: C 599 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8495 (tm-30) REVERT: C 625 ARG cc_start: 0.6988 (ttt-90) cc_final: 0.6494 (tpt90) REVERT: D 63 GLN cc_start: 0.8650 (tm-30) cc_final: 0.7745 (tm-30) REVERT: D 83 MET cc_start: 0.8295 (mmp) cc_final: 0.7839 (mmm) REVERT: D 85 GLN cc_start: 0.9042 (tp40) cc_final: 0.8774 (tp40) REVERT: D 101 VAL cc_start: 0.9153 (p) cc_final: 0.8770 (p) REVERT: D 105 LEU cc_start: 0.9481 (mt) cc_final: 0.9157 (mt) REVERT: D 195 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7713 (mt-10) REVERT: D 201 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8241 (mm-40) REVERT: D 227 LEU cc_start: 0.8863 (tt) cc_final: 0.8560 (tp) REVERT: D 277 TYR cc_start: 0.8202 (m-80) cc_final: 0.7910 (m-80) REVERT: D 281 LYS cc_start: 0.8500 (tttt) cc_final: 0.8098 (tttt) REVERT: D 297 ARG cc_start: 0.9231 (ttt-90) cc_final: 0.8761 (ttt-90) REVERT: D 491 LEU cc_start: 0.9511 (pt) cc_final: 0.9298 (pp) REVERT: D 523 SER cc_start: 0.8767 (p) cc_final: 0.8403 (p) REVERT: D 536 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7609 (tm-30) REVERT: D 546 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8494 (tm-30) REVERT: D 578 LEU cc_start: 0.9277 (mt) cc_final: 0.8973 (mt) REVERT: D 599 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8418 (tm-30) REVERT: D 600 LEU cc_start: 0.9494 (tt) cc_final: 0.9277 (tt) REVERT: D 618 TYR cc_start: 0.7958 (m-80) cc_final: 0.7690 (m-80) REVERT: G 83 MET cc_start: 0.9254 (tpp) cc_final: 0.8586 (tpp) REVERT: G 91 CYS cc_start: 0.8352 (m) cc_final: 0.7452 (m) REVERT: G 101 VAL cc_start: 0.9124 (p) cc_final: 0.8769 (p) REVERT: G 105 LEU cc_start: 0.9545 (mt) cc_final: 0.9117 (mt) REVERT: G 116 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8151 (tp30) REVERT: G 195 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7658 (mt-10) REVERT: G 234 ARG cc_start: 0.7872 (ttm170) cc_final: 0.7563 (ttp-170) REVERT: G 264 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8171 (mtpp) REVERT: G 296 LEU cc_start: 0.9662 (tp) cc_final: 0.9438 (tp) REVERT: G 317 LYS cc_start: 0.8797 (mtmm) cc_final: 0.8513 (mtmt) REVERT: G 498 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8242 (mm-30) REVERT: G 512 LEU cc_start: 0.9009 (pt) cc_final: 0.8571 (pt) REVERT: G 538 PHE cc_start: 0.9251 (t80) cc_final: 0.8945 (t80) REVERT: G 548 PHE cc_start: 0.9245 (m-10) cc_final: 0.8941 (m-10) REVERT: G 578 LEU cc_start: 0.9347 (tp) cc_final: 0.9075 (tp) REVERT: G 599 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8477 (tm-30) REVERT: G 618 TYR cc_start: 0.8439 (m-10) cc_final: 0.8239 (m-10) REVERT: G 625 ARG cc_start: 0.7791 (tmt170) cc_final: 0.7173 (tpt90) REVERT: J 63 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8162 (tm-30) REVERT: J 81 GLN cc_start: 0.8362 (tp-100) cc_final: 0.7772 (tp-100) REVERT: J 85 GLN cc_start: 0.9002 (tp-100) cc_final: 0.8585 (tp-100) REVERT: J 88 ARG cc_start: 0.8062 (tmt-80) cc_final: 0.7780 (tpt-90) REVERT: J 101 VAL cc_start: 0.9333 (p) cc_final: 0.8968 (p) REVERT: J 105 LEU cc_start: 0.9521 (mt) cc_final: 0.9236 (mt) REVERT: J 195 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7811 (mt-10) REVERT: J 225 LEU cc_start: 0.9387 (tp) cc_final: 0.9063 (tt) REVERT: J 245 GLU cc_start: 0.8033 (mp0) cc_final: 0.7629 (mp0) REVERT: J 301 LEU cc_start: 0.8994 (tt) cc_final: 0.8785 (tt) REVERT: J 305 GLN cc_start: 0.9278 (tm-30) cc_final: 0.8865 (tt0) REVERT: J 309 GLN cc_start: 0.9357 (mt0) cc_final: 0.9071 (mt0) REVERT: J 491 LEU cc_start: 0.9352 (pt) cc_final: 0.9136 (pt) REVERT: J 502 LYS cc_start: 0.9191 (ttmt) cc_final: 0.8957 (mtpp) REVERT: J 528 PHE cc_start: 0.8925 (t80) cc_final: 0.8617 (t80) REVERT: J 536 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7605 (tm-30) REVERT: J 546 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8421 (tm-30) REVERT: J 548 PHE cc_start: 0.9252 (m-10) cc_final: 0.8991 (m-10) REVERT: J 599 GLN cc_start: 0.8976 (tm-30) cc_final: 0.8486 (tm-30) REVERT: J 625 ARG cc_start: 0.6993 (ttt-90) cc_final: 0.6499 (tpt90) REVERT: E 63 GLN cc_start: 0.8358 (tm-30) cc_final: 0.7834 (tm-30) REVERT: E 83 MET cc_start: 0.8343 (mmp) cc_final: 0.7862 (mmm) REVERT: E 85 GLN cc_start: 0.9055 (tp40) cc_final: 0.8734 (tp40) REVERT: E 99 TYR cc_start: 0.8810 (t80) cc_final: 0.8597 (t80) REVERT: E 105 LEU cc_start: 0.9479 (mt) cc_final: 0.9203 (mt) REVERT: E 195 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7710 (mt-10) REVERT: E 201 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8227 (mm-40) REVERT: E 227 LEU cc_start: 0.8873 (tt) cc_final: 0.8610 (tp) REVERT: E 277 TYR cc_start: 0.8195 (m-80) cc_final: 0.7927 (m-80) REVERT: E 281 LYS cc_start: 0.8498 (tttt) cc_final: 0.8099 (tttt) REVERT: E 297 ARG cc_start: 0.9231 (ttt-90) cc_final: 0.8750 (ttt-90) REVERT: E 491 LEU cc_start: 0.9506 (pt) cc_final: 0.9288 (pp) REVERT: E 523 SER cc_start: 0.8738 (p) cc_final: 0.8368 (p) REVERT: E 536 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7600 (tm-30) REVERT: E 546 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8474 (tm-30) REVERT: E 548 PHE cc_start: 0.9318 (m-10) cc_final: 0.9076 (m-10) REVERT: E 578 LEU cc_start: 0.9281 (mt) cc_final: 0.8967 (mt) REVERT: E 599 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8422 (tm-30) REVERT: E 600 LEU cc_start: 0.9489 (tt) cc_final: 0.9281 (tt) REVERT: E 614 LYS cc_start: 0.8970 (mtpt) cc_final: 0.8736 (mtmm) REVERT: E 618 TYR cc_start: 0.7995 (m-80) cc_final: 0.7675 (m-80) REVERT: H 83 MET cc_start: 0.9233 (tpp) cc_final: 0.8568 (tpp) REVERT: H 91 CYS cc_start: 0.8330 (m) cc_final: 0.7395 (m) REVERT: H 101 VAL cc_start: 0.9180 (p) cc_final: 0.8840 (p) REVERT: H 105 LEU cc_start: 0.9542 (mt) cc_final: 0.9122 (mt) REVERT: H 116 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8146 (tp30) REVERT: H 195 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7650 (mt-10) REVERT: H 234 ARG cc_start: 0.7712 (ttm170) cc_final: 0.7360 (ttp-170) REVERT: H 264 LYS cc_start: 0.8458 (mmtt) cc_final: 0.8166 (mtpp) REVERT: H 295 ILE cc_start: 0.9734 (tt) cc_final: 0.9530 (tt) REVERT: H 296 LEU cc_start: 0.9662 (tp) cc_final: 0.9457 (tp) REVERT: H 317 LYS cc_start: 0.8788 (mtmm) cc_final: 0.8512 (mtmt) REVERT: H 498 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8251 (mm-30) REVERT: H 512 LEU cc_start: 0.9002 (pt) cc_final: 0.8582 (pt) REVERT: H 538 PHE cc_start: 0.9244 (t80) cc_final: 0.8987 (t80) REVERT: H 546 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8414 (tm-30) REVERT: H 548 PHE cc_start: 0.9254 (m-10) cc_final: 0.8963 (m-10) REVERT: H 550 THR cc_start: 0.8722 (p) cc_final: 0.8070 (p) REVERT: H 578 LEU cc_start: 0.9333 (tp) cc_final: 0.9060 (tp) REVERT: H 599 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8430 (tm-30) REVERT: H 625 ARG cc_start: 0.7791 (tmt170) cc_final: 0.7170 (tpt90) REVERT: K 63 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8175 (tm-30) REVERT: K 71 LEU cc_start: 0.9066 (tp) cc_final: 0.8852 (tp) REVERT: K 81 GLN cc_start: 0.8317 (tp-100) cc_final: 0.7766 (tp-100) REVERT: K 85 GLN cc_start: 0.9055 (tp-100) cc_final: 0.8671 (tp-100) REVERT: K 88 ARG cc_start: 0.8095 (tmt-80) cc_final: 0.7829 (tpt-90) REVERT: K 101 VAL cc_start: 0.9320 (p) cc_final: 0.8969 (p) REVERT: K 105 LEU cc_start: 0.9413 (mt) cc_final: 0.9177 (mt) REVERT: K 195 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7811 (mt-10) REVERT: K 225 LEU cc_start: 0.9390 (tp) cc_final: 0.9112 (tt) REVERT: K 245 GLU cc_start: 0.8011 (mp0) cc_final: 0.7573 (mp0) REVERT: K 247 ARG cc_start: 0.8570 (ptp90) cc_final: 0.8210 (ttp-170) REVERT: K 301 LEU cc_start: 0.8988 (tt) cc_final: 0.8778 (tt) REVERT: K 305 GLN cc_start: 0.9257 (tm-30) cc_final: 0.8857 (tt0) REVERT: K 309 GLN cc_start: 0.9349 (mt0) cc_final: 0.9062 (mt0) REVERT: K 502 LYS cc_start: 0.9190 (ttmt) cc_final: 0.8959 (mtpp) REVERT: K 528 PHE cc_start: 0.8924 (t80) cc_final: 0.8617 (t80) REVERT: K 536 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7616 (tm-30) REVERT: K 546 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8421 (tm-30) REVERT: K 548 PHE cc_start: 0.9219 (m-10) cc_final: 0.8958 (m-10) REVERT: K 583 HIS cc_start: 0.8629 (m-70) cc_final: 0.8289 (m-70) REVERT: K 599 GLN cc_start: 0.8982 (tm-30) cc_final: 0.8490 (tm-30) REVERT: K 625 ARG cc_start: 0.6987 (ttt-90) cc_final: 0.6499 (tpt90) REVERT: F 63 GLN cc_start: 0.8349 (tm-30) cc_final: 0.7812 (tm-30) REVERT: F 81 GLN cc_start: 0.8451 (tp-100) cc_final: 0.7894 (tp-100) REVERT: F 83 MET cc_start: 0.8425 (mmp) cc_final: 0.7869 (tpp) REVERT: F 85 GLN cc_start: 0.9086 (tp40) cc_final: 0.8133 (tp-100) REVERT: F 101 VAL cc_start: 0.9165 (p) cc_final: 0.8777 (p) REVERT: F 105 LEU cc_start: 0.9474 (mt) cc_final: 0.9155 (mt) REVERT: F 195 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7729 (mt-10) REVERT: F 227 LEU cc_start: 0.8868 (tt) cc_final: 0.8561 (tp) REVERT: F 277 TYR cc_start: 0.8209 (m-80) cc_final: 0.7905 (m-80) REVERT: F 281 LYS cc_start: 0.8549 (tttt) cc_final: 0.8189 (tttt) REVERT: F 295 ILE cc_start: 0.9630 (tt) cc_final: 0.9399 (tt) REVERT: F 297 ARG cc_start: 0.9235 (ttt-90) cc_final: 0.8752 (ttt-90) REVERT: F 305 GLN cc_start: 0.9109 (tp40) cc_final: 0.8754 (tp40) REVERT: F 306 LYS cc_start: 0.8902 (tttt) cc_final: 0.8693 (ttmm) REVERT: F 307 ILE cc_start: 0.9509 (tp) cc_final: 0.9295 (tp) REVERT: F 309 GLN cc_start: 0.9349 (mt0) cc_final: 0.8951 (mt0) REVERT: F 491 LEU cc_start: 0.9507 (pt) cc_final: 0.9298 (pp) REVERT: F 523 SER cc_start: 0.8770 (p) cc_final: 0.8408 (p) REVERT: F 536 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7556 (tm-30) REVERT: F 578 LEU cc_start: 0.9251 (mt) cc_final: 0.8945 (mt) REVERT: F 599 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8398 (tm-30) REVERT: F 600 LEU cc_start: 0.9490 (tt) cc_final: 0.9275 (tt) REVERT: I 69 ARG cc_start: 0.8378 (mmm-85) cc_final: 0.8139 (mmm160) REVERT: I 83 MET cc_start: 0.9018 (tpp) cc_final: 0.8683 (tpp) REVERT: I 91 CYS cc_start: 0.8344 (m) cc_final: 0.7431 (m) REVERT: I 101 VAL cc_start: 0.9176 (p) cc_final: 0.8842 (p) REVERT: I 105 LEU cc_start: 0.9537 (mt) cc_final: 0.9117 (mt) REVERT: I 116 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8152 (tp30) REVERT: I 195 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7655 (mt-10) REVERT: I 234 ARG cc_start: 0.7863 (ttm170) cc_final: 0.7563 (ttp-170) REVERT: I 264 LYS cc_start: 0.8468 (mmtt) cc_final: 0.8167 (mtpp) REVERT: I 295 ILE cc_start: 0.9714 (tt) cc_final: 0.9507 (tt) REVERT: I 296 LEU cc_start: 0.9656 (tp) cc_final: 0.9449 (tp) REVERT: I 317 LYS cc_start: 0.8783 (mtmm) cc_final: 0.8533 (mtmt) REVERT: I 498 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8300 (mm-30) REVERT: I 512 LEU cc_start: 0.9002 (pt) cc_final: 0.8575 (pt) REVERT: I 538 PHE cc_start: 0.9256 (t80) cc_final: 0.8930 (t80) REVERT: I 548 PHE cc_start: 0.9254 (m-10) cc_final: 0.8999 (m-10) REVERT: I 599 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8425 (tm-30) REVERT: I 625 ARG cc_start: 0.7784 (tmt170) cc_final: 0.7167 (tpt90) REVERT: L 81 GLN cc_start: 0.8367 (tp-100) cc_final: 0.7946 (tp-100) REVERT: L 101 VAL cc_start: 0.9331 (p) cc_final: 0.8978 (p) REVERT: L 105 LEU cc_start: 0.9529 (mt) cc_final: 0.9240 (mt) REVERT: L 177 TRP cc_start: 0.9309 (m100) cc_final: 0.8998 (m100) REVERT: L 195 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7797 (mt-10) REVERT: L 225 LEU cc_start: 0.9385 (tp) cc_final: 0.9093 (tt) REVERT: L 245 GLU cc_start: 0.8115 (mp0) cc_final: 0.7715 (mp0) REVERT: L 305 GLN cc_start: 0.9253 (tm-30) cc_final: 0.8851 (tt0) REVERT: L 309 GLN cc_start: 0.9350 (mt0) cc_final: 0.9079 (mt0) REVERT: L 502 LYS cc_start: 0.9202 (ttmt) cc_final: 0.8985 (mtpp) REVERT: L 528 PHE cc_start: 0.8928 (t80) cc_final: 0.8623 (t80) REVERT: L 536 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7579 (tm-30) REVERT: L 546 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8418 (tm-30) REVERT: L 548 PHE cc_start: 0.9227 (m-10) cc_final: 0.8991 (m-10) REVERT: L 599 GLN cc_start: 0.8978 (tm-30) cc_final: 0.8478 (tm-30) REVERT: L 625 ARG cc_start: 0.6976 (ttt-90) cc_final: 0.6484 (tpt90) outliers start: 4 outliers final: 4 residues processed: 2210 average time/residue: 0.2473 time to fit residues: 880.1550 Evaluate side-chains 2081 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 2077 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 377 optimal weight: 7.9990 chunk 147 optimal weight: 7.9990 chunk 455 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 362 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 266 optimal weight: 0.0980 chunk 334 optimal weight: 8.9990 chunk 138 optimal weight: 8.9990 chunk 409 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 GLN B 260 GLN B 632 GLN C 632 GLN D 309 GLN D 632 GLN G 72 HIS G 260 GLN G 632 GLN J 632 GLN E 309 GLN E 632 GLN H 260 GLN H 632 GLN K 632 GLN F 632 GLN I 260 GLN I 632 GLN L 72 HIS L 85 GLN L 632 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.156479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.130537 restraints weight = 68569.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.134673 restraints weight = 38085.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.137480 restraints weight = 24646.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.139401 restraints weight = 17752.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.140652 restraints weight = 13898.494| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 39672 Z= 0.175 Angle : 0.667 8.077 53820 Z= 0.339 Chirality : 0.043 0.138 6168 Planarity : 0.006 0.050 6888 Dihedral : 5.521 21.201 5424 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.12), residues: 4740 helix: -2.07 (0.09), residues: 2376 sheet: -2.38 (0.37), residues: 120 loop : -1.65 (0.14), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 159 TYR 0.020 0.002 TYR L 568 PHE 0.021 0.002 PHE A 538 TRP 0.047 0.003 TRP C 118 HIS 0.005 0.001 HIS L 583 Details of bonding type rmsd covalent geometry : bond 0.00389 (39672) covalent geometry : angle 0.66705 (53820) hydrogen bonds : bond 0.03663 ( 1410) hydrogen bonds : angle 4.98052 ( 3909) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2209 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2209 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.8627 (tm-30) cc_final: 0.7890 (tm-30) REVERT: A 85 GLN cc_start: 0.9144 (tp40) cc_final: 0.8813 (tp40) REVERT: A 99 TYR cc_start: 0.8833 (t80) cc_final: 0.8626 (t80) REVERT: A 103 LYS cc_start: 0.8879 (tttt) cc_final: 0.8664 (tppt) REVERT: A 105 LEU cc_start: 0.9531 (mt) cc_final: 0.9204 (mt) REVERT: A 116 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8406 (tp30) REVERT: A 118 TRP cc_start: 0.8300 (t60) cc_final: 0.7887 (t60) REVERT: A 177 TRP cc_start: 0.9061 (m100) cc_final: 0.8698 (t-100) REVERT: A 187 LEU cc_start: 0.9347 (mm) cc_final: 0.9062 (mm) REVERT: A 227 LEU cc_start: 0.8869 (tt) cc_final: 0.8663 (tp) REVERT: A 267 ARG cc_start: 0.8719 (tmm-80) cc_final: 0.8519 (tmm-80) REVERT: A 281 LYS cc_start: 0.8518 (tttt) cc_final: 0.7991 (tttt) REVERT: A 306 LYS cc_start: 0.9037 (tttt) cc_final: 0.8758 (ttmm) REVERT: A 307 ILE cc_start: 0.9547 (tp) cc_final: 0.9321 (tp) REVERT: A 309 GLN cc_start: 0.9362 (mt0) cc_final: 0.8649 (mt0) REVERT: A 523 SER cc_start: 0.8746 (p) cc_final: 0.8312 (p) REVERT: A 536 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7595 (tm-30) REVERT: A 574 GLU cc_start: 0.9261 (tm-30) cc_final: 0.8954 (tm-30) REVERT: A 578 LEU cc_start: 0.9410 (mt) cc_final: 0.9126 (mt) REVERT: A 599 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8381 (tm-30) REVERT: A 600 LEU cc_start: 0.9486 (tt) cc_final: 0.9282 (tt) REVERT: A 610 TYR cc_start: 0.8572 (t80) cc_final: 0.7608 (t80) REVERT: A 618 TYR cc_start: 0.8247 (m-80) cc_final: 0.7709 (m-80) REVERT: B 83 MET cc_start: 0.8948 (tpp) cc_final: 0.8277 (tpp) REVERT: B 91 CYS cc_start: 0.8179 (m) cc_final: 0.7614 (m) REVERT: B 105 LEU cc_start: 0.9594 (mt) cc_final: 0.9214 (mt) REVERT: B 195 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7630 (mt-10) REVERT: B 234 ARG cc_start: 0.7881 (ttm170) cc_final: 0.7473 (ttp-170) REVERT: B 264 LYS cc_start: 0.8347 (mmtt) cc_final: 0.8023 (mtpp) REVERT: B 296 LEU cc_start: 0.9579 (tp) cc_final: 0.9357 (tp) REVERT: B 317 LYS cc_start: 0.8708 (mtmm) cc_final: 0.8437 (mtmt) REVERT: B 498 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8035 (mm-30) REVERT: B 512 LEU cc_start: 0.9047 (pt) cc_final: 0.8684 (pt) REVERT: B 548 PHE cc_start: 0.9269 (m-10) cc_final: 0.9038 (m-10) REVERT: B 599 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8416 (tm-30) REVERT: B 625 ARG cc_start: 0.7861 (tmt170) cc_final: 0.7146 (tpt90) REVERT: C 63 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8228 (tm-30) REVERT: C 85 GLN cc_start: 0.9086 (tp-100) cc_final: 0.8667 (tp-100) REVERT: C 101 VAL cc_start: 0.9247 (p) cc_final: 0.8946 (p) REVERT: C 105 LEU cc_start: 0.9536 (mt) cc_final: 0.9228 (mt) REVERT: C 116 GLU cc_start: 0.8805 (tp30) cc_final: 0.8554 (tp30) REVERT: C 195 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7816 (mt-10) REVERT: C 213 THR cc_start: 0.8695 (t) cc_final: 0.7774 (t) REVERT: C 225 LEU cc_start: 0.9428 (tp) cc_final: 0.9070 (tt) REVERT: C 245 GLU cc_start: 0.8015 (mp0) cc_final: 0.7661 (mp0) REVERT: C 297 ARG cc_start: 0.9158 (ttt-90) cc_final: 0.8843 (ttt180) REVERT: C 305 GLN cc_start: 0.9303 (tm-30) cc_final: 0.8782 (tt0) REVERT: C 309 GLN cc_start: 0.9340 (mt0) cc_final: 0.9058 (mt0) REVERT: C 498 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8411 (mm-30) REVERT: C 502 LYS cc_start: 0.9173 (ttmt) cc_final: 0.8903 (mtpp) REVERT: C 528 PHE cc_start: 0.8794 (t80) cc_final: 0.8511 (t80) REVERT: C 536 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7666 (tm-30) REVERT: C 545 ASN cc_start: 0.8658 (t0) cc_final: 0.8284 (t0) REVERT: C 574 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8467 (tm-30) REVERT: C 583 HIS cc_start: 0.8537 (m-70) cc_final: 0.8318 (m-70) REVERT: C 599 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8497 (tm-30) REVERT: C 625 ARG cc_start: 0.6909 (ttt-90) cc_final: 0.6267 (tmt170) REVERT: D 63 GLN cc_start: 0.8616 (tm-30) cc_final: 0.7903 (tm-30) REVERT: D 85 GLN cc_start: 0.9042 (tp40) cc_final: 0.8578 (tp40) REVERT: D 105 LEU cc_start: 0.9533 (mt) cc_final: 0.9231 (mt) REVERT: D 117 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7975 (mm-30) REVERT: D 118 TRP cc_start: 0.8304 (t60) cc_final: 0.7879 (t60) REVERT: D 177 TRP cc_start: 0.9120 (m100) cc_final: 0.8751 (t-100) REVERT: D 187 LEU cc_start: 0.9179 (mm) cc_final: 0.8926 (mm) REVERT: D 281 LYS cc_start: 0.8566 (tttt) cc_final: 0.8050 (tttt) REVERT: D 306 LYS cc_start: 0.9153 (ttmm) cc_final: 0.8615 (ttpt) REVERT: D 523 SER cc_start: 0.8761 (p) cc_final: 0.8335 (p) REVERT: D 536 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7643 (tm-30) REVERT: D 545 ASN cc_start: 0.8851 (t0) cc_final: 0.8616 (t0) REVERT: D 546 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8346 (tm-30) REVERT: D 578 LEU cc_start: 0.9412 (mt) cc_final: 0.9118 (mt) REVERT: D 599 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8408 (tm-30) REVERT: D 618 TYR cc_start: 0.8223 (m-80) cc_final: 0.7695 (m-80) REVERT: G 83 MET cc_start: 0.8928 (tpp) cc_final: 0.8340 (tpp) REVERT: G 91 CYS cc_start: 0.8123 (m) cc_final: 0.7244 (m) REVERT: G 105 LEU cc_start: 0.9609 (mt) cc_final: 0.9233 (mt) REVERT: G 195 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7631 (mt-10) REVERT: G 264 LYS cc_start: 0.8357 (mmtt) cc_final: 0.8021 (mtpp) REVERT: G 277 TYR cc_start: 0.8352 (m-80) cc_final: 0.7905 (m-80) REVERT: G 317 LYS cc_start: 0.8754 (mtmm) cc_final: 0.8504 (mtmt) REVERT: G 498 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8044 (mm-30) REVERT: G 512 LEU cc_start: 0.9057 (pt) cc_final: 0.8668 (pt) REVERT: G 538 PHE cc_start: 0.9243 (t80) cc_final: 0.9017 (t80) REVERT: G 545 ASN cc_start: 0.8761 (t0) cc_final: 0.8407 (t0) REVERT: G 548 PHE cc_start: 0.9272 (m-10) cc_final: 0.9000 (m-10) REVERT: G 599 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8425 (tm-30) REVERT: G 625 ARG cc_start: 0.7878 (tmt170) cc_final: 0.7144 (tpt90) REVERT: J 63 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8225 (tm-30) REVERT: J 85 GLN cc_start: 0.9072 (tp-100) cc_final: 0.8666 (tp-100) REVERT: J 101 VAL cc_start: 0.9220 (p) cc_final: 0.8867 (p) REVERT: J 105 LEU cc_start: 0.9544 (mt) cc_final: 0.9218 (mt) REVERT: J 116 GLU cc_start: 0.8810 (tp30) cc_final: 0.8558 (tp30) REVERT: J 195 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7813 (mt-10) REVERT: J 213 THR cc_start: 0.8728 (t) cc_final: 0.7729 (t) REVERT: J 225 LEU cc_start: 0.9435 (tp) cc_final: 0.9124 (tt) REVERT: J 245 GLU cc_start: 0.8019 (mp0) cc_final: 0.7659 (mp0) REVERT: J 297 ARG cc_start: 0.9279 (ttt-90) cc_final: 0.9020 (ttt-90) REVERT: J 305 GLN cc_start: 0.9324 (tm-30) cc_final: 0.8819 (tt0) REVERT: J 309 GLN cc_start: 0.9344 (mt0) cc_final: 0.9061 (mt0) REVERT: J 502 LYS cc_start: 0.9164 (ttmt) cc_final: 0.8896 (mtpp) REVERT: J 528 PHE cc_start: 0.8782 (t80) cc_final: 0.8502 (t80) REVERT: J 536 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7720 (tm-30) REVERT: J 545 ASN cc_start: 0.8780 (t0) cc_final: 0.8493 (t0) REVERT: J 599 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8486 (tm-30) REVERT: J 625 ARG cc_start: 0.6919 (ttt-90) cc_final: 0.6273 (tmt170) REVERT: E 85 GLN cc_start: 0.9067 (tp40) cc_final: 0.8574 (tp40) REVERT: E 99 TYR cc_start: 0.8861 (t80) cc_final: 0.8525 (t80) REVERT: E 105 LEU cc_start: 0.9533 (mt) cc_final: 0.9220 (mt) REVERT: E 117 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8004 (mm-30) REVERT: E 118 TRP cc_start: 0.8298 (t60) cc_final: 0.7862 (t60) REVERT: E 177 TRP cc_start: 0.9120 (m100) cc_final: 0.8749 (t-100) REVERT: E 187 LEU cc_start: 0.9176 (mm) cc_final: 0.8919 (mm) REVERT: E 267 ARG cc_start: 0.8693 (tmm-80) cc_final: 0.8493 (tmm-80) REVERT: E 281 LYS cc_start: 0.8570 (tttt) cc_final: 0.8038 (tttt) REVERT: E 306 LYS cc_start: 0.9144 (ttmm) cc_final: 0.8631 (tttt) REVERT: E 523 SER cc_start: 0.8747 (p) cc_final: 0.8308 (p) REVERT: E 536 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7617 (tm-30) REVERT: E 545 ASN cc_start: 0.8880 (t0) cc_final: 0.8656 (t0) REVERT: E 546 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8359 (tm-30) REVERT: E 578 LEU cc_start: 0.9405 (mt) cc_final: 0.9129 (mt) REVERT: E 599 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8419 (tm-30) REVERT: E 610 TYR cc_start: 0.8565 (t80) cc_final: 0.7635 (t80) REVERT: E 618 TYR cc_start: 0.8242 (m-80) cc_final: 0.7674 (m-80) REVERT: H 83 MET cc_start: 0.8921 (tpp) cc_final: 0.8356 (tpp) REVERT: H 91 CYS cc_start: 0.8014 (m) cc_final: 0.7161 (m) REVERT: H 105 LEU cc_start: 0.9602 (mt) cc_final: 0.9228 (mt) REVERT: H 163 TYR cc_start: 0.7985 (m-80) cc_final: 0.7720 (m-80) REVERT: H 195 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7623 (mt-10) REVERT: H 234 ARG cc_start: 0.7940 (ttm170) cc_final: 0.7529 (ttp-170) REVERT: H 264 LYS cc_start: 0.8333 (mmtt) cc_final: 0.8013 (mtpp) REVERT: H 277 TYR cc_start: 0.8375 (m-80) cc_final: 0.7919 (m-80) REVERT: H 295 ILE cc_start: 0.9666 (tt) cc_final: 0.9464 (tt) REVERT: H 317 LYS cc_start: 0.8702 (mtmm) cc_final: 0.8464 (mtmt) REVERT: H 498 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8022 (mm-30) REVERT: H 512 LEU cc_start: 0.9047 (pt) cc_final: 0.8694 (pt) REVERT: H 545 ASN cc_start: 0.8808 (t0) cc_final: 0.8444 (t0) REVERT: H 548 PHE cc_start: 0.9282 (m-10) cc_final: 0.9019 (m-10) REVERT: H 599 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8439 (tm-30) REVERT: H 625 ARG cc_start: 0.7865 (tmt170) cc_final: 0.7138 (tpt90) REVERT: K 63 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8256 (tm-30) REVERT: K 81 GLN cc_start: 0.8644 (tp-100) cc_final: 0.8259 (tp-100) REVERT: K 85 GLN cc_start: 0.9007 (tp-100) cc_final: 0.8630 (tp-100) REVERT: K 101 VAL cc_start: 0.9244 (p) cc_final: 0.8958 (p) REVERT: K 105 LEU cc_start: 0.9534 (mt) cc_final: 0.9224 (mt) REVERT: K 116 GLU cc_start: 0.8805 (tp30) cc_final: 0.8552 (tp30) REVERT: K 195 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7832 (mt-10) REVERT: K 213 THR cc_start: 0.8686 (t) cc_final: 0.7795 (t) REVERT: K 225 LEU cc_start: 0.9397 (tp) cc_final: 0.9046 (tt) REVERT: K 245 GLU cc_start: 0.8037 (mp0) cc_final: 0.7668 (mp0) REVERT: K 305 GLN cc_start: 0.9301 (tm-30) cc_final: 0.8806 (tt0) REVERT: K 309 GLN cc_start: 0.9342 (mt0) cc_final: 0.9053 (mt0) REVERT: K 498 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8371 (mm-30) REVERT: K 528 PHE cc_start: 0.8786 (t80) cc_final: 0.8507 (t80) REVERT: K 536 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7734 (tm-30) REVERT: K 545 ASN cc_start: 0.8786 (t0) cc_final: 0.8490 (t0) REVERT: K 583 HIS cc_start: 0.8547 (m-70) cc_final: 0.8318 (m-70) REVERT: K 599 GLN cc_start: 0.8935 (tm-30) cc_final: 0.8492 (tm-30) REVERT: K 625 ARG cc_start: 0.6909 (ttt-90) cc_final: 0.6269 (tmt170) REVERT: F 63 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7918 (tm-30) REVERT: F 85 GLN cc_start: 0.9147 (tp40) cc_final: 0.8240 (tp-100) REVERT: F 105 LEU cc_start: 0.9529 (mt) cc_final: 0.9232 (mt) REVERT: F 117 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7902 (mm-30) REVERT: F 118 TRP cc_start: 0.8270 (t60) cc_final: 0.7906 (t60) REVERT: F 177 TRP cc_start: 0.9127 (m100) cc_final: 0.8803 (t-100) REVERT: F 187 LEU cc_start: 0.9177 (mm) cc_final: 0.8921 (mm) REVERT: F 267 ARG cc_start: 0.8698 (tmm-80) cc_final: 0.8493 (tmm-80) REVERT: F 281 LYS cc_start: 0.8543 (tttt) cc_final: 0.8013 (tttt) REVERT: F 295 ILE cc_start: 0.9638 (tt) cc_final: 0.9435 (tt) REVERT: F 309 GLN cc_start: 0.9364 (mt0) cc_final: 0.9147 (mt0) REVERT: F 523 SER cc_start: 0.8769 (p) cc_final: 0.8328 (p) REVERT: F 536 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7605 (tm-30) REVERT: F 578 LEU cc_start: 0.9400 (mt) cc_final: 0.9088 (mt) REVERT: F 599 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8398 (tm-30) REVERT: F 610 TYR cc_start: 0.8511 (t80) cc_final: 0.7597 (t80) REVERT: F 625 ARG cc_start: 0.6591 (ttt-90) cc_final: 0.6276 (tmt170) REVERT: I 83 MET cc_start: 0.8947 (tpp) cc_final: 0.8521 (tpp) REVERT: I 91 CYS cc_start: 0.8100 (m) cc_final: 0.7249 (m) REVERT: I 105 LEU cc_start: 0.9593 (mt) cc_final: 0.9219 (mt) REVERT: I 195 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7616 (mt-10) REVERT: I 264 LYS cc_start: 0.8357 (mmtt) cc_final: 0.8028 (mtpp) REVERT: I 317 LYS cc_start: 0.8697 (mtmm) cc_final: 0.8455 (mtmt) REVERT: I 498 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8029 (mm-30) REVERT: I 512 LEU cc_start: 0.9052 (pt) cc_final: 0.8667 (pt) REVERT: I 538 PHE cc_start: 0.9251 (t80) cc_final: 0.9005 (t80) REVERT: I 545 ASN cc_start: 0.8921 (t0) cc_final: 0.8696 (t0) REVERT: I 548 PHE cc_start: 0.9264 (m-10) cc_final: 0.9056 (m-10) REVERT: I 599 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8414 (tm-30) REVERT: I 625 ARG cc_start: 0.7866 (tmt170) cc_final: 0.7143 (tpt90) REVERT: L 101 VAL cc_start: 0.9213 (p) cc_final: 0.8859 (p) REVERT: L 105 LEU cc_start: 0.9548 (mt) cc_final: 0.9222 (mt) REVERT: L 116 GLU cc_start: 0.8800 (tp30) cc_final: 0.8553 (tp30) REVERT: L 177 TRP cc_start: 0.9383 (m100) cc_final: 0.9020 (m100) REVERT: L 195 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7804 (mt-10) REVERT: L 213 THR cc_start: 0.8691 (t) cc_final: 0.7780 (t) REVERT: L 225 LEU cc_start: 0.9407 (tp) cc_final: 0.9047 (tt) REVERT: L 245 GLU cc_start: 0.8051 (mp0) cc_final: 0.7688 (mp0) REVERT: L 297 ARG cc_start: 0.9282 (ttt-90) cc_final: 0.9027 (ttt-90) REVERT: L 305 GLN cc_start: 0.9305 (tm-30) cc_final: 0.8809 (tt0) REVERT: L 309 GLN cc_start: 0.9354 (mt0) cc_final: 0.9087 (mt0) REVERT: L 498 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8381 (mm-30) REVERT: L 528 PHE cc_start: 0.8794 (t80) cc_final: 0.8522 (t80) REVERT: L 536 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7655 (tm-30) REVERT: L 545 ASN cc_start: 0.8791 (t0) cc_final: 0.8489 (t0) REVERT: L 599 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8489 (tm-30) REVERT: L 625 ARG cc_start: 0.6910 (ttt-90) cc_final: 0.6273 (tmt170) outliers start: 0 outliers final: 0 residues processed: 2209 average time/residue: 0.2468 time to fit residues: 879.3460 Evaluate side-chains 2060 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2060 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 379 optimal weight: 7.9990 chunk 460 optimal weight: 0.6980 chunk 436 optimal weight: 8.9990 chunk 318 optimal weight: 3.9990 chunk 462 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 237 optimal weight: 7.9990 chunk 403 optimal weight: 5.9990 chunk 293 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 290 optimal weight: 9.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 GLN B 96 GLN B 632 GLN C 632 GLN D 632 GLN G 85 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 632 GLN J 632 GLN ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 632 GLN H 96 GLN ** H 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 632 GLN K 632 GLN F 632 GLN I 96 GLN I 632 GLN L 632 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.157683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.131185 restraints weight = 68183.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.135422 restraints weight = 37382.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.138274 restraints weight = 24096.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.140218 restraints weight = 17323.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.141555 restraints weight = 13623.037| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 39672 Z= 0.159 Angle : 0.648 6.692 53820 Z= 0.325 Chirality : 0.042 0.139 6168 Planarity : 0.005 0.048 6888 Dihedral : 5.325 20.314 5424 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.12), residues: 4740 helix: -1.73 (0.10), residues: 2412 sheet: -2.14 (0.39), residues: 120 loop : -1.60 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 234 TYR 0.016 0.002 TYR A 568 PHE 0.024 0.002 PHE E 538 TRP 0.031 0.002 TRP C 118 HIS 0.004 0.001 HIS L 583 Details of bonding type rmsd covalent geometry : bond 0.00357 (39672) covalent geometry : angle 0.64791 (53820) hydrogen bonds : bond 0.03488 ( 1410) hydrogen bonds : angle 4.76167 ( 3909) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2208 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2208 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.8643 (tm-30) cc_final: 0.7919 (tm-30) REVERT: A 83 MET cc_start: 0.8799 (mmp) cc_final: 0.8585 (mmp) REVERT: A 85 GLN cc_start: 0.9112 (tp40) cc_final: 0.8782 (tp40) REVERT: A 105 LEU cc_start: 0.9547 (mt) cc_final: 0.9224 (mt) REVERT: A 117 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7969 (mm-30) REVERT: A 177 TRP cc_start: 0.9140 (m100) cc_final: 0.8780 (t-100) REVERT: A 187 LEU cc_start: 0.9373 (mm) cc_final: 0.9105 (mm) REVERT: A 225 LEU cc_start: 0.9232 (tt) cc_final: 0.8997 (tt) REVERT: A 281 LYS cc_start: 0.8540 (tttt) cc_final: 0.8003 (tttt) REVERT: A 297 ARG cc_start: 0.9126 (ttt-90) cc_final: 0.8788 (ttt-90) REVERT: A 306 LYS cc_start: 0.8911 (tttt) cc_final: 0.8671 (ttmm) REVERT: A 309 GLN cc_start: 0.9366 (mt0) cc_final: 0.9163 (mt0) REVERT: A 523 SER cc_start: 0.8712 (p) cc_final: 0.8266 (p) REVERT: A 536 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7556 (tm-30) REVERT: A 571 TYR cc_start: 0.8912 (t80) cc_final: 0.8565 (t80) REVERT: A 574 GLU cc_start: 0.9280 (tm-30) cc_final: 0.8907 (tm-30) REVERT: A 575 ARG cc_start: 0.8702 (ttt-90) cc_final: 0.8135 (ttt-90) REVERT: A 578 LEU cc_start: 0.9389 (mt) cc_final: 0.9093 (mt) REVERT: A 599 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8420 (tm-30) REVERT: A 600 LEU cc_start: 0.9495 (tt) cc_final: 0.9293 (tt) REVERT: A 610 TYR cc_start: 0.8537 (t80) cc_final: 0.7626 (t80) REVERT: A 618 TYR cc_start: 0.8144 (m-80) cc_final: 0.7943 (m-80) REVERT: A 631 ARG cc_start: 0.6040 (ttp-110) cc_final: 0.5318 (tpp-160) REVERT: B 83 MET cc_start: 0.8947 (tpp) cc_final: 0.8370 (tpp) REVERT: B 91 CYS cc_start: 0.8114 (m) cc_final: 0.7533 (m) REVERT: B 105 LEU cc_start: 0.9601 (mt) cc_final: 0.9253 (mt) REVERT: B 195 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7661 (mt-10) REVERT: B 264 LYS cc_start: 0.8300 (mmtt) cc_final: 0.7990 (mtpp) REVERT: B 277 TYR cc_start: 0.8469 (m-80) cc_final: 0.7386 (m-80) REVERT: B 281 LYS cc_start: 0.8445 (tttt) cc_final: 0.8169 (tttt) REVERT: B 317 LYS cc_start: 0.8738 (mtmm) cc_final: 0.8445 (mtmt) REVERT: B 498 GLU cc_start: 0.8568 (mm-30) cc_final: 0.7974 (mm-30) REVERT: B 512 LEU cc_start: 0.9048 (pt) cc_final: 0.8736 (pt) REVERT: B 538 PHE cc_start: 0.9102 (t80) cc_final: 0.8821 (t80) REVERT: B 548 PHE cc_start: 0.9238 (m-10) cc_final: 0.9018 (m-10) REVERT: B 599 GLN cc_start: 0.8990 (tm-30) cc_final: 0.8460 (tm-30) REVERT: B 625 ARG cc_start: 0.7827 (tmt170) cc_final: 0.7166 (tpt90) REVERT: C 63 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8266 (tm-30) REVERT: C 81 GLN cc_start: 0.8694 (tp-100) cc_final: 0.8363 (tp-100) REVERT: C 85 GLN cc_start: 0.9065 (tp-100) cc_final: 0.8532 (tp-100) REVERT: C 101 VAL cc_start: 0.9223 (p) cc_final: 0.8919 (p) REVERT: C 105 LEU cc_start: 0.9539 (mt) cc_final: 0.9231 (mt) REVERT: C 195 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7845 (mt-10) REVERT: C 213 THR cc_start: 0.8567 (t) cc_final: 0.7239 (t) REVERT: C 225 LEU cc_start: 0.9413 (tp) cc_final: 0.9093 (tt) REVERT: C 245 GLU cc_start: 0.8171 (mp0) cc_final: 0.7705 (mp0) REVERT: C 249 PHE cc_start: 0.9026 (m-10) cc_final: 0.8481 (m-10) REVERT: C 250 LYS cc_start: 0.8455 (tptm) cc_final: 0.8015 (tptm) REVERT: C 268 LEU cc_start: 0.9289 (pt) cc_final: 0.9085 (pt) REVERT: C 305 GLN cc_start: 0.9308 (tm-30) cc_final: 0.8236 (tm-30) REVERT: C 498 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8364 (mm-30) REVERT: C 528 PHE cc_start: 0.8714 (t80) cc_final: 0.8430 (t80) REVERT: C 536 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7778 (tm-30) REVERT: C 545 ASN cc_start: 0.8613 (t0) cc_final: 0.8350 (t0) REVERT: C 574 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8402 (tm-30) REVERT: C 599 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8538 (tm-30) REVERT: C 625 ARG cc_start: 0.6882 (ttt-90) cc_final: 0.6300 (tmt170) REVERT: D 63 GLN cc_start: 0.8646 (tm-30) cc_final: 0.7942 (tm-30) REVERT: D 79 ARG cc_start: 0.9209 (mtm-85) cc_final: 0.8993 (mtm-85) REVERT: D 85 GLN cc_start: 0.8921 (tp40) cc_final: 0.8413 (tp40) REVERT: D 99 TYR cc_start: 0.8849 (t80) cc_final: 0.8587 (t80) REVERT: D 105 LEU cc_start: 0.9569 (mt) cc_final: 0.9264 (mt) REVERT: D 117 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7860 (mm-30) REVERT: D 177 TRP cc_start: 0.9141 (m100) cc_final: 0.8806 (t-100) REVERT: D 187 LEU cc_start: 0.9113 (mm) cc_final: 0.8906 (mm) REVERT: D 225 LEU cc_start: 0.9254 (tt) cc_final: 0.8984 (tt) REVERT: D 244 PRO cc_start: 0.9404 (Cg_exo) cc_final: 0.8511 (Cg_endo) REVERT: D 245 GLU cc_start: 0.8357 (mp0) cc_final: 0.7963 (mp0) REVERT: D 281 LYS cc_start: 0.8557 (tttt) cc_final: 0.8036 (tttt) REVERT: D 297 ARG cc_start: 0.9123 (ttt-90) cc_final: 0.8884 (ttt-90) REVERT: D 306 LYS cc_start: 0.9050 (ttmm) cc_final: 0.8603 (tttt) REVERT: D 309 GLN cc_start: 0.9374 (mt0) cc_final: 0.9106 (mt0) REVERT: D 523 SER cc_start: 0.8726 (p) cc_final: 0.8286 (p) REVERT: D 536 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7484 (tm-30) REVERT: D 546 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8364 (tm-30) REVERT: D 571 TYR cc_start: 0.8939 (t80) cc_final: 0.8454 (t80) REVERT: D 578 LEU cc_start: 0.9365 (mt) cc_final: 0.9059 (mt) REVERT: D 599 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8438 (tm-30) REVERT: D 610 TYR cc_start: 0.8532 (t80) cc_final: 0.7614 (t80) REVERT: D 631 ARG cc_start: 0.6039 (ttp-110) cc_final: 0.5312 (tpp-160) REVERT: G 83 MET cc_start: 0.8919 (tpp) cc_final: 0.8391 (tpp) REVERT: G 91 CYS cc_start: 0.8014 (m) cc_final: 0.7479 (m) REVERT: G 105 LEU cc_start: 0.9608 (mt) cc_final: 0.9278 (mt) REVERT: G 195 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7641 (mt-10) REVERT: G 264 LYS cc_start: 0.8309 (mmtt) cc_final: 0.7990 (mtpp) REVERT: G 273 GLU cc_start: 0.9050 (tt0) cc_final: 0.8596 (tt0) REVERT: G 277 TYR cc_start: 0.8460 (m-80) cc_final: 0.7353 (m-80) REVERT: G 281 LYS cc_start: 0.8436 (tttt) cc_final: 0.8180 (tttt) REVERT: G 295 ILE cc_start: 0.9662 (tt) cc_final: 0.9460 (tt) REVERT: G 296 LEU cc_start: 0.9672 (tp) cc_final: 0.9461 (tp) REVERT: G 309 GLN cc_start: 0.9369 (tt0) cc_final: 0.8365 (mt0) REVERT: G 317 LYS cc_start: 0.8732 (mtmm) cc_final: 0.8462 (mtmt) REVERT: G 498 GLU cc_start: 0.8577 (mm-30) cc_final: 0.7987 (mm-30) REVERT: G 512 LEU cc_start: 0.9052 (pt) cc_final: 0.8722 (pt) REVERT: G 538 PHE cc_start: 0.9256 (t80) cc_final: 0.8991 (t80) REVERT: G 545 ASN cc_start: 0.8742 (t0) cc_final: 0.8407 (t0) REVERT: G 599 GLN cc_start: 0.8989 (tm-30) cc_final: 0.8472 (tm-30) REVERT: G 625 ARG cc_start: 0.7829 (tmt170) cc_final: 0.7170 (tpt90) REVERT: J 63 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8234 (tm-30) REVERT: J 81 GLN cc_start: 0.8684 (tp-100) cc_final: 0.8331 (tp-100) REVERT: J 85 GLN cc_start: 0.9059 (tp-100) cc_final: 0.8546 (tp-100) REVERT: J 101 VAL cc_start: 0.9242 (p) cc_final: 0.8933 (p) REVERT: J 105 LEU cc_start: 0.9543 (mt) cc_final: 0.9191 (mt) REVERT: J 195 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7846 (mt-10) REVERT: J 213 THR cc_start: 0.8571 (t) cc_final: 0.7236 (t) REVERT: J 225 LEU cc_start: 0.9406 (tp) cc_final: 0.9150 (tt) REVERT: J 245 GLU cc_start: 0.8172 (mp0) cc_final: 0.7708 (mp0) REVERT: J 249 PHE cc_start: 0.9015 (m-10) cc_final: 0.8490 (m-10) REVERT: J 250 LYS cc_start: 0.8460 (tptm) cc_final: 0.8154 (tptm) REVERT: J 281 LYS cc_start: 0.8118 (tttt) cc_final: 0.7729 (tttt) REVERT: J 297 ARG cc_start: 0.9274 (ttt-90) cc_final: 0.8960 (ttt-90) REVERT: J 305 GLN cc_start: 0.9321 (tm-30) cc_final: 0.8870 (tt0) REVERT: J 309 GLN cc_start: 0.9327 (mt0) cc_final: 0.8925 (mt0) REVERT: J 498 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8353 (mm-30) REVERT: J 528 PHE cc_start: 0.8717 (t80) cc_final: 0.8431 (t80) REVERT: J 536 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7780 (tm-30) REVERT: J 545 ASN cc_start: 0.8724 (t0) cc_final: 0.8484 (t0) REVERT: J 574 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8551 (tm-30) REVERT: J 599 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8498 (tm-30) REVERT: J 625 ARG cc_start: 0.6884 (ttt-90) cc_final: 0.6293 (tmt170) REVERT: E 85 GLN cc_start: 0.8938 (tp40) cc_final: 0.8449 (tp40) REVERT: E 99 TYR cc_start: 0.8859 (t80) cc_final: 0.8653 (t80) REVERT: E 105 LEU cc_start: 0.9545 (mt) cc_final: 0.9248 (mt) REVERT: E 177 TRP cc_start: 0.9120 (m100) cc_final: 0.8772 (t-100) REVERT: E 187 LEU cc_start: 0.9223 (mm) cc_final: 0.9013 (mm) REVERT: E 225 LEU cc_start: 0.9253 (tt) cc_final: 0.8976 (tt) REVERT: E 281 LYS cc_start: 0.8541 (tttt) cc_final: 0.8021 (tttt) REVERT: E 297 ARG cc_start: 0.9125 (ttt-90) cc_final: 0.8784 (ttt-90) REVERT: E 306 LYS cc_start: 0.9073 (ttmm) cc_final: 0.8582 (tttt) REVERT: E 491 LEU cc_start: 0.9303 (pt) cc_final: 0.8916 (pt) REVERT: E 523 SER cc_start: 0.8724 (p) cc_final: 0.8282 (p) REVERT: E 528 PHE cc_start: 0.9206 (t80) cc_final: 0.8999 (t80) REVERT: E 532 THR cc_start: 0.9144 (t) cc_final: 0.8932 (t) REVERT: E 536 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7686 (tm-30) REVERT: E 546 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8352 (tm-30) REVERT: E 571 TYR cc_start: 0.8882 (t80) cc_final: 0.8678 (t80) REVERT: E 578 LEU cc_start: 0.9363 (mt) cc_final: 0.9082 (mt) REVERT: E 599 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8425 (tm-30) REVERT: E 610 TYR cc_start: 0.8534 (t80) cc_final: 0.7645 (t80) REVERT: H 83 MET cc_start: 0.8877 (tpp) cc_final: 0.8402 (tpp) REVERT: H 91 CYS cc_start: 0.8026 (m) cc_final: 0.7498 (m) REVERT: H 105 LEU cc_start: 0.9607 (mt) cc_final: 0.9255 (mt) REVERT: H 195 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7778 (mt-10) REVERT: H 264 LYS cc_start: 0.8287 (mmtt) cc_final: 0.7984 (mtpp) REVERT: H 273 GLU cc_start: 0.9072 (tt0) cc_final: 0.8612 (tt0) REVERT: H 277 TYR cc_start: 0.8460 (m-80) cc_final: 0.7368 (m-80) REVERT: H 281 LYS cc_start: 0.8428 (tttt) cc_final: 0.8169 (tttt) REVERT: H 295 ILE cc_start: 0.9660 (tt) cc_final: 0.9442 (tt) REVERT: H 306 LYS cc_start: 0.9148 (tttt) cc_final: 0.8807 (ttmm) REVERT: H 309 GLN cc_start: 0.9365 (tt0) cc_final: 0.8385 (mt0) REVERT: H 317 LYS cc_start: 0.8746 (mtmm) cc_final: 0.8476 (mtmt) REVERT: H 498 GLU cc_start: 0.8549 (mm-30) cc_final: 0.7954 (mm-30) REVERT: H 538 PHE cc_start: 0.9129 (t80) cc_final: 0.8854 (t80) REVERT: H 545 ASN cc_start: 0.8819 (t0) cc_final: 0.8467 (t0) REVERT: H 599 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8490 (tm-30) REVERT: H 625 ARG cc_start: 0.7815 (tmt170) cc_final: 0.7152 (tpt90) REVERT: K 63 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8294 (tm-30) REVERT: K 81 GLN cc_start: 0.8737 (tp-100) cc_final: 0.8393 (tp-100) REVERT: K 85 GLN cc_start: 0.9033 (tp-100) cc_final: 0.8619 (tp-100) REVERT: K 101 VAL cc_start: 0.9230 (p) cc_final: 0.8929 (p) REVERT: K 105 LEU cc_start: 0.9542 (mt) cc_final: 0.9236 (mt) REVERT: K 195 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7861 (mt-10) REVERT: K 213 THR cc_start: 0.8567 (t) cc_final: 0.7238 (t) REVERT: K 225 LEU cc_start: 0.9413 (tp) cc_final: 0.9154 (tt) REVERT: K 245 GLU cc_start: 0.8056 (mp0) cc_final: 0.7663 (mp0) REVERT: K 249 PHE cc_start: 0.9055 (m-10) cc_final: 0.8643 (m-10) REVERT: K 268 LEU cc_start: 0.9276 (pt) cc_final: 0.9073 (pt) REVERT: K 305 GLN cc_start: 0.9287 (tm-30) cc_final: 0.8871 (tt0) REVERT: K 309 GLN cc_start: 0.9318 (mt0) cc_final: 0.8927 (mt0) REVERT: K 498 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8372 (mm-30) REVERT: K 528 PHE cc_start: 0.8591 (t80) cc_final: 0.8237 (t80) REVERT: K 536 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7747 (tm-30) REVERT: K 545 ASN cc_start: 0.8740 (t0) cc_final: 0.8455 (t0) REVERT: K 574 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8504 (tm-30) REVERT: K 599 GLN cc_start: 0.8968 (tm-30) cc_final: 0.8527 (tm-30) REVERT: K 625 ARG cc_start: 0.6884 (ttt-90) cc_final: 0.6297 (tmt170) REVERT: F 63 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8113 (tm-30) REVERT: F 83 MET cc_start: 0.9118 (tpt) cc_final: 0.8076 (tpp) REVERT: F 85 GLN cc_start: 0.9166 (tp40) cc_final: 0.8738 (tp40) REVERT: F 99 TYR cc_start: 0.8867 (t80) cc_final: 0.8634 (t80) REVERT: F 105 LEU cc_start: 0.9562 (mt) cc_final: 0.9275 (mt) REVERT: F 117 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7890 (mm-30) REVERT: F 118 TRP cc_start: 0.8234 (t60) cc_final: 0.7911 (t60) REVERT: F 177 TRP cc_start: 0.9113 (m100) cc_final: 0.8778 (t-100) REVERT: F 187 LEU cc_start: 0.9229 (mm) cc_final: 0.8993 (mm) REVERT: F 225 LEU cc_start: 0.9244 (tt) cc_final: 0.8970 (tt) REVERT: F 281 LYS cc_start: 0.8539 (tttt) cc_final: 0.8004 (tttt) REVERT: F 297 ARG cc_start: 0.9126 (ttt-90) cc_final: 0.8764 (ttt-90) REVERT: F 523 SER cc_start: 0.8721 (p) cc_final: 0.8282 (p) REVERT: F 536 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7610 (tm-30) REVERT: F 578 LEU cc_start: 0.9399 (mt) cc_final: 0.9085 (mt) REVERT: F 599 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8436 (tm-30) REVERT: F 610 TYR cc_start: 0.8517 (t80) cc_final: 0.7601 (t80) REVERT: F 625 ARG cc_start: 0.6569 (ttt-90) cc_final: 0.6280 (tmt170) REVERT: I 83 MET cc_start: 0.8929 (tpp) cc_final: 0.8575 (tpp) REVERT: I 91 CYS cc_start: 0.7998 (m) cc_final: 0.7133 (m) REVERT: I 95 LYS cc_start: 0.8877 (mttp) cc_final: 0.8670 (mttp) REVERT: I 105 LEU cc_start: 0.9602 (mt) cc_final: 0.9262 (mt) REVERT: I 195 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7649 (mt-10) REVERT: I 264 LYS cc_start: 0.8305 (mmtt) cc_final: 0.7989 (mtpp) REVERT: I 273 GLU cc_start: 0.9064 (tt0) cc_final: 0.8588 (tt0) REVERT: I 277 TYR cc_start: 0.8454 (m-80) cc_final: 0.7383 (m-80) REVERT: I 281 LYS cc_start: 0.8429 (tttt) cc_final: 0.8169 (tttt) REVERT: I 309 GLN cc_start: 0.9327 (tt0) cc_final: 0.8249 (mt0) REVERT: I 317 LYS cc_start: 0.8726 (mtmm) cc_final: 0.8462 (mtmt) REVERT: I 498 GLU cc_start: 0.8576 (mm-30) cc_final: 0.7989 (mm-30) REVERT: I 512 LEU cc_start: 0.9046 (pt) cc_final: 0.8713 (pt) REVERT: I 538 PHE cc_start: 0.9245 (t80) cc_final: 0.8976 (t80) REVERT: I 599 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8478 (tm-30) REVERT: I 625 ARG cc_start: 0.7817 (tmt170) cc_final: 0.7151 (tpt90) REVERT: L 81 GLN cc_start: 0.8687 (tp-100) cc_final: 0.8345 (tp-100) REVERT: L 101 VAL cc_start: 0.9234 (p) cc_final: 0.8921 (p) REVERT: L 105 LEU cc_start: 0.9556 (mt) cc_final: 0.9198 (mt) REVERT: L 177 TRP cc_start: 0.9353 (m100) cc_final: 0.8971 (m100) REVERT: L 195 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7839 (mt-10) REVERT: L 225 LEU cc_start: 0.9435 (tp) cc_final: 0.9171 (tt) REVERT: L 245 GLU cc_start: 0.8055 (mp0) cc_final: 0.7688 (mp0) REVERT: L 281 LYS cc_start: 0.8146 (tttt) cc_final: 0.7738 (tttt) REVERT: L 297 ARG cc_start: 0.9267 (ttt-90) cc_final: 0.8956 (ttt-90) REVERT: L 305 GLN cc_start: 0.9312 (tm-30) cc_final: 0.8880 (tt0) REVERT: L 309 GLN cc_start: 0.9333 (mt0) cc_final: 0.8953 (mt0) REVERT: L 491 LEU cc_start: 0.9225 (pt) cc_final: 0.8984 (pt) REVERT: L 498 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8338 (mm-30) REVERT: L 528 PHE cc_start: 0.8596 (t80) cc_final: 0.8246 (t80) REVERT: L 536 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7731 (tm-30) REVERT: L 545 ASN cc_start: 0.8723 (t0) cc_final: 0.8469 (t0) REVERT: L 599 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8538 (tm-30) REVERT: L 625 ARG cc_start: 0.6866 (ttt-90) cc_final: 0.6293 (tmt170) outliers start: 0 outliers final: 0 residues processed: 2208 average time/residue: 0.2429 time to fit residues: 867.7969 Evaluate side-chains 1983 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1983 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 253 optimal weight: 30.0000 chunk 203 optimal weight: 1.9990 chunk 235 optimal weight: 8.9990 chunk 440 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 312 optimal weight: 0.7980 chunk 360 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 370 optimal weight: 10.0000 chunk 254 optimal weight: 7.9990 chunk 449 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 632 GLN B 583 HIS B 632 GLN C 632 GLN D 305 GLN D 632 GLN G 309 GLN G 583 HIS G 632 GLN J 632 GLN E 632 GLN H 309 GLN H 583 HIS H 632 GLN K 632 GLN F 305 GLN F 632 GLN I 309 GLN I 583 HIS I 632 GLN L 632 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.162543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.135739 restraints weight = 68125.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.140116 restraints weight = 36972.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.143055 restraints weight = 23676.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.145034 restraints weight = 17010.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.146423 restraints weight = 13349.896| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 39672 Z= 0.108 Angle : 0.630 7.073 53820 Z= 0.310 Chirality : 0.041 0.132 6168 Planarity : 0.005 0.061 6888 Dihedral : 4.999 19.607 5424 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.12), residues: 4740 helix: -1.51 (0.10), residues: 2412 sheet: -1.94 (0.39), residues: 120 loop : -1.57 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 617 TYR 0.020 0.002 TYR F 571 PHE 0.025 0.002 PHE A 538 TRP 0.047 0.003 TRP L 118 HIS 0.004 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00245 (39672) covalent geometry : angle 0.62991 (53820) hydrogen bonds : bond 0.03361 ( 1410) hydrogen bonds : angle 4.49361 ( 3909) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2174 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2174 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8271 (tm-30) REVERT: A 83 MET cc_start: 0.8962 (mmp) cc_final: 0.8697 (mmp) REVERT: A 85 GLN cc_start: 0.8604 (tp40) cc_final: 0.8317 (tp40) REVERT: A 105 LEU cc_start: 0.9584 (mt) cc_final: 0.9271 (mt) REVERT: A 177 TRP cc_start: 0.9112 (m100) cc_final: 0.8755 (t-100) REVERT: A 187 LEU cc_start: 0.9175 (mm) cc_final: 0.8941 (mm) REVERT: A 195 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7678 (mt-10) REVERT: A 244 PRO cc_start: 0.9411 (Cg_exo) cc_final: 0.8627 (Cg_endo) REVERT: A 245 GLU cc_start: 0.8401 (mp0) cc_final: 0.7926 (mp0) REVERT: A 267 ARG cc_start: 0.8814 (tmm-80) cc_final: 0.8586 (tmm-80) REVERT: A 281 LYS cc_start: 0.8486 (tttt) cc_final: 0.7973 (tttt) REVERT: A 297 ARG cc_start: 0.9055 (ttt-90) cc_final: 0.8851 (ttt-90) REVERT: A 306 LYS cc_start: 0.8910 (tttt) cc_final: 0.8597 (ttmm) REVERT: A 309 GLN cc_start: 0.9193 (mt0) cc_final: 0.8981 (mt0) REVERT: A 491 LEU cc_start: 0.9237 (pt) cc_final: 0.8843 (pp) REVERT: A 523 SER cc_start: 0.8672 (p) cc_final: 0.8208 (p) REVERT: A 536 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7623 (tm-30) REVERT: A 550 THR cc_start: 0.8768 (p) cc_final: 0.8527 (p) REVERT: A 574 GLU cc_start: 0.9305 (tm-30) cc_final: 0.8879 (tm-30) REVERT: A 578 LEU cc_start: 0.9297 (mt) cc_final: 0.8956 (mt) REVERT: A 599 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8430 (tm-30) REVERT: A 610 TYR cc_start: 0.8438 (t80) cc_final: 0.7579 (t80) REVERT: B 83 MET cc_start: 0.8934 (tpp) cc_final: 0.8479 (tpp) REVERT: B 91 CYS cc_start: 0.7746 (m) cc_final: 0.7517 (m) REVERT: B 105 LEU cc_start: 0.9505 (mt) cc_final: 0.9086 (mt) REVERT: B 195 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7746 (mt-10) REVERT: B 264 LYS cc_start: 0.8251 (mmtt) cc_final: 0.7979 (mtpp) REVERT: B 277 TYR cc_start: 0.8489 (m-80) cc_final: 0.7629 (m-80) REVERT: B 281 LYS cc_start: 0.8508 (tttt) cc_final: 0.8216 (tttt) REVERT: B 296 LEU cc_start: 0.9437 (tp) cc_final: 0.9233 (tp) REVERT: B 309 GLN cc_start: 0.9476 (tt0) cc_final: 0.8616 (mt0) REVERT: B 317 LYS cc_start: 0.8684 (mtmm) cc_final: 0.8380 (mtmt) REVERT: B 498 GLU cc_start: 0.8561 (mm-30) cc_final: 0.7976 (mm-30) REVERT: B 504 ARG cc_start: 0.9082 (ttm170) cc_final: 0.8663 (ttm170) REVERT: B 510 ARG cc_start: 0.8227 (mtp85) cc_final: 0.8027 (mtp85) REVERT: B 532 THR cc_start: 0.8325 (t) cc_final: 0.7804 (t) REVERT: B 536 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7675 (tm-30) REVERT: B 538 PHE cc_start: 0.9235 (t80) cc_final: 0.8886 (t80) REVERT: B 599 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8471 (tm-30) REVERT: B 625 ARG cc_start: 0.7813 (tmt170) cc_final: 0.7164 (tpt90) REVERT: C 81 GLN cc_start: 0.8802 (tp-100) cc_final: 0.8540 (tp-100) REVERT: C 83 MET cc_start: 0.9086 (tpp) cc_final: 0.7254 (tpp) REVERT: C 85 GLN cc_start: 0.9002 (tp-100) cc_final: 0.8549 (tp-100) REVERT: C 86 VAL cc_start: 0.9438 (p) cc_final: 0.9191 (p) REVERT: C 101 VAL cc_start: 0.9178 (p) cc_final: 0.8895 (p) REVERT: C 105 LEU cc_start: 0.9548 (mt) cc_final: 0.9217 (mt) REVERT: C 195 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7811 (mt-10) REVERT: C 225 LEU cc_start: 0.9379 (tp) cc_final: 0.9064 (tt) REVERT: C 245 GLU cc_start: 0.8232 (mp0) cc_final: 0.7804 (mp0) REVERT: C 305 GLN cc_start: 0.9303 (tm-30) cc_final: 0.8954 (tt0) REVERT: C 309 GLN cc_start: 0.9300 (mt0) cc_final: 0.9004 (mt0) REVERT: C 498 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8482 (mm-30) REVERT: C 501 ARG cc_start: 0.8752 (tmm-80) cc_final: 0.8411 (tmm-80) REVERT: C 528 PHE cc_start: 0.8845 (t80) cc_final: 0.8431 (t80) REVERT: C 536 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7760 (tm-30) REVERT: C 574 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8743 (tm-30) REVERT: C 599 GLN cc_start: 0.8967 (tm-30) cc_final: 0.8503 (tm-30) REVERT: C 622 ILE cc_start: 0.8913 (tt) cc_final: 0.8522 (tt) REVERT: C 626 GLU cc_start: 0.8817 (mp0) cc_final: 0.8584 (mp0) REVERT: D 63 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8288 (tm-30) REVERT: D 85 GLN cc_start: 0.8829 (tp40) cc_final: 0.8455 (tp40) REVERT: D 99 TYR cc_start: 0.8781 (t80) cc_final: 0.8567 (t80) REVERT: D 105 LEU cc_start: 0.9557 (mt) cc_final: 0.9234 (mt) REVERT: D 116 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8086 (tp30) REVERT: D 117 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7760 (mm-30) REVERT: D 163 TYR cc_start: 0.8247 (m-80) cc_final: 0.7115 (m-80) REVERT: D 177 TRP cc_start: 0.9126 (m100) cc_final: 0.8750 (t-100) REVERT: D 225 LEU cc_start: 0.9260 (tt) cc_final: 0.8998 (tt) REVERT: D 244 PRO cc_start: 0.9405 (Cg_exo) cc_final: 0.8605 (Cg_endo) REVERT: D 245 GLU cc_start: 0.8405 (mp0) cc_final: 0.7971 (mp0) REVERT: D 281 LYS cc_start: 0.8532 (tttt) cc_final: 0.7997 (tttt) REVERT: D 297 ARG cc_start: 0.9053 (ttt-90) cc_final: 0.8822 (ttt-90) REVERT: D 306 LYS cc_start: 0.8891 (ttmm) cc_final: 0.8629 (ttpt) REVERT: D 523 SER cc_start: 0.8639 (p) cc_final: 0.8186 (p) REVERT: D 536 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7462 (tm-30) REVERT: D 578 LEU cc_start: 0.9197 (mt) cc_final: 0.8914 (mt) REVERT: D 599 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8437 (tm-30) REVERT: D 610 TYR cc_start: 0.8456 (t80) cc_final: 0.7566 (t80) REVERT: G 83 MET cc_start: 0.8938 (tpp) cc_final: 0.8618 (tpp) REVERT: G 91 CYS cc_start: 0.7597 (m) cc_final: 0.7145 (m) REVERT: G 105 LEU cc_start: 0.9523 (mt) cc_final: 0.9096 (mt) REVERT: G 195 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7710 (mt-10) REVERT: G 264 LYS cc_start: 0.8254 (mmtt) cc_final: 0.7974 (mtpp) REVERT: G 273 GLU cc_start: 0.9047 (tt0) cc_final: 0.8579 (tt0) REVERT: G 277 TYR cc_start: 0.8490 (m-80) cc_final: 0.7606 (m-80) REVERT: G 281 LYS cc_start: 0.8436 (tttt) cc_final: 0.8182 (tttt) REVERT: G 295 ILE cc_start: 0.9646 (tt) cc_final: 0.9390 (tt) REVERT: G 317 LYS cc_start: 0.8679 (mtmm) cc_final: 0.8388 (mtmt) REVERT: G 498 GLU cc_start: 0.8555 (mm-30) cc_final: 0.7949 (mm-30) REVERT: G 504 ARG cc_start: 0.9074 (ttm170) cc_final: 0.8636 (ttm170) REVERT: G 536 GLU cc_start: 0.8510 (tm-30) cc_final: 0.7988 (tm-30) REVERT: G 538 PHE cc_start: 0.9241 (t80) cc_final: 0.8982 (t80) REVERT: G 599 GLN cc_start: 0.8982 (tm-30) cc_final: 0.8472 (tm-30) REVERT: G 625 ARG cc_start: 0.7809 (tmt170) cc_final: 0.7155 (tpt90) REVERT: J 81 GLN cc_start: 0.8798 (tp-100) cc_final: 0.8525 (tp-100) REVERT: J 83 MET cc_start: 0.9105 (tpp) cc_final: 0.7247 (tpp) REVERT: J 85 GLN cc_start: 0.8996 (tp-100) cc_final: 0.8536 (tp-100) REVERT: J 86 VAL cc_start: 0.9378 (p) cc_final: 0.9128 (p) REVERT: J 101 VAL cc_start: 0.9161 (p) cc_final: 0.8815 (p) REVERT: J 105 LEU cc_start: 0.9543 (mt) cc_final: 0.9179 (mt) REVERT: J 195 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7826 (mt-10) REVERT: J 225 LEU cc_start: 0.9382 (tp) cc_final: 0.9059 (tt) REVERT: J 245 GLU cc_start: 0.8224 (mp0) cc_final: 0.7810 (mp0) REVERT: J 297 ARG cc_start: 0.9223 (ttt-90) cc_final: 0.8898 (ttp-170) REVERT: J 309 GLN cc_start: 0.9311 (mt0) cc_final: 0.8742 (mt0) REVERT: J 498 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8477 (mm-30) REVERT: J 528 PHE cc_start: 0.8837 (t80) cc_final: 0.8473 (t80) REVERT: J 536 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7828 (tm-30) REVERT: J 599 GLN cc_start: 0.8963 (tm-30) cc_final: 0.8468 (tm-30) REVERT: J 622 ILE cc_start: 0.8947 (tt) cc_final: 0.8542 (tt) REVERT: J 626 GLU cc_start: 0.8824 (mp0) cc_final: 0.8591 (mp0) REVERT: E 85 GLN cc_start: 0.8891 (tp40) cc_final: 0.8510 (tp40) REVERT: E 105 LEU cc_start: 0.9547 (mt) cc_final: 0.9228 (mt) REVERT: E 163 TYR cc_start: 0.8349 (m-80) cc_final: 0.7110 (m-80) REVERT: E 177 TRP cc_start: 0.9123 (m100) cc_final: 0.8762 (t-100) REVERT: E 187 LEU cc_start: 0.9141 (mm) cc_final: 0.8862 (mm) REVERT: E 195 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7704 (mt-10) REVERT: E 225 LEU cc_start: 0.9262 (tt) cc_final: 0.8999 (tt) REVERT: E 244 PRO cc_start: 0.9399 (Cg_exo) cc_final: 0.8663 (Cg_endo) REVERT: E 245 GLU cc_start: 0.8414 (mp0) cc_final: 0.8001 (mp0) REVERT: E 281 LYS cc_start: 0.8519 (tttt) cc_final: 0.7992 (tttt) REVERT: E 297 ARG cc_start: 0.9056 (ttt-90) cc_final: 0.8836 (ttt-90) REVERT: E 306 LYS cc_start: 0.8974 (ttmm) cc_final: 0.8604 (tttt) REVERT: E 307 ILE cc_start: 0.9505 (tp) cc_final: 0.9304 (tp) REVERT: E 491 LEU cc_start: 0.9326 (pt) cc_final: 0.8983 (pp) REVERT: E 523 SER cc_start: 0.8693 (p) cc_final: 0.8234 (p) REVERT: E 536 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7707 (tm-30) REVERT: E 578 LEU cc_start: 0.9258 (mt) cc_final: 0.8937 (mt) REVERT: E 599 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8415 (tm-30) REVERT: H 83 MET cc_start: 0.8890 (tpp) cc_final: 0.8593 (tpp) REVERT: H 91 CYS cc_start: 0.7346 (m) cc_final: 0.7054 (m) REVERT: H 105 LEU cc_start: 0.9502 (mt) cc_final: 0.9084 (mt) REVERT: H 195 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7747 (mt-10) REVERT: H 264 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7971 (mtpp) REVERT: H 273 GLU cc_start: 0.9063 (tt0) cc_final: 0.8609 (tt0) REVERT: H 277 TYR cc_start: 0.8495 (m-80) cc_final: 0.7668 (m-80) REVERT: H 281 LYS cc_start: 0.8491 (tttt) cc_final: 0.8197 (tttt) REVERT: H 295 ILE cc_start: 0.9654 (tt) cc_final: 0.9408 (tt) REVERT: H 296 LEU cc_start: 0.9685 (tp) cc_final: 0.9461 (tp) REVERT: H 317 LYS cc_start: 0.8693 (mtmm) cc_final: 0.8416 (mtmt) REVERT: H 498 GLU cc_start: 0.8568 (mm-30) cc_final: 0.7974 (mm-30) REVERT: H 504 ARG cc_start: 0.9081 (ttm170) cc_final: 0.8645 (ttm170) REVERT: H 536 GLU cc_start: 0.8499 (tm-30) cc_final: 0.7971 (tm-30) REVERT: H 538 PHE cc_start: 0.9184 (t80) cc_final: 0.8834 (t80) REVERT: H 545 ASN cc_start: 0.8725 (t0) cc_final: 0.8299 (t0) REVERT: H 599 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8473 (tm-30) REVERT: H 625 ARG cc_start: 0.7799 (tmt170) cc_final: 0.7154 (tpt90) REVERT: K 81 GLN cc_start: 0.8753 (tp-100) cc_final: 0.8419 (tp-100) REVERT: K 101 VAL cc_start: 0.9184 (p) cc_final: 0.8902 (p) REVERT: K 105 LEU cc_start: 0.9539 (mt) cc_final: 0.9219 (mt) REVERT: K 195 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7826 (mt-10) REVERT: K 225 LEU cc_start: 0.9387 (tp) cc_final: 0.9073 (tt) REVERT: K 245 GLU cc_start: 0.8105 (mp0) cc_final: 0.7767 (mp0) REVERT: K 309 GLN cc_start: 0.9303 (mt0) cc_final: 0.8739 (mt0) REVERT: K 498 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8446 (mm-30) REVERT: K 501 ARG cc_start: 0.8732 (tmm-80) cc_final: 0.8409 (tmm-80) REVERT: K 528 PHE cc_start: 0.8854 (t80) cc_final: 0.8477 (t80) REVERT: K 536 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7733 (tm-30) REVERT: K 599 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8480 (tm-30) REVERT: K 622 ILE cc_start: 0.8951 (tt) cc_final: 0.8566 (tt) REVERT: K 626 GLU cc_start: 0.8823 (mp0) cc_final: 0.8599 (mp0) REVERT: F 85 GLN cc_start: 0.8988 (tp40) cc_final: 0.8559 (tp40) REVERT: F 99 TYR cc_start: 0.8876 (t80) cc_final: 0.8662 (t80) REVERT: F 105 LEU cc_start: 0.9569 (mt) cc_final: 0.9281 (mt) REVERT: F 117 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7854 (mm-30) REVERT: F 177 TRP cc_start: 0.9090 (m100) cc_final: 0.8770 (t-100) REVERT: F 225 LEU cc_start: 0.9201 (tt) cc_final: 0.8912 (tt) REVERT: F 244 PRO cc_start: 0.9419 (Cg_exo) cc_final: 0.8655 (Cg_endo) REVERT: F 245 GLU cc_start: 0.8410 (mp0) cc_final: 0.7993 (mp0) REVERT: F 281 LYS cc_start: 0.8519 (tttt) cc_final: 0.7969 (tttt) REVERT: F 295 ILE cc_start: 0.9601 (tt) cc_final: 0.9390 (tt) REVERT: F 297 ARG cc_start: 0.9056 (ttt-90) cc_final: 0.8837 (ttt-90) REVERT: F 523 SER cc_start: 0.8633 (p) cc_final: 0.8165 (p) REVERT: F 536 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7408 (tm-30) REVERT: F 546 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8672 (tm-30) REVERT: F 578 LEU cc_start: 0.9235 (mt) cc_final: 0.8881 (mt) REVERT: F 599 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8421 (tm-30) REVERT: F 610 TYR cc_start: 0.8717 (t80) cc_final: 0.7904 (t80) REVERT: I 83 MET cc_start: 0.8919 (tpp) cc_final: 0.8600 (tpp) REVERT: I 91 CYS cc_start: 0.7902 (m) cc_final: 0.7536 (m) REVERT: I 105 LEU cc_start: 0.9520 (mt) cc_final: 0.9089 (mt) REVERT: I 195 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7711 (mt-10) REVERT: I 209 ARG cc_start: 0.8242 (tpt90) cc_final: 0.8039 (tpt90) REVERT: I 264 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7982 (mtpp) REVERT: I 273 GLU cc_start: 0.9029 (tt0) cc_final: 0.8555 (tt0) REVERT: I 277 TYR cc_start: 0.8500 (m-80) cc_final: 0.7671 (m-80) REVERT: I 281 LYS cc_start: 0.8445 (tttt) cc_final: 0.8190 (tttt) REVERT: I 295 ILE cc_start: 0.9646 (tt) cc_final: 0.9392 (tt) REVERT: I 305 GLN cc_start: 0.9116 (tt0) cc_final: 0.8896 (tt0) REVERT: I 309 GLN cc_start: 0.9203 (tt0) cc_final: 0.8890 (mt0) REVERT: I 317 LYS cc_start: 0.8672 (mtmm) cc_final: 0.8394 (mtmt) REVERT: I 498 GLU cc_start: 0.8577 (mm-30) cc_final: 0.7970 (mm-30) REVERT: I 504 ARG cc_start: 0.9081 (ttm170) cc_final: 0.8651 (ttm170) REVERT: I 510 ARG cc_start: 0.8242 (mtp85) cc_final: 0.8039 (mtp85) REVERT: I 536 GLU cc_start: 0.8558 (tm-30) cc_final: 0.7973 (tm-30) REVERT: I 538 PHE cc_start: 0.9241 (t80) cc_final: 0.8967 (t80) REVERT: I 599 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8471 (tm-30) REVERT: I 625 ARG cc_start: 0.7783 (tmt170) cc_final: 0.7147 (tpt90) REVERT: L 81 GLN cc_start: 0.8713 (tp-100) cc_final: 0.8476 (tp-100) REVERT: L 83 MET cc_start: 0.9117 (tpp) cc_final: 0.7328 (tpp) REVERT: L 86 VAL cc_start: 0.9476 (p) cc_final: 0.9159 (p) REVERT: L 101 VAL cc_start: 0.9152 (p) cc_final: 0.8799 (p) REVERT: L 105 LEU cc_start: 0.9556 (mt) cc_final: 0.9194 (mt) REVERT: L 177 TRP cc_start: 0.9347 (m100) cc_final: 0.8993 (m100) REVERT: L 195 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7804 (mt-10) REVERT: L 225 LEU cc_start: 0.9386 (tp) cc_final: 0.9070 (tt) REVERT: L 245 GLU cc_start: 0.8143 (mp0) cc_final: 0.7784 (mp0) REVERT: L 297 ARG cc_start: 0.9303 (ttt-90) cc_final: 0.8971 (ttp-170) REVERT: L 309 GLN cc_start: 0.9319 (mt0) cc_final: 0.8785 (mt0) REVERT: L 491 LEU cc_start: 0.9140 (pt) cc_final: 0.8814 (pt) REVERT: L 498 GLU cc_start: 0.8636 (mm-30) cc_final: 0.7707 (mm-30) REVERT: L 501 ARG cc_start: 0.8772 (tmm-80) cc_final: 0.7529 (tmm-80) REVERT: L 504 ARG cc_start: 0.8760 (ttm170) cc_final: 0.8264 (ttt180) REVERT: L 528 PHE cc_start: 0.8858 (t80) cc_final: 0.8472 (t80) REVERT: L 599 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8443 (tm-30) REVERT: L 622 ILE cc_start: 0.8926 (tt) cc_final: 0.8543 (tt) REVERT: L 626 GLU cc_start: 0.8820 (mp0) cc_final: 0.8603 (mp0) outliers start: 0 outliers final: 0 residues processed: 2174 average time/residue: 0.2485 time to fit residues: 876.2483 Evaluate side-chains 1989 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1989 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 28 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 192 optimal weight: 20.0000 chunk 139 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 286 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 349 optimal weight: 0.0770 chunk 211 optimal weight: 30.0000 chunk 382 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 265 HIS A 632 GLN B 632 GLN C 137 GLN C 632 GLN D 137 GLN D 148 GLN D 265 HIS ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 632 GLN G 85 GLN G 137 GLN G 632 GLN J 137 GLN J 632 GLN E 148 GLN E 632 GLN H 632 GLN K 137 GLN K 632 GLN F 137 GLN F 265 HIS ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 632 GLN I 632 GLN L 137 GLN L 632 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.157649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.131471 restraints weight = 68476.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.135696 restraints weight = 37219.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.138552 restraints weight = 23847.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.140482 restraints weight = 17111.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.141728 restraints weight = 13415.835| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 39672 Z= 0.178 Angle : 0.671 7.982 53820 Z= 0.337 Chirality : 0.043 0.190 6168 Planarity : 0.005 0.063 6888 Dihedral : 5.153 20.918 5424 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.19 % Allowed : 3.54 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.12), residues: 4740 helix: -1.29 (0.10), residues: 2388 sheet: -1.94 (0.40), residues: 120 loop : -1.56 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 617 TYR 0.019 0.002 TYR I 568 PHE 0.023 0.002 PHE J 538 TRP 0.060 0.003 TRP D 118 HIS 0.003 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00400 (39672) covalent geometry : angle 0.67080 (53820) hydrogen bonds : bond 0.03453 ( 1410) hydrogen bonds : angle 4.60373 ( 3909) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2182 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 2174 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8313 (tm-30) REVERT: A 83 MET cc_start: 0.9106 (mmp) cc_final: 0.8576 (mmp) REVERT: A 105 LEU cc_start: 0.9620 (mt) cc_final: 0.9262 (mt) REVERT: A 177 TRP cc_start: 0.9127 (m100) cc_final: 0.8798 (t-100) REVERT: A 187 LEU cc_start: 0.9298 (mm) cc_final: 0.9054 (mm) REVERT: A 267 ARG cc_start: 0.8834 (tmm-80) cc_final: 0.8594 (tmm-80) REVERT: A 281 LYS cc_start: 0.8598 (tttt) cc_final: 0.8055 (tttt) REVERT: A 306 LYS cc_start: 0.8908 (tttt) cc_final: 0.8546 (ttmm) REVERT: A 309 GLN cc_start: 0.9315 (mt0) cc_final: 0.8973 (mt0) REVERT: A 491 LEU cc_start: 0.9256 (pt) cc_final: 0.8788 (pp) REVERT: A 523 SER cc_start: 0.8686 (p) cc_final: 0.8225 (p) REVERT: A 536 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7684 (tm-30) REVERT: A 574 GLU cc_start: 0.9293 (tm-30) cc_final: 0.8888 (tm-30) REVERT: A 578 LEU cc_start: 0.9372 (mt) cc_final: 0.9032 (mt) REVERT: A 599 GLN cc_start: 0.8896 (tm-30) cc_final: 0.8455 (tm-30) REVERT: A 610 TYR cc_start: 0.8636 (t80) cc_final: 0.7779 (t80) REVERT: B 83 MET cc_start: 0.8868 (tpp) cc_final: 0.8551 (tpp) REVERT: B 105 LEU cc_start: 0.9470 (mt) cc_final: 0.9060 (mt) REVERT: B 195 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7837 (mt-10) REVERT: B 209 ARG cc_start: 0.7956 (tpt90) cc_final: 0.7253 (tpt90) REVERT: B 264 LYS cc_start: 0.8364 (mmtt) cc_final: 0.8070 (mtpp) REVERT: B 273 GLU cc_start: 0.8915 (tt0) cc_final: 0.8641 (tt0) REVERT: B 277 TYR cc_start: 0.8689 (m-80) cc_final: 0.7774 (m-80) REVERT: B 281 LYS cc_start: 0.8475 (tttt) cc_final: 0.8186 (tttt) REVERT: B 296 LEU cc_start: 0.9548 (tp) cc_final: 0.9347 (tp) REVERT: B 317 LYS cc_start: 0.8723 (mtmm) cc_final: 0.8427 (mtmt) REVERT: B 498 GLU cc_start: 0.8623 (mm-30) cc_final: 0.7930 (mm-30) REVERT: B 510 ARG cc_start: 0.8323 (mtp85) cc_final: 0.8119 (mtp85) REVERT: B 536 GLU cc_start: 0.8470 (tm-30) cc_final: 0.7849 (tm-30) REVERT: B 599 GLN cc_start: 0.9019 (tm-30) cc_final: 0.8540 (tm-30) REVERT: B 625 ARG cc_start: 0.7847 (tmt170) cc_final: 0.7222 (tpt90) REVERT: C 63 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8427 (tm-30) REVERT: C 81 GLN cc_start: 0.8785 (tp-100) cc_final: 0.8454 (tp-100) REVERT: C 83 MET cc_start: 0.9090 (tpp) cc_final: 0.8834 (tpp) REVERT: C 105 LEU cc_start: 0.9583 (mt) cc_final: 0.9260 (mt) REVERT: C 195 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8022 (mt-10) REVERT: C 225 LEU cc_start: 0.9450 (tp) cc_final: 0.9129 (tt) REVERT: C 245 GLU cc_start: 0.8244 (mp0) cc_final: 0.7841 (mp0) REVERT: C 268 LEU cc_start: 0.9385 (pt) cc_final: 0.9176 (pt) REVERT: C 301 LEU cc_start: 0.9093 (tt) cc_final: 0.8812 (tt) REVERT: C 309 GLN cc_start: 0.9307 (mt0) cc_final: 0.8710 (mt0) REVERT: C 498 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8587 (mm-30) REVERT: C 501 ARG cc_start: 0.8703 (tmm-80) cc_final: 0.8298 (tmm-80) REVERT: C 536 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7715 (tm-30) REVERT: C 574 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8549 (tm-30) REVERT: C 597 TYR cc_start: 0.8607 (m-10) cc_final: 0.8383 (m-80) REVERT: C 599 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8656 (tm-30) REVERT: D 63 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8375 (tm-30) REVERT: D 70 LEU cc_start: 0.9420 (mm) cc_final: 0.9184 (mm) REVERT: D 85 GLN cc_start: 0.8899 (tp40) cc_final: 0.8433 (tp40) REVERT: D 105 LEU cc_start: 0.9632 (mt) cc_final: 0.9299 (mt) REVERT: D 177 TRP cc_start: 0.9113 (m100) cc_final: 0.8799 (t-100) REVERT: D 187 LEU cc_start: 0.9103 (mm) cc_final: 0.8802 (mm) REVERT: D 195 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7638 (mt-10) REVERT: D 225 LEU cc_start: 0.9365 (tt) cc_final: 0.9038 (tt) REVERT: D 244 PRO cc_start: 0.9442 (Cg_exo) cc_final: 0.8527 (Cg_endo) REVERT: D 245 GLU cc_start: 0.8381 (mp0) cc_final: 0.8004 (mp0) REVERT: D 281 LYS cc_start: 0.8618 (tttt) cc_final: 0.8076 (tttt) REVERT: D 306 LYS cc_start: 0.9129 (ttmm) cc_final: 0.8706 (tttt) REVERT: D 491 LEU cc_start: 0.9254 (pt) cc_final: 0.8854 (pp) REVERT: D 523 SER cc_start: 0.8712 (p) cc_final: 0.8262 (p) REVERT: D 578 LEU cc_start: 0.9254 (mt) cc_final: 0.8940 (mt) REVERT: D 599 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8504 (tm-30) REVERT: G 83 MET cc_start: 0.9067 (tpp) cc_final: 0.8460 (tpp) REVERT: G 105 LEU cc_start: 0.9488 (mt) cc_final: 0.9103 (mt) REVERT: G 195 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7815 (mt-10) REVERT: G 209 ARG cc_start: 0.7908 (tpt90) cc_final: 0.7462 (tpt90) REVERT: G 264 LYS cc_start: 0.8358 (mmtt) cc_final: 0.8067 (mtpp) REVERT: G 273 GLU cc_start: 0.9063 (tt0) cc_final: 0.8674 (tt0) REVERT: G 277 TYR cc_start: 0.8683 (m-80) cc_final: 0.7741 (m-80) REVERT: G 281 LYS cc_start: 0.8461 (tttt) cc_final: 0.8178 (tttt) REVERT: G 296 LEU cc_start: 0.9650 (tp) cc_final: 0.9419 (tp) REVERT: G 309 GLN cc_start: 0.9124 (mt0) cc_final: 0.8913 (mt0) REVERT: G 317 LYS cc_start: 0.8731 (mtmm) cc_final: 0.8429 (mtmt) REVERT: G 498 GLU cc_start: 0.8614 (mm-30) cc_final: 0.7903 (mm-30) REVERT: G 510 ARG cc_start: 0.8348 (mtp85) cc_final: 0.8140 (mtp85) REVERT: G 536 GLU cc_start: 0.8447 (tm-30) cc_final: 0.7834 (tm-30) REVERT: G 545 ASN cc_start: 0.8587 (t0) cc_final: 0.8210 (t0) REVERT: G 599 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8532 (tm-30) REVERT: G 625 ARG cc_start: 0.7847 (tmt170) cc_final: 0.7223 (tpt90) REVERT: J 63 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8419 (tm-30) REVERT: J 81 GLN cc_start: 0.8777 (tp-100) cc_final: 0.8456 (tp-100) REVERT: J 83 MET cc_start: 0.9103 (tpp) cc_final: 0.7418 (tpp) REVERT: J 86 VAL cc_start: 0.9489 (p) cc_final: 0.9176 (p) REVERT: J 105 LEU cc_start: 0.9590 (mt) cc_final: 0.9220 (mt) REVERT: J 195 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8056 (mt-10) REVERT: J 225 LEU cc_start: 0.9453 (tp) cc_final: 0.9130 (tt) REVERT: J 245 GLU cc_start: 0.8253 (mp0) cc_final: 0.7845 (mp0) REVERT: J 268 LEU cc_start: 0.9353 (pt) cc_final: 0.9130 (pt) REVERT: J 281 LYS cc_start: 0.8295 (tttt) cc_final: 0.7784 (tttt) REVERT: J 297 ARG cc_start: 0.9317 (ttt-90) cc_final: 0.8733 (ttt180) REVERT: J 498 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8553 (mm-30) REVERT: J 501 ARG cc_start: 0.8688 (tmm-80) cc_final: 0.8272 (tmm-80) REVERT: J 528 PHE cc_start: 0.8574 (t80) cc_final: 0.8214 (t80) REVERT: J 536 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7888 (tm-30) REVERT: J 574 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8568 (tm-30) REVERT: J 597 TYR cc_start: 0.8576 (m-10) cc_final: 0.8359 (m-80) REVERT: J 599 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8591 (tm-30) REVERT: E 63 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8134 (tm-30) REVERT: E 85 GLN cc_start: 0.8937 (tp40) cc_final: 0.8462 (tp40) REVERT: E 105 LEU cc_start: 0.9595 (mt) cc_final: 0.9284 (mt) REVERT: E 177 TRP cc_start: 0.9107 (m100) cc_final: 0.8839 (t-100) REVERT: E 187 LEU cc_start: 0.9126 (mm) cc_final: 0.8813 (mm) REVERT: E 195 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7625 (mt-10) REVERT: E 225 LEU cc_start: 0.9373 (tt) cc_final: 0.9057 (tt) REVERT: E 244 PRO cc_start: 0.9427 (Cg_exo) cc_final: 0.8548 (Cg_endo) REVERT: E 245 GLU cc_start: 0.8533 (mp0) cc_final: 0.8144 (mp0) REVERT: E 281 LYS cc_start: 0.8610 (tttt) cc_final: 0.8068 (tttt) REVERT: E 306 LYS cc_start: 0.9160 (ttmm) cc_final: 0.8756 (tttt) REVERT: E 491 LEU cc_start: 0.9173 (pt) cc_final: 0.8706 (pp) REVERT: E 523 SER cc_start: 0.8706 (p) cc_final: 0.8230 (p) REVERT: E 578 LEU cc_start: 0.9253 (mt) cc_final: 0.8949 (mt) REVERT: E 599 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8464 (tm-30) REVERT: E 610 TYR cc_start: 0.8668 (t80) cc_final: 0.7890 (t80) REVERT: E 625 ARG cc_start: 0.6855 (tmt170) cc_final: 0.6459 (tmt170) REVERT: H 83 MET cc_start: 0.8912 (tpp) cc_final: 0.8558 (tpp) REVERT: H 105 LEU cc_start: 0.9488 (mt) cc_final: 0.9084 (mt) REVERT: H 195 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7841 (mt-10) REVERT: H 225 LEU cc_start: 0.9079 (tt) cc_final: 0.8762 (tt) REVERT: H 264 LYS cc_start: 0.8354 (mmtt) cc_final: 0.8060 (mtpp) REVERT: H 273 GLU cc_start: 0.9100 (tt0) cc_final: 0.8711 (tt0) REVERT: H 281 LYS cc_start: 0.8467 (tttt) cc_final: 0.8174 (tttt) REVERT: H 295 ILE cc_start: 0.9680 (tt) cc_final: 0.9428 (tt) REVERT: H 296 LEU cc_start: 0.9686 (tp) cc_final: 0.9462 (tp) REVERT: H 309 GLN cc_start: 0.9107 (mt0) cc_final: 0.8902 (mt0) REVERT: H 317 LYS cc_start: 0.8722 (mtmm) cc_final: 0.8440 (mtmt) REVERT: H 498 GLU cc_start: 0.8630 (mm-30) cc_final: 0.7914 (mm-30) REVERT: H 510 ARG cc_start: 0.8313 (mtp85) cc_final: 0.8086 (mtp85) REVERT: H 536 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7705 (tm-30) REVERT: H 545 ASN cc_start: 0.8862 (t0) cc_final: 0.8419 (t0) REVERT: H 599 GLN cc_start: 0.9021 (tm-30) cc_final: 0.8529 (tm-30) REVERT: H 625 ARG cc_start: 0.7841 (tmt170) cc_final: 0.7211 (tpt90) REVERT: K 63 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8446 (tm-30) REVERT: K 81 GLN cc_start: 0.8681 (tp-100) cc_final: 0.8364 (tp-100) REVERT: K 105 LEU cc_start: 0.9538 (mt) cc_final: 0.9225 (mt) REVERT: K 195 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8055 (mt-10) REVERT: K 225 LEU cc_start: 0.9453 (tp) cc_final: 0.9130 (tt) REVERT: K 245 GLU cc_start: 0.8203 (mp0) cc_final: 0.7796 (mp0) REVERT: K 264 LYS cc_start: 0.8409 (mmtt) cc_final: 0.8174 (mtpp) REVERT: K 498 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8603 (mm-30) REVERT: K 501 ARG cc_start: 0.8681 (tmm-80) cc_final: 0.8325 (tmm-80) REVERT: K 528 PHE cc_start: 0.8589 (t80) cc_final: 0.8215 (t80) REVERT: K 536 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7827 (tm-30) REVERT: K 548 PHE cc_start: 0.9281 (m-10) cc_final: 0.8935 (m-10) REVERT: K 574 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8511 (tm-30) REVERT: K 597 TYR cc_start: 0.8594 (m-10) cc_final: 0.8379 (m-80) REVERT: K 599 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8671 (tm-30) REVERT: F 63 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8252 (tm-30) REVERT: F 83 MET cc_start: 0.9127 (tpt) cc_final: 0.8482 (tpp) REVERT: F 85 GLN cc_start: 0.9073 (tp40) cc_final: 0.8564 (tp40) REVERT: F 105 LEU cc_start: 0.9635 (mt) cc_final: 0.9306 (mt) REVERT: F 177 TRP cc_start: 0.9113 (m100) cc_final: 0.8846 (t-100) REVERT: F 187 LEU cc_start: 0.9095 (mm) cc_final: 0.8800 (mm) REVERT: F 195 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7647 (mt-10) REVERT: F 225 LEU cc_start: 0.9353 (tt) cc_final: 0.9018 (tt) REVERT: F 244 PRO cc_start: 0.9447 (Cg_exo) cc_final: 0.8537 (Cg_endo) REVERT: F 245 GLU cc_start: 0.8523 (mp0) cc_final: 0.8129 (mp0) REVERT: F 281 LYS cc_start: 0.8614 (tttt) cc_final: 0.8051 (tttt) REVERT: F 295 ILE cc_start: 0.9626 (tt) cc_final: 0.9403 (tt) REVERT: F 306 LYS cc_start: 0.8929 (ttpt) cc_final: 0.8493 (tttt) REVERT: F 309 GLN cc_start: 0.9368 (mt0) cc_final: 0.9104 (mt0) REVERT: F 491 LEU cc_start: 0.9257 (pt) cc_final: 0.8847 (pp) REVERT: F 523 SER cc_start: 0.8690 (p) cc_final: 0.8230 (p) REVERT: F 546 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8638 (tm-30) REVERT: F 578 LEU cc_start: 0.9395 (mt) cc_final: 0.9038 (mt) REVERT: F 599 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8468 (tm-30) REVERT: F 610 TYR cc_start: 0.8771 (t80) cc_final: 0.8170 (t80) REVERT: F 625 ARG cc_start: 0.6501 (ttt-90) cc_final: 0.6242 (tmt170) REVERT: I 83 MET cc_start: 0.8969 (tpp) cc_final: 0.8508 (tpp) REVERT: I 91 CYS cc_start: 0.8009 (m) cc_final: 0.7492 (m) REVERT: I 105 LEU cc_start: 0.9500 (mt) cc_final: 0.9087 (mt) REVERT: I 195 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7824 (mt-10) REVERT: I 209 ARG cc_start: 0.8275 (tpt90) cc_final: 0.8054 (tpt90) REVERT: I 264 LYS cc_start: 0.8307 (mmtt) cc_final: 0.8020 (mtpp) REVERT: I 273 GLU cc_start: 0.8988 (tt0) cc_final: 0.8511 (tt0) REVERT: I 277 TYR cc_start: 0.8674 (m-80) cc_final: 0.7778 (m-80) REVERT: I 281 LYS cc_start: 0.8454 (tttt) cc_final: 0.8169 (tttt) REVERT: I 295 ILE cc_start: 0.9650 (tt) cc_final: 0.9449 (tt) REVERT: I 296 LEU cc_start: 0.9652 (tp) cc_final: 0.9442 (tp) REVERT: I 309 GLN cc_start: 0.9313 (tt0) cc_final: 0.8142 (pt0) REVERT: I 317 LYS cc_start: 0.8695 (mtmm) cc_final: 0.8431 (mtmt) REVERT: I 498 GLU cc_start: 0.8625 (mm-30) cc_final: 0.7919 (mm-30) REVERT: I 536 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7705 (tm-30) REVERT: I 538 PHE cc_start: 0.9173 (t80) cc_final: 0.8971 (t80) REVERT: I 599 GLN cc_start: 0.9015 (tm-30) cc_final: 0.8538 (tm-30) REVERT: I 625 ARG cc_start: 0.7833 (tmt170) cc_final: 0.7210 (tpt90) REVERT: L 83 MET cc_start: 0.9151 (tpp) cc_final: 0.7495 (tpp) REVERT: L 85 GLN cc_start: 0.8873 (tp40) cc_final: 0.8654 (tp40) REVERT: L 105 LEU cc_start: 0.9598 (mt) cc_final: 0.9240 (mt) REVERT: L 177 TRP cc_start: 0.9342 (m100) cc_final: 0.8986 (m100) REVERT: L 195 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8024 (mt-10) REVERT: L 225 LEU cc_start: 0.9448 (tp) cc_final: 0.9127 (tt) REVERT: L 245 GLU cc_start: 0.8234 (mp0) cc_final: 0.7826 (mp0) REVERT: L 281 LYS cc_start: 0.8321 (tttt) cc_final: 0.7810 (tttt) REVERT: L 301 LEU cc_start: 0.9093 (tt) cc_final: 0.8843 (tt) REVERT: L 491 LEU cc_start: 0.9145 (pt) cc_final: 0.8845 (pt) REVERT: L 498 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8525 (mm-30) REVERT: L 528 PHE cc_start: 0.8603 (t80) cc_final: 0.8206 (t80) REVERT: L 536 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7764 (tm-30) REVERT: L 599 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8558 (tm-30) outliers start: 8 outliers final: 0 residues processed: 2174 average time/residue: 0.2434 time to fit residues: 860.9575 Evaluate side-chains 1939 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1939 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 256 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 431 optimal weight: 0.9990 chunk 354 optimal weight: 5.9990 chunk 291 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 395 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 243 optimal weight: 0.9990 chunk 303 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 265 HIS A 305 GLN A 545 ASN A 632 GLN B 632 GLN C 137 GLN C 632 GLN D 137 GLN D 265 HIS D 632 GLN G 137 GLN G 632 GLN J 137 GLN J 632 GLN E 137 GLN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS E 305 GLN E 632 GLN H 632 GLN K 137 GLN K 632 GLN F 137 GLN F 265 HIS ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 632 GLN ** I 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 632 GLN L 137 GLN L 632 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.160313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.134329 restraints weight = 67947.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.138598 restraints weight = 36833.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.141485 restraints weight = 23524.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.143444 restraints weight = 16776.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.144705 restraints weight = 13116.972| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39672 Z= 0.136 Angle : 0.665 7.558 53820 Z= 0.329 Chirality : 0.042 0.160 6168 Planarity : 0.005 0.071 6888 Dihedral : 5.129 20.764 5424 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.24 % Allowed : 2.14 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.12), residues: 4740 helix: -1.23 (0.10), residues: 2400 sheet: -1.89 (0.40), residues: 120 loop : -1.50 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 617 TYR 0.019 0.002 TYR C 138 PHE 0.021 0.002 PHE L 249 TRP 0.081 0.003 TRP D 118 HIS 0.004 0.001 HIS I 214 Details of bonding type rmsd covalent geometry : bond 0.00315 (39672) covalent geometry : angle 0.66516 (53820) hydrogen bonds : bond 0.03399 ( 1410) hydrogen bonds : angle 4.52707 ( 3909) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2152 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 2142 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8371 (tm-30) REVERT: A 83 MET cc_start: 0.8991 (mmp) cc_final: 0.8533 (mmp) REVERT: A 105 LEU cc_start: 0.9635 (mt) cc_final: 0.9316 (mt) REVERT: A 177 TRP cc_start: 0.9105 (m100) cc_final: 0.8782 (t-100) REVERT: A 187 LEU cc_start: 0.9282 (mm) cc_final: 0.9043 (mm) REVERT: A 195 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7772 (mt-10) REVERT: A 225 LEU cc_start: 0.9305 (tt) cc_final: 0.8983 (tt) REVERT: A 281 LYS cc_start: 0.8600 (tttt) cc_final: 0.8046 (tttt) REVERT: A 306 LYS cc_start: 0.8851 (tttt) cc_final: 0.8640 (ttmm) REVERT: A 523 SER cc_start: 0.8637 (p) cc_final: 0.8170 (p) REVERT: A 532 THR cc_start: 0.8692 (t) cc_final: 0.8231 (t) REVERT: A 574 GLU cc_start: 0.9293 (tm-30) cc_final: 0.8880 (tm-30) REVERT: A 578 LEU cc_start: 0.9347 (mt) cc_final: 0.9009 (mt) REVERT: A 599 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8435 (tm-30) REVERT: A 610 TYR cc_start: 0.8801 (t80) cc_final: 0.8082 (t80) REVERT: A 625 ARG cc_start: 0.7414 (tmt170) cc_final: 0.6095 (ttt90) REVERT: B 83 MET cc_start: 0.8882 (tpp) cc_final: 0.8636 (tpp) REVERT: B 105 LEU cc_start: 0.9471 (mt) cc_final: 0.9109 (mt) REVERT: B 195 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7839 (mt-10) REVERT: B 209 ARG cc_start: 0.8159 (tpt90) cc_final: 0.7614 (tpt90) REVERT: B 264 LYS cc_start: 0.8289 (mmtt) cc_final: 0.7967 (tttp) REVERT: B 273 GLU cc_start: 0.8936 (tt0) cc_final: 0.8703 (tt0) REVERT: B 277 TYR cc_start: 0.8325 (m-80) cc_final: 0.7729 (m-80) REVERT: B 281 LYS cc_start: 0.8554 (tttt) cc_final: 0.8231 (tttt) REVERT: B 296 LEU cc_start: 0.9536 (tp) cc_final: 0.9319 (tp) REVERT: B 317 LYS cc_start: 0.8719 (mtmm) cc_final: 0.8439 (mtmt) REVERT: B 498 GLU cc_start: 0.8595 (mm-30) cc_final: 0.7899 (mm-30) REVERT: B 504 ARG cc_start: 0.9077 (ttm170) cc_final: 0.8612 (ttm170) REVERT: B 510 ARG cc_start: 0.8277 (mtp85) cc_final: 0.8077 (mtp85) REVERT: B 536 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7654 (tm-30) REVERT: B 538 PHE cc_start: 0.9024 (t80) cc_final: 0.8821 (t80) REVERT: B 599 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8506 (tm-30) REVERT: C 63 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8399 (tm-30) REVERT: C 81 GLN cc_start: 0.8723 (tp-100) cc_final: 0.8447 (tp-100) REVERT: C 91 CYS cc_start: 0.8245 (m) cc_final: 0.7921 (m) REVERT: C 105 LEU cc_start: 0.9565 (mt) cc_final: 0.9206 (mt) REVERT: C 195 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8026 (mt-10) REVERT: C 225 LEU cc_start: 0.9445 (tp) cc_final: 0.9107 (tt) REVERT: C 245 GLU cc_start: 0.8227 (mp0) cc_final: 0.7822 (mp0) REVERT: C 301 LEU cc_start: 0.9107 (tt) cc_final: 0.8822 (tt) REVERT: C 309 GLN cc_start: 0.9276 (mt0) cc_final: 0.8645 (mt0) REVERT: C 498 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8526 (mm-30) REVERT: C 501 ARG cc_start: 0.8722 (tmm-80) cc_final: 0.8343 (tmm-80) REVERT: C 536 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7626 (tm-30) REVERT: C 574 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8560 (tm-30) REVERT: C 599 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8485 (tm-30) REVERT: D 63 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8341 (tm-30) REVERT: D 85 GLN cc_start: 0.8893 (tp40) cc_final: 0.8504 (tp40) REVERT: D 105 LEU cc_start: 0.9617 (mt) cc_final: 0.9283 (mt) REVERT: D 113 ARG cc_start: 0.8518 (tpm170) cc_final: 0.8146 (tpm170) REVERT: D 177 TRP cc_start: 0.9103 (m100) cc_final: 0.8809 (t-100) REVERT: D 187 LEU cc_start: 0.9161 (mm) cc_final: 0.8827 (mm) REVERT: D 225 LEU cc_start: 0.9337 (tt) cc_final: 0.8965 (tt) REVERT: D 244 PRO cc_start: 0.9459 (Cg_exo) cc_final: 0.8499 (Cg_endo) REVERT: D 245 GLU cc_start: 0.8375 (mp0) cc_final: 0.7993 (mp0) REVERT: D 281 LYS cc_start: 0.8530 (tttt) cc_final: 0.8059 (tttt) REVERT: D 297 ARG cc_start: 0.9104 (ttt-90) cc_final: 0.8876 (ttt-90) REVERT: D 306 LYS cc_start: 0.9059 (ttmm) cc_final: 0.8679 (tttt) REVERT: D 491 LEU cc_start: 0.9163 (pt) cc_final: 0.8685 (pp) REVERT: D 523 SER cc_start: 0.8712 (p) cc_final: 0.8242 (p) REVERT: D 578 LEU cc_start: 0.9192 (mt) cc_final: 0.8909 (mt) REVERT: D 599 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8468 (tm-30) REVERT: D 610 TYR cc_start: 0.8869 (t80) cc_final: 0.8136 (t80) REVERT: G 83 MET cc_start: 0.8944 (tpp) cc_final: 0.8463 (tpp) REVERT: G 91 CYS cc_start: 0.7683 (m) cc_final: 0.6895 (m) REVERT: G 99 TYR cc_start: 0.8697 (t80) cc_final: 0.8476 (t80) REVERT: G 105 LEU cc_start: 0.9502 (mt) cc_final: 0.9163 (mt) REVERT: G 195 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7833 (mt-10) REVERT: G 209 ARG cc_start: 0.7888 (tpt90) cc_final: 0.7620 (tpt90) REVERT: G 264 LYS cc_start: 0.8288 (mmtt) cc_final: 0.8013 (mtpp) REVERT: G 273 GLU cc_start: 0.8979 (tt0) cc_final: 0.8486 (tt0) REVERT: G 277 TYR cc_start: 0.8370 (m-80) cc_final: 0.7748 (m-80) REVERT: G 281 LYS cc_start: 0.8524 (tttt) cc_final: 0.8221 (tttt) REVERT: G 296 LEU cc_start: 0.9676 (tp) cc_final: 0.9466 (tp) REVERT: G 297 ARG cc_start: 0.9182 (ttt180) cc_final: 0.8069 (ttt180) REVERT: G 309 GLN cc_start: 0.9062 (mt0) cc_final: 0.8762 (mt0) REVERT: G 317 LYS cc_start: 0.8729 (mtmm) cc_final: 0.8467 (mtmt) REVERT: G 498 GLU cc_start: 0.8581 (mm-30) cc_final: 0.7877 (mm-30) REVERT: G 504 ARG cc_start: 0.9100 (ttm170) cc_final: 0.8636 (ttm170) REVERT: G 510 ARG cc_start: 0.8333 (mtp85) cc_final: 0.8125 (mtp85) REVERT: G 536 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7766 (tm-30) REVERT: G 538 PHE cc_start: 0.9072 (t80) cc_final: 0.8850 (t80) REVERT: G 599 GLN cc_start: 0.9036 (tm-30) cc_final: 0.8529 (tm-30) REVERT: G 625 ARG cc_start: 0.7391 (tmt170) cc_final: 0.6950 (tpt90) REVERT: J 63 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8373 (tm-30) REVERT: J 81 GLN cc_start: 0.8708 (tp-100) cc_final: 0.8435 (tp-100) REVERT: J 83 MET cc_start: 0.9125 (tpp) cc_final: 0.8885 (tpp) REVERT: J 91 CYS cc_start: 0.8129 (m) cc_final: 0.7855 (m) REVERT: J 105 LEU cc_start: 0.9526 (mt) cc_final: 0.9198 (mt) REVERT: J 195 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8044 (mt-10) REVERT: J 225 LEU cc_start: 0.9444 (tp) cc_final: 0.9112 (tt) REVERT: J 245 GLU cc_start: 0.8213 (mp0) cc_final: 0.7817 (mp0) REVERT: J 309 GLN cc_start: 0.9254 (mt0) cc_final: 0.8675 (mt0) REVERT: J 491 LEU cc_start: 0.9158 (pt) cc_final: 0.8857 (pt) REVERT: J 498 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8476 (mm-30) REVERT: J 501 ARG cc_start: 0.8719 (tmm-80) cc_final: 0.8307 (tmm-80) REVERT: J 528 PHE cc_start: 0.8778 (t80) cc_final: 0.8388 (t80) REVERT: J 536 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7857 (tm-30) REVERT: J 599 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8494 (tm-30) REVERT: E 63 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8236 (tm-30) REVERT: E 85 GLN cc_start: 0.8848 (tp40) cc_final: 0.8390 (tp40) REVERT: E 105 LEU cc_start: 0.9577 (mt) cc_final: 0.9261 (mt) REVERT: E 177 TRP cc_start: 0.9101 (m100) cc_final: 0.8785 (t-100) REVERT: E 187 LEU cc_start: 0.9175 (mm) cc_final: 0.8848 (mm) REVERT: E 195 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7727 (mt-10) REVERT: E 225 LEU cc_start: 0.9354 (tt) cc_final: 0.8995 (tt) REVERT: E 244 PRO cc_start: 0.9466 (Cg_exo) cc_final: 0.8535 (Cg_endo) REVERT: E 245 GLU cc_start: 0.8399 (mp0) cc_final: 0.7998 (mp0) REVERT: E 281 LYS cc_start: 0.8476 (tttt) cc_final: 0.7984 (tttt) REVERT: E 491 LEU cc_start: 0.9243 (pt) cc_final: 0.8818 (pp) REVERT: E 523 SER cc_start: 0.8646 (p) cc_final: 0.8157 (p) REVERT: E 536 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7709 (tm-30) REVERT: E 574 GLU cc_start: 0.9259 (tm-30) cc_final: 0.8782 (tm-30) REVERT: E 578 LEU cc_start: 0.9255 (mt) cc_final: 0.8945 (mt) REVERT: E 599 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8472 (tm-30) REVERT: E 610 TYR cc_start: 0.8693 (t80) cc_final: 0.8037 (t80) REVERT: E 625 ARG cc_start: 0.7243 (tmt170) cc_final: 0.6808 (tmt170) REVERT: H 83 MET cc_start: 0.8954 (tpp) cc_final: 0.8654 (tpp) REVERT: H 91 CYS cc_start: 0.7562 (m) cc_final: 0.7137 (m) REVERT: H 105 LEU cc_start: 0.9489 (mt) cc_final: 0.9149 (mt) REVERT: H 195 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7855 (mt-10) REVERT: H 209 ARG cc_start: 0.7885 (tpt90) cc_final: 0.7399 (tpt90) REVERT: H 264 LYS cc_start: 0.8283 (mmtt) cc_final: 0.8004 (mtpp) REVERT: H 273 GLU cc_start: 0.9073 (tt0) cc_final: 0.8597 (tt0) REVERT: H 277 TYR cc_start: 0.8316 (m-80) cc_final: 0.7730 (m-80) REVERT: H 281 LYS cc_start: 0.8539 (tttt) cc_final: 0.8230 (tttt) REVERT: H 295 ILE cc_start: 0.9666 (tt) cc_final: 0.9416 (tt) REVERT: H 296 LEU cc_start: 0.9689 (tp) cc_final: 0.9488 (tp) REVERT: H 317 LYS cc_start: 0.8727 (mtmm) cc_final: 0.8459 (mtmt) REVERT: H 498 GLU cc_start: 0.8599 (mm-30) cc_final: 0.7901 (mm-30) REVERT: H 504 ARG cc_start: 0.9104 (ttm170) cc_final: 0.8649 (ttm170) REVERT: H 510 ARG cc_start: 0.8247 (mtp85) cc_final: 0.8034 (mtp85) REVERT: H 536 GLU cc_start: 0.8408 (tm-30) cc_final: 0.7824 (tm-30) REVERT: H 545 ASN cc_start: 0.8853 (t0) cc_final: 0.8397 (t0) REVERT: H 599 GLN cc_start: 0.9040 (tm-30) cc_final: 0.8510 (tm-30) REVERT: H 625 ARG cc_start: 0.7383 (tmt170) cc_final: 0.6951 (tpt90) REVERT: K 63 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8398 (tm-30) REVERT: K 81 GLN cc_start: 0.8646 (tp-100) cc_final: 0.8317 (tp-100) REVERT: K 91 CYS cc_start: 0.8168 (m) cc_final: 0.7647 (m) REVERT: K 105 LEU cc_start: 0.9571 (mt) cc_final: 0.9217 (mt) REVERT: K 195 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8041 (mt-10) REVERT: K 225 LEU cc_start: 0.9455 (tp) cc_final: 0.9118 (tt) REVERT: K 245 GLU cc_start: 0.8265 (mp0) cc_final: 0.7871 (mp0) REVERT: K 264 LYS cc_start: 0.8349 (mmtt) cc_final: 0.8101 (mtpp) REVERT: K 309 GLN cc_start: 0.9289 (mt0) cc_final: 0.8798 (mt0) REVERT: K 498 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8573 (mm-30) REVERT: K 501 ARG cc_start: 0.8692 (tmm-80) cc_final: 0.8365 (tmm-80) REVERT: K 528 PHE cc_start: 0.8784 (t80) cc_final: 0.8398 (t80) REVERT: K 536 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7893 (tm-30) REVERT: K 548 PHE cc_start: 0.9185 (m-10) cc_final: 0.8906 (m-10) REVERT: K 574 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8652 (tm-30) REVERT: K 599 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8506 (tm-30) REVERT: F 63 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8249 (tm-30) REVERT: F 83 MET cc_start: 0.9144 (tpt) cc_final: 0.8137 (tpp) REVERT: F 85 GLN cc_start: 0.9033 (tp40) cc_final: 0.8547 (tp40) REVERT: F 105 LEU cc_start: 0.9611 (mt) cc_final: 0.9299 (mt) REVERT: F 177 TRP cc_start: 0.9090 (m100) cc_final: 0.8793 (t-100) REVERT: F 187 LEU cc_start: 0.9156 (mm) cc_final: 0.8839 (mm) REVERT: F 225 LEU cc_start: 0.9325 (tt) cc_final: 0.8950 (tt) REVERT: F 244 PRO cc_start: 0.9466 (Cg_exo) cc_final: 0.8544 (Cg_endo) REVERT: F 245 GLU cc_start: 0.8395 (mp0) cc_final: 0.7992 (mp0) REVERT: F 281 LYS cc_start: 0.8516 (tttt) cc_final: 0.8033 (tttt) REVERT: F 295 ILE cc_start: 0.9623 (tt) cc_final: 0.9400 (tt) REVERT: F 491 LEU cc_start: 0.9157 (pt) cc_final: 0.8955 (pt) REVERT: F 523 SER cc_start: 0.8651 (p) cc_final: 0.8185 (p) REVERT: F 532 THR cc_start: 0.9174 (p) cc_final: 0.8938 (p) REVERT: F 546 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8506 (tm-30) REVERT: F 578 LEU cc_start: 0.9346 (mt) cc_final: 0.8978 (mt) REVERT: F 599 GLN cc_start: 0.8907 (tm-30) cc_final: 0.8448 (tm-30) REVERT: F 610 TYR cc_start: 0.8754 (t80) cc_final: 0.8085 (t80) REVERT: F 625 ARG cc_start: 0.6785 (ttt-90) cc_final: 0.6110 (tmt170) REVERT: I 83 MET cc_start: 0.8944 (tpp) cc_final: 0.8631 (tpp) REVERT: I 91 CYS cc_start: 0.7714 (m) cc_final: 0.7211 (m) REVERT: I 105 LEU cc_start: 0.9500 (mt) cc_final: 0.9131 (mt) REVERT: I 195 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7842 (mt-10) REVERT: I 209 ARG cc_start: 0.8257 (tpt90) cc_final: 0.8001 (tpt90) REVERT: I 264 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7968 (tttp) REVERT: I 273 GLU cc_start: 0.9019 (tt0) cc_final: 0.8542 (tt0) REVERT: I 277 TYR cc_start: 0.8338 (m-80) cc_final: 0.7738 (m-80) REVERT: I 281 LYS cc_start: 0.8535 (tttt) cc_final: 0.8232 (tttt) REVERT: I 296 LEU cc_start: 0.9645 (tp) cc_final: 0.9424 (tp) REVERT: I 309 GLN cc_start: 0.9467 (tt0) cc_final: 0.8397 (pt0) REVERT: I 317 LYS cc_start: 0.8675 (mtmm) cc_final: 0.8404 (mtmt) REVERT: I 498 GLU cc_start: 0.8603 (mm-30) cc_final: 0.7896 (mm-30) REVERT: I 504 ARG cc_start: 0.9124 (ttm170) cc_final: 0.8670 (ttm170) REVERT: I 510 ARG cc_start: 0.8242 (mtp85) cc_final: 0.8038 (mtp85) REVERT: I 536 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7796 (tm-30) REVERT: I 538 PHE cc_start: 0.9213 (t80) cc_final: 0.8923 (t80) REVERT: I 599 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8517 (tm-30) REVERT: L 83 MET cc_start: 0.9184 (tpp) cc_final: 0.7497 (tpp) REVERT: L 105 LEU cc_start: 0.9532 (mt) cc_final: 0.9212 (mt) REVERT: L 177 TRP cc_start: 0.9319 (m100) cc_final: 0.8944 (m100) REVERT: L 195 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8021 (mt-10) REVERT: L 225 LEU cc_start: 0.9451 (tp) cc_final: 0.9125 (tt) REVERT: L 245 GLU cc_start: 0.8230 (mp0) cc_final: 0.7833 (mp0) REVERT: L 250 LYS cc_start: 0.8303 (tptm) cc_final: 0.8052 (tptm) REVERT: L 301 LEU cc_start: 0.9099 (tt) cc_final: 0.8864 (tt) REVERT: L 309 GLN cc_start: 0.9241 (mt0) cc_final: 0.8696 (mt0) REVERT: L 491 LEU cc_start: 0.9142 (pt) cc_final: 0.8785 (pt) REVERT: L 498 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8581 (mm-30) REVERT: L 501 ARG cc_start: 0.8789 (tmm-80) cc_final: 0.8466 (tmm-80) REVERT: L 528 PHE cc_start: 0.8839 (t80) cc_final: 0.8421 (t80) REVERT: L 536 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7776 (tm-30) REVERT: L 597 TYR cc_start: 0.8946 (m-80) cc_final: 0.8703 (m-80) REVERT: L 599 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8500 (tm-30) outliers start: 10 outliers final: 0 residues processed: 2146 average time/residue: 0.2395 time to fit residues: 840.2511 Evaluate side-chains 1977 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1977 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 2.9990 chunk 369 optimal weight: 8.9990 chunk 336 optimal weight: 0.0570 chunk 342 optimal weight: 8.9990 chunk 361 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 404 optimal weight: 10.0000 chunk 466 optimal weight: 0.1980 chunk 465 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 overall best weight: 3.6504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 148 GLN A 265 HIS A 545 ASN A 632 GLN B 632 GLN C 137 GLN C 632 GLN D 137 GLN D 632 GLN G 137 GLN ** G 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 632 GLN J 137 GLN J 632 GLN E 137 GLN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS E 305 GLN E 632 GLN ** H 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 632 GLN K 137 GLN K 632 GLN F 137 GLN F 265 HIS F 632 GLN I 305 GLN I 632 GLN L 137 GLN L 632 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.159364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.133694 restraints weight = 67802.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.137969 restraints weight = 36625.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.140840 restraints weight = 23310.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.142779 restraints weight = 16641.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.144071 restraints weight = 12983.480| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39672 Z= 0.145 Angle : 0.680 7.570 53820 Z= 0.336 Chirality : 0.042 0.168 6168 Planarity : 0.005 0.061 6888 Dihedral : 5.113 21.416 5424 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.22 % Allowed : 1.66 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.12), residues: 4740 helix: -1.14 (0.10), residues: 2400 sheet: -1.86 (0.40), residues: 120 loop : -1.46 (0.14), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 575 TYR 0.019 0.002 TYR L 568 PHE 0.019 0.002 PHE I 74 TRP 0.068 0.003 TRP F 118 HIS 0.004 0.001 HIS I 214 Details of bonding type rmsd covalent geometry : bond 0.00331 (39672) covalent geometry : angle 0.67957 (53820) hydrogen bonds : bond 0.03420 ( 1410) hydrogen bonds : angle 4.54391 ( 3909) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2129 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 2120 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8377 (tm-30) REVERT: A 83 MET cc_start: 0.8978 (mmp) cc_final: 0.8498 (mmp) REVERT: A 85 GLN cc_start: 0.8775 (tp40) cc_final: 0.8535 (tp40) REVERT: A 105 LEU cc_start: 0.9619 (mt) cc_final: 0.9272 (mt) REVERT: A 177 TRP cc_start: 0.9148 (m100) cc_final: 0.8753 (t-100) REVERT: A 187 LEU cc_start: 0.9163 (mm) cc_final: 0.8929 (mm) REVERT: A 195 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7919 (mt-10) REVERT: A 225 LEU cc_start: 0.9311 (tt) cc_final: 0.8965 (tt) REVERT: A 244 PRO cc_start: 0.9428 (Cg_exo) cc_final: 0.8624 (Cg_endo) REVERT: A 245 GLU cc_start: 0.8366 (mp0) cc_final: 0.8003 (mp0) REVERT: A 255 GLU cc_start: 0.9209 (pp20) cc_final: 0.8773 (pp20) REVERT: A 281 LYS cc_start: 0.8619 (tttt) cc_final: 0.8068 (tttt) REVERT: A 295 ILE cc_start: 0.9601 (tt) cc_final: 0.9395 (tt) REVERT: A 306 LYS cc_start: 0.9011 (tttt) cc_final: 0.8712 (ttmm) REVERT: A 309 GLN cc_start: 0.9118 (mt0) cc_final: 0.8914 (mt0) REVERT: A 491 LEU cc_start: 0.9162 (pt) cc_final: 0.8921 (pt) REVERT: A 523 SER cc_start: 0.8611 (p) cc_final: 0.8273 (p) REVERT: A 524 PHE cc_start: 0.9009 (m-80) cc_final: 0.8800 (m-80) REVERT: A 574 GLU cc_start: 0.9407 (tm-30) cc_final: 0.8969 (tm-30) REVERT: A 578 LEU cc_start: 0.9284 (mt) cc_final: 0.8906 (mt) REVERT: A 599 GLN cc_start: 0.8874 (tm-30) cc_final: 0.8454 (tm-30) REVERT: A 610 TYR cc_start: 0.8771 (t80) cc_final: 0.8090 (t80) REVERT: A 625 ARG cc_start: 0.7304 (tmt170) cc_final: 0.5509 (ttt180) REVERT: B 83 MET cc_start: 0.8941 (tpp) cc_final: 0.8693 (tpp) REVERT: B 105 LEU cc_start: 0.9463 (mt) cc_final: 0.9102 (mt) REVERT: B 151 GLN cc_start: 0.8620 (tt0) cc_final: 0.8396 (tt0) REVERT: B 195 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7957 (mt-10) REVERT: B 209 ARG cc_start: 0.8276 (tpt90) cc_final: 0.7799 (tpt90) REVERT: B 264 LYS cc_start: 0.8297 (mmtt) cc_final: 0.7975 (tttp) REVERT: B 273 GLU cc_start: 0.8920 (tt0) cc_final: 0.8656 (tt0) REVERT: B 277 TYR cc_start: 0.8523 (m-80) cc_final: 0.7792 (m-80) REVERT: B 281 LYS cc_start: 0.8545 (tttt) cc_final: 0.8231 (tttt) REVERT: B 296 LEU cc_start: 0.9502 (tp) cc_final: 0.9286 (tp) REVERT: B 317 LYS cc_start: 0.8644 (mtmm) cc_final: 0.8348 (mtmt) REVERT: B 498 GLU cc_start: 0.8637 (mm-30) cc_final: 0.7893 (mm-30) REVERT: B 504 ARG cc_start: 0.9107 (ttm170) cc_final: 0.8624 (ttm170) REVERT: B 510 ARG cc_start: 0.8241 (mtp85) cc_final: 0.8016 (mtp85) REVERT: B 536 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7978 (tm-30) REVERT: B 599 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8619 (tm-30) REVERT: C 63 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8396 (tm-30) REVERT: C 81 GLN cc_start: 0.8790 (tp-100) cc_final: 0.8514 (tp-100) REVERT: C 91 CYS cc_start: 0.8471 (m) cc_final: 0.8047 (m) REVERT: C 105 LEU cc_start: 0.9558 (mt) cc_final: 0.9221 (mt) REVERT: C 195 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8003 (mt-10) REVERT: C 201 GLN cc_start: 0.8856 (mp10) cc_final: 0.8436 (mp10) REVERT: C 225 LEU cc_start: 0.9448 (tp) cc_final: 0.9102 (tt) REVERT: C 245 GLU cc_start: 0.8256 (mp0) cc_final: 0.7846 (mp0) REVERT: C 297 ARG cc_start: 0.9243 (ttp80) cc_final: 0.8723 (ttt-90) REVERT: C 301 LEU cc_start: 0.9101 (tt) cc_final: 0.8854 (tt) REVERT: C 309 GLN cc_start: 0.9307 (mt0) cc_final: 0.8728 (mt0) REVERT: C 498 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8490 (mm-30) REVERT: C 501 ARG cc_start: 0.8752 (tmm-80) cc_final: 0.8354 (tmm-80) REVERT: C 536 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7858 (tm-30) REVERT: C 574 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8558 (tm-30) REVERT: C 597 TYR cc_start: 0.9270 (m-80) cc_final: 0.8956 (m-80) REVERT: C 599 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8645 (tm-30) REVERT: D 63 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8242 (tm-30) REVERT: D 85 GLN cc_start: 0.8831 (tp40) cc_final: 0.8372 (tp40) REVERT: D 105 LEU cc_start: 0.9644 (mt) cc_final: 0.9332 (mt) REVERT: D 177 TRP cc_start: 0.9131 (m100) cc_final: 0.8756 (t-100) REVERT: D 187 LEU cc_start: 0.9172 (mm) cc_final: 0.8837 (mm) REVERT: D 195 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7733 (mt-10) REVERT: D 225 LEU cc_start: 0.9350 (tt) cc_final: 0.8946 (tt) REVERT: D 244 PRO cc_start: 0.9448 (Cg_exo) cc_final: 0.8474 (Cg_endo) REVERT: D 245 GLU cc_start: 0.8272 (mp0) cc_final: 0.7923 (mp0) REVERT: D 281 LYS cc_start: 0.8517 (tttt) cc_final: 0.8045 (tttt) REVERT: D 306 LYS cc_start: 0.9135 (ttmm) cc_final: 0.8584 (tttt) REVERT: D 491 LEU cc_start: 0.9112 (pt) cc_final: 0.8873 (pt) REVERT: D 523 SER cc_start: 0.8671 (p) cc_final: 0.8204 (p) REVERT: D 536 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7624 (tm-30) REVERT: D 540 THR cc_start: 0.9410 (m) cc_final: 0.9198 (m) REVERT: D 571 TYR cc_start: 0.8893 (t80) cc_final: 0.8675 (t80) REVERT: D 578 LEU cc_start: 0.9195 (mt) cc_final: 0.8916 (mt) REVERT: D 599 GLN cc_start: 0.8933 (tm-30) cc_final: 0.8549 (tm-30) REVERT: D 610 TYR cc_start: 0.8884 (t80) cc_final: 0.8149 (t80) REVERT: G 83 MET cc_start: 0.9050 (tpp) cc_final: 0.8660 (tpp) REVERT: G 85 GLN cc_start: 0.8835 (tp40) cc_final: 0.8491 (tp40) REVERT: G 91 CYS cc_start: 0.7721 (m) cc_final: 0.6995 (m) REVERT: G 105 LEU cc_start: 0.9492 (mt) cc_final: 0.9148 (mt) REVERT: G 195 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7952 (mt-10) REVERT: G 264 LYS cc_start: 0.8293 (mmtt) cc_final: 0.7973 (tttp) REVERT: G 273 GLU cc_start: 0.8970 (tt0) cc_final: 0.8496 (tt0) REVERT: G 277 TYR cc_start: 0.8539 (m-80) cc_final: 0.7744 (m-80) REVERT: G 281 LYS cc_start: 0.8632 (tttt) cc_final: 0.8302 (tttt) REVERT: G 297 ARG cc_start: 0.8792 (ttt180) cc_final: 0.8085 (ttt180) REVERT: G 317 LYS cc_start: 0.8714 (mtmm) cc_final: 0.8459 (mtmt) REVERT: G 498 GLU cc_start: 0.8638 (mm-30) cc_final: 0.7937 (mm-30) REVERT: G 504 ARG cc_start: 0.9123 (ttm170) cc_final: 0.8645 (ttm170) REVERT: G 510 ARG cc_start: 0.8347 (mtp85) cc_final: 0.8131 (mtp85) REVERT: G 528 PHE cc_start: 0.8679 (t80) cc_final: 0.8059 (t80) REVERT: G 536 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7949 (tm-30) REVERT: G 538 PHE cc_start: 0.9281 (t80) cc_final: 0.8823 (t80) REVERT: G 599 GLN cc_start: 0.9166 (tm-30) cc_final: 0.8644 (tm-30) REVERT: J 63 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8395 (tm-30) REVERT: J 81 GLN cc_start: 0.8763 (tp-100) cc_final: 0.8459 (tp-100) REVERT: J 91 CYS cc_start: 0.8345 (m) cc_final: 0.8088 (m) REVERT: J 105 LEU cc_start: 0.9536 (mt) cc_final: 0.9213 (mt) REVERT: J 195 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8029 (mt-10) REVERT: J 201 GLN cc_start: 0.8853 (mp10) cc_final: 0.8435 (mp10) REVERT: J 225 LEU cc_start: 0.9453 (tp) cc_final: 0.9108 (tt) REVERT: J 245 GLU cc_start: 0.8257 (mp0) cc_final: 0.7850 (mp0) REVERT: J 301 LEU cc_start: 0.9142 (tt) cc_final: 0.8851 (tt) REVERT: J 309 GLN cc_start: 0.9195 (mt0) cc_final: 0.8572 (mt0) REVERT: J 498 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8498 (mm-30) REVERT: J 501 ARG cc_start: 0.8736 (tmm-80) cc_final: 0.8337 (tmm-80) REVERT: J 528 PHE cc_start: 0.8660 (t80) cc_final: 0.8277 (t80) REVERT: J 536 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7936 (tm-30) REVERT: J 597 TYR cc_start: 0.9258 (m-80) cc_final: 0.8992 (m-80) REVERT: J 599 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8629 (tm-30) REVERT: E 63 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8248 (tm-30) REVERT: E 85 GLN cc_start: 0.8882 (tp40) cc_final: 0.8401 (tp40) REVERT: E 105 LEU cc_start: 0.9603 (mt) cc_final: 0.9326 (mt) REVERT: E 177 TRP cc_start: 0.9107 (m100) cc_final: 0.8770 (t-100) REVERT: E 187 LEU cc_start: 0.9184 (mm) cc_final: 0.8846 (mm) REVERT: E 195 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7733 (mt-10) REVERT: E 225 LEU cc_start: 0.9405 (tt) cc_final: 0.9056 (tt) REVERT: E 244 PRO cc_start: 0.9441 (Cg_exo) cc_final: 0.8500 (Cg_endo) REVERT: E 245 GLU cc_start: 0.8388 (mp0) cc_final: 0.8020 (mp0) REVERT: E 281 LYS cc_start: 0.8359 (tttt) cc_final: 0.7950 (tttt) REVERT: E 306 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8571 (tttt) REVERT: E 540 THR cc_start: 0.9425 (m) cc_final: 0.9178 (m) REVERT: E 578 LEU cc_start: 0.9195 (mt) cc_final: 0.8907 (mt) REVERT: E 599 GLN cc_start: 0.8935 (tm-30) cc_final: 0.8502 (tm-30) REVERT: E 610 TYR cc_start: 0.8698 (t80) cc_final: 0.7926 (t80) REVERT: E 625 ARG cc_start: 0.7262 (tmt170) cc_final: 0.6910 (tmt170) REVERT: H 83 MET cc_start: 0.8966 (tpp) cc_final: 0.8664 (tpp) REVERT: H 91 CYS cc_start: 0.7951 (m) cc_final: 0.7506 (m) REVERT: H 105 LEU cc_start: 0.9460 (mt) cc_final: 0.9103 (mt) REVERT: H 195 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7976 (mt-10) REVERT: H 209 ARG cc_start: 0.8015 (tpt90) cc_final: 0.7649 (tpt90) REVERT: H 264 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7964 (tttp) REVERT: H 273 GLU cc_start: 0.9007 (tt0) cc_final: 0.8538 (tt0) REVERT: H 277 TYR cc_start: 0.8526 (m-80) cc_final: 0.7785 (m-80) REVERT: H 281 LYS cc_start: 0.8488 (tttt) cc_final: 0.8235 (tttt) REVERT: H 295 ILE cc_start: 0.9641 (tt) cc_final: 0.9429 (tt) REVERT: H 296 LEU cc_start: 0.9680 (tp) cc_final: 0.9468 (tp) REVERT: H 297 ARG cc_start: 0.9202 (ttt180) cc_final: 0.8158 (ttt180) REVERT: H 317 LYS cc_start: 0.8679 (mtmm) cc_final: 0.8386 (mtmt) REVERT: H 498 GLU cc_start: 0.8648 (mm-30) cc_final: 0.7942 (mm-30) REVERT: H 504 ARG cc_start: 0.9122 (ttm170) cc_final: 0.8662 (ttm170) REVERT: H 510 ARG cc_start: 0.8264 (mtp85) cc_final: 0.8043 (mtp85) REVERT: H 528 PHE cc_start: 0.8700 (t80) cc_final: 0.8095 (t80) REVERT: H 536 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7763 (tm-30) REVERT: H 599 GLN cc_start: 0.9165 (tm-30) cc_final: 0.8636 (tm-30) REVERT: K 63 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8394 (tm-30) REVERT: K 81 GLN cc_start: 0.8688 (tp-100) cc_final: 0.8350 (tp-100) REVERT: K 83 MET cc_start: 0.9180 (tpp) cc_final: 0.7403 (tpp) REVERT: K 105 LEU cc_start: 0.9518 (mt) cc_final: 0.9200 (mt) REVERT: K 195 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8021 (mt-10) REVERT: K 201 GLN cc_start: 0.8856 (mp10) cc_final: 0.8444 (mp10) REVERT: K 225 LEU cc_start: 0.9459 (tp) cc_final: 0.9111 (tt) REVERT: K 245 GLU cc_start: 0.8255 (mp0) cc_final: 0.7816 (mp0) REVERT: K 301 LEU cc_start: 0.9175 (tt) cc_final: 0.8859 (tt) REVERT: K 305 GLN cc_start: 0.9317 (tm-30) cc_final: 0.8314 (tm-30) REVERT: K 498 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8546 (mm-30) REVERT: K 501 ARG cc_start: 0.8738 (tmm-80) cc_final: 0.8395 (tmm-80) REVERT: K 504 ARG cc_start: 0.8975 (ttm170) cc_final: 0.8283 (ttt180) REVERT: K 528 PHE cc_start: 0.8670 (t80) cc_final: 0.8247 (t80) REVERT: K 536 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7885 (tm-30) REVERT: K 574 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8725 (tm-30) REVERT: K 599 GLN cc_start: 0.8983 (tm-30) cc_final: 0.8698 (tm-30) REVERT: F 83 MET cc_start: 0.9200 (tpt) cc_final: 0.8228 (tpp) REVERT: F 85 GLN cc_start: 0.9010 (tp40) cc_final: 0.8535 (tp40) REVERT: F 105 LEU cc_start: 0.9652 (mt) cc_final: 0.9345 (mt) REVERT: F 177 TRP cc_start: 0.9108 (m100) cc_final: 0.8821 (t-100) REVERT: F 187 LEU cc_start: 0.9161 (mm) cc_final: 0.8845 (mm) REVERT: F 195 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7629 (mt-10) REVERT: F 225 LEU cc_start: 0.9352 (tt) cc_final: 0.8950 (tt) REVERT: F 244 PRO cc_start: 0.9443 (Cg_exo) cc_final: 0.8509 (Cg_endo) REVERT: F 245 GLU cc_start: 0.8386 (mp0) cc_final: 0.8019 (mp0) REVERT: F 281 LYS cc_start: 0.8542 (tttt) cc_final: 0.8068 (tttt) REVERT: F 295 ILE cc_start: 0.9622 (tt) cc_final: 0.9377 (tt) REVERT: F 306 LYS cc_start: 0.8931 (ttpt) cc_final: 0.8424 (ttpt) REVERT: F 491 LEU cc_start: 0.9216 (pt) cc_final: 0.8722 (pp) REVERT: F 536 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7740 (tm-30) REVERT: F 540 THR cc_start: 0.9367 (m) cc_final: 0.8992 (m) REVERT: F 546 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8537 (tm-30) REVERT: F 578 LEU cc_start: 0.9314 (mt) cc_final: 0.8966 (mt) REVERT: F 599 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8512 (tm-30) REVERT: F 610 TYR cc_start: 0.8745 (t80) cc_final: 0.8062 (t80) REVERT: I 83 MET cc_start: 0.8981 (tpp) cc_final: 0.8668 (tpp) REVERT: I 91 CYS cc_start: 0.8111 (m) cc_final: 0.7539 (m) REVERT: I 105 LEU cc_start: 0.9476 (mt) cc_final: 0.9118 (mt) REVERT: I 195 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7944 (mt-10) REVERT: I 209 ARG cc_start: 0.8279 (tpt90) cc_final: 0.7995 (tpt90) REVERT: I 264 LYS cc_start: 0.8300 (mmtt) cc_final: 0.7976 (tttp) REVERT: I 273 GLU cc_start: 0.8967 (tt0) cc_final: 0.8469 (tt0) REVERT: I 277 TYR cc_start: 0.8505 (m-80) cc_final: 0.7787 (m-80) REVERT: I 281 LYS cc_start: 0.8593 (tttt) cc_final: 0.8311 (tttt) REVERT: I 309 GLN cc_start: 0.9424 (tt0) cc_final: 0.8255 (pt0) REVERT: I 317 LYS cc_start: 0.8654 (mtmm) cc_final: 0.8372 (mtmt) REVERT: I 498 GLU cc_start: 0.8648 (mm-30) cc_final: 0.7937 (mm-30) REVERT: I 510 ARG cc_start: 0.8260 (mtp85) cc_final: 0.8058 (mtp85) REVERT: I 536 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7831 (tm-30) REVERT: I 599 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8628 (tm-30) REVERT: L 83 MET cc_start: 0.9149 (tpp) cc_final: 0.7539 (tpp) REVERT: L 105 LEU cc_start: 0.9571 (mt) cc_final: 0.9225 (mt) REVERT: L 177 TRP cc_start: 0.9338 (m100) cc_final: 0.8939 (m100) REVERT: L 195 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8009 (mt-10) REVERT: L 201 GLN cc_start: 0.8869 (mp10) cc_final: 0.8452 (mp10) REVERT: L 225 LEU cc_start: 0.9457 (tp) cc_final: 0.9112 (tt) REVERT: L 245 GLU cc_start: 0.8286 (mp0) cc_final: 0.7876 (mp0) REVERT: L 301 LEU cc_start: 0.9117 (tt) cc_final: 0.8848 (tt) REVERT: L 305 GLN cc_start: 0.9489 (tm-30) cc_final: 0.8188 (tm-30) REVERT: L 491 LEU cc_start: 0.9124 (pt) cc_final: 0.8776 (pt) REVERT: L 498 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8606 (mm-30) REVERT: L 501 ARG cc_start: 0.8807 (tmm-80) cc_final: 0.8518 (tmm-80) REVERT: L 504 ARG cc_start: 0.8978 (ttm170) cc_final: 0.8278 (ttt180) REVERT: L 528 PHE cc_start: 0.8666 (t80) cc_final: 0.8124 (t80) REVERT: L 597 TYR cc_start: 0.9249 (m-80) cc_final: 0.8963 (m-80) REVERT: L 599 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8620 (tm-30) outliers start: 9 outliers final: 0 residues processed: 2124 average time/residue: 0.2391 time to fit residues: 830.9292 Evaluate side-chains 1910 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1910 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 105 optimal weight: 5.9990 chunk 364 optimal weight: 9.9990 chunk 313 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 363 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 247 optimal weight: 20.0000 chunk 337 optimal weight: 20.0000 chunk 381 optimal weight: 0.8980 chunk 474 optimal weight: 9.9990 chunk 174 optimal weight: 20.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 632 GLN B 632 GLN C 137 GLN C 632 GLN D 137 GLN D 265 HIS D 305 GLN D 632 GLN G 85 GLN ** G 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 632 GLN J 137 GLN ** J 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 632 GLN E 137 GLN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 632 GLN ** H 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 632 GLN K 137 GLN K 632 GLN F 137 GLN ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 632 GLN I 632 GLN L 137 GLN L 632 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.157127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.131375 restraints weight = 68404.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.135585 restraints weight = 37293.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.138405 restraints weight = 23888.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.140333 restraints weight = 17110.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.141592 restraints weight = 13421.444| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 39672 Z= 0.180 Angle : 0.722 7.599 53820 Z= 0.358 Chirality : 0.044 0.172 6168 Planarity : 0.005 0.073 6888 Dihedral : 5.315 26.036 5424 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.19 % Allowed : 1.25 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.12), residues: 4740 helix: -1.06 (0.10), residues: 2400 sheet: -1.88 (0.39), residues: 120 loop : -1.50 (0.14), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 617 TYR 0.022 0.002 TYR D 568 PHE 0.023 0.002 PHE B 538 TRP 0.062 0.003 TRP F 118 HIS 0.004 0.001 HIS I 214 Details of bonding type rmsd covalent geometry : bond 0.00408 (39672) covalent geometry : angle 0.72218 (53820) hydrogen bonds : bond 0.03558 ( 1410) hydrogen bonds : angle 4.69577 ( 3909) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2101 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 2093 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8318 (tm-30) REVERT: A 83 MET cc_start: 0.9216 (mmp) cc_final: 0.8711 (mmp) REVERT: A 105 LEU cc_start: 0.9647 (mt) cc_final: 0.9332 (mt) REVERT: A 177 TRP cc_start: 0.9148 (m100) cc_final: 0.8815 (t-100) REVERT: A 187 LEU cc_start: 0.9190 (mm) cc_final: 0.8897 (mm) REVERT: A 195 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8108 (mt-10) REVERT: A 225 LEU cc_start: 0.9352 (tt) cc_final: 0.8994 (tt) REVERT: A 244 PRO cc_start: 0.9421 (Cg_exo) cc_final: 0.9205 (Cg_endo) REVERT: A 281 LYS cc_start: 0.8650 (tttt) cc_final: 0.8102 (tttt) REVERT: A 295 ILE cc_start: 0.9596 (tt) cc_final: 0.9365 (tt) REVERT: A 297 ARG cc_start: 0.9165 (ttt-90) cc_final: 0.8890 (ttt-90) REVERT: A 306 LYS cc_start: 0.8968 (tttt) cc_final: 0.8619 (ttmm) REVERT: A 309 GLN cc_start: 0.9177 (mt0) cc_final: 0.8920 (mt0) REVERT: A 314 PHE cc_start: 0.8847 (t80) cc_final: 0.8408 (t80) REVERT: A 523 SER cc_start: 0.8620 (p) cc_final: 0.8274 (p) REVERT: A 524 PHE cc_start: 0.9006 (m-80) cc_final: 0.8770 (m-80) REVERT: A 536 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7409 (tm-30) REVERT: A 540 THR cc_start: 0.9317 (m) cc_final: 0.9113 (m) REVERT: A 574 GLU cc_start: 0.9322 (tm-30) cc_final: 0.8888 (tm-30) REVERT: A 578 LEU cc_start: 0.9236 (mt) cc_final: 0.8874 (mt) REVERT: A 599 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8498 (tm-30) REVERT: A 610 TYR cc_start: 0.8796 (t80) cc_final: 0.8139 (t80) REVERT: A 625 ARG cc_start: 0.7175 (tmt170) cc_final: 0.5458 (ttt180) REVERT: B 83 MET cc_start: 0.8994 (tpp) cc_final: 0.8789 (tpp) REVERT: B 91 CYS cc_start: 0.7928 (m) cc_final: 0.7351 (m) REVERT: B 105 LEU cc_start: 0.9460 (mt) cc_final: 0.9153 (mt) REVERT: B 195 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8066 (mt-10) REVERT: B 264 LYS cc_start: 0.8381 (mmtt) cc_final: 0.8088 (mtpp) REVERT: B 277 TYR cc_start: 0.8623 (m-80) cc_final: 0.7717 (m-80) REVERT: B 281 LYS cc_start: 0.8678 (tttt) cc_final: 0.8403 (tttt) REVERT: B 296 LEU cc_start: 0.9584 (tp) cc_final: 0.9365 (tp) REVERT: B 317 LYS cc_start: 0.8641 (mtmm) cc_final: 0.8367 (mtmt) REVERT: B 498 GLU cc_start: 0.8617 (mm-30) cc_final: 0.7872 (mm-30) REVERT: B 504 ARG cc_start: 0.9122 (ttm170) cc_final: 0.8664 (ttm170) REVERT: B 510 ARG cc_start: 0.8298 (mtp85) cc_final: 0.8073 (mtp85) REVERT: B 536 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7825 (tm-30) REVERT: B 538 PHE cc_start: 0.9197 (t80) cc_final: 0.8755 (t80) REVERT: B 599 GLN cc_start: 0.9196 (tm-30) cc_final: 0.8706 (tm-30) REVERT: C 63 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8418 (tm-30) REVERT: C 67 PHE cc_start: 0.8918 (t80) cc_final: 0.8386 (t80) REVERT: C 81 GLN cc_start: 0.8761 (tp-100) cc_final: 0.8492 (tp-100) REVERT: C 85 GLN cc_start: 0.9068 (tp-100) cc_final: 0.8585 (tp-100) REVERT: C 105 LEU cc_start: 0.9553 (mt) cc_final: 0.9210 (mt) REVERT: C 164 GLN cc_start: 0.8056 (tt0) cc_final: 0.7678 (tt0) REVERT: C 177 TRP cc_start: 0.9159 (m100) cc_final: 0.8915 (m100) REVERT: C 201 GLN cc_start: 0.8906 (mp10) cc_final: 0.8452 (mp10) REVERT: C 225 LEU cc_start: 0.9453 (tp) cc_final: 0.9103 (tt) REVERT: C 245 GLU cc_start: 0.8245 (mp0) cc_final: 0.7881 (mp0) REVERT: C 297 ARG cc_start: 0.9244 (ttp80) cc_final: 0.8789 (ttt180) REVERT: C 301 LEU cc_start: 0.9113 (tt) cc_final: 0.8840 (tt) REVERT: C 305 GLN cc_start: 0.9518 (tm-30) cc_final: 0.8112 (tm-30) REVERT: C 498 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8368 (mm-30) REVERT: C 501 ARG cc_start: 0.8770 (tmm-80) cc_final: 0.8341 (tmm-80) REVERT: C 536 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7868 (tm-30) REVERT: C 574 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8544 (tm-30) REVERT: C 597 TYR cc_start: 0.9280 (m-80) cc_final: 0.8965 (m-80) REVERT: C 599 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8649 (tm-30) REVERT: D 63 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8296 (tm-30) REVERT: D 85 GLN cc_start: 0.8960 (tp40) cc_final: 0.8536 (tp40) REVERT: D 105 LEU cc_start: 0.9590 (mt) cc_final: 0.9273 (mt) REVERT: D 177 TRP cc_start: 0.9130 (m100) cc_final: 0.8745 (t-100) REVERT: D 187 LEU cc_start: 0.9200 (mm) cc_final: 0.8855 (mm) REVERT: D 195 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7719 (mt-10) REVERT: D 201 GLN cc_start: 0.8534 (mt0) cc_final: 0.8083 (mm110) REVERT: D 225 LEU cc_start: 0.9353 (tt) cc_final: 0.8937 (tt) REVERT: D 244 PRO cc_start: 0.9432 (Cg_exo) cc_final: 0.9199 (Cg_endo) REVERT: D 281 LYS cc_start: 0.8575 (tttt) cc_final: 0.8098 (tttt) REVERT: D 306 LYS cc_start: 0.9243 (ttmm) cc_final: 0.8574 (tttt) REVERT: D 491 LEU cc_start: 0.9166 (pt) cc_final: 0.8935 (pt) REVERT: D 523 SER cc_start: 0.8687 (p) cc_final: 0.8201 (p) REVERT: D 536 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7684 (tm-30) REVERT: D 578 LEU cc_start: 0.9173 (mt) cc_final: 0.8883 (mt) REVERT: D 595 GLU cc_start: 0.7647 (pt0) cc_final: 0.7400 (pt0) REVERT: D 599 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8478 (tm-30) REVERT: D 610 TYR cc_start: 0.8715 (t80) cc_final: 0.7989 (t80) REVERT: D 625 ARG cc_start: 0.6508 (tmt170) cc_final: 0.5044 (ttt180) REVERT: G 83 MET cc_start: 0.9052 (tpp) cc_final: 0.8595 (tpp) REVERT: G 91 CYS cc_start: 0.7824 (m) cc_final: 0.7073 (m) REVERT: G 105 LEU cc_start: 0.9485 (mt) cc_final: 0.9162 (mt) REVERT: G 195 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8048 (mt-10) REVERT: G 208 GLN cc_start: 0.8079 (pm20) cc_final: 0.7862 (pm20) REVERT: G 209 ARG cc_start: 0.8438 (tpt90) cc_final: 0.8029 (tpt90) REVERT: G 225 LEU cc_start: 0.9194 (tt) cc_final: 0.8839 (tt) REVERT: G 264 LYS cc_start: 0.8373 (mmtt) cc_final: 0.8078 (mtpp) REVERT: G 273 GLU cc_start: 0.8969 (tt0) cc_final: 0.8507 (tt0) REVERT: G 277 TYR cc_start: 0.8663 (m-80) cc_final: 0.7665 (m-80) REVERT: G 281 LYS cc_start: 0.8662 (tttt) cc_final: 0.8393 (tttt) REVERT: G 296 LEU cc_start: 0.9611 (tp) cc_final: 0.9407 (tp) REVERT: G 317 LYS cc_start: 0.8661 (mtmm) cc_final: 0.8391 (mtmt) REVERT: G 498 GLU cc_start: 0.8617 (mm-30) cc_final: 0.7863 (mm-30) REVERT: G 504 ARG cc_start: 0.9103 (ttm170) cc_final: 0.8640 (ttm170) REVERT: G 510 ARG cc_start: 0.8313 (mtp85) cc_final: 0.8091 (mtp85) REVERT: G 536 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7953 (tm-30) REVERT: G 538 PHE cc_start: 0.9322 (t80) cc_final: 0.8965 (t80) REVERT: G 599 GLN cc_start: 0.9219 (tm-30) cc_final: 0.8719 (tm-30) REVERT: J 63 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8384 (tm-30) REVERT: J 67 PHE cc_start: 0.8890 (t80) cc_final: 0.8367 (t80) REVERT: J 81 GLN cc_start: 0.8811 (tp-100) cc_final: 0.8559 (tp-100) REVERT: J 85 GLN cc_start: 0.9071 (tp-100) cc_final: 0.8620 (tp-100) REVERT: J 91 CYS cc_start: 0.8281 (m) cc_final: 0.7890 (m) REVERT: J 105 LEU cc_start: 0.9539 (mt) cc_final: 0.9209 (mt) REVERT: J 164 GLN cc_start: 0.8078 (tt0) cc_final: 0.7806 (tt0) REVERT: J 177 TRP cc_start: 0.9170 (m100) cc_final: 0.8931 (m100) REVERT: J 201 GLN cc_start: 0.8899 (mp10) cc_final: 0.8448 (mp10) REVERT: J 225 LEU cc_start: 0.9465 (tp) cc_final: 0.9118 (tt) REVERT: J 245 GLU cc_start: 0.8240 (mp0) cc_final: 0.7878 (mp0) REVERT: J 281 LYS cc_start: 0.8302 (tttt) cc_final: 0.7807 (tttt) REVERT: J 301 LEU cc_start: 0.9130 (tt) cc_final: 0.8824 (tt) REVERT: J 305 GLN cc_start: 0.9364 (tm-30) cc_final: 0.8351 (tm-30) REVERT: J 498 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8388 (mm-30) REVERT: J 501 ARG cc_start: 0.8770 (tmm-80) cc_final: 0.8348 (tmm-80) REVERT: J 528 PHE cc_start: 0.8670 (t80) cc_final: 0.8304 (t80) REVERT: J 536 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7922 (tm-30) REVERT: J 597 TYR cc_start: 0.9219 (m-80) cc_final: 0.8959 (m-80) REVERT: J 599 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8658 (tm-30) REVERT: E 85 GLN cc_start: 0.8934 (tp40) cc_final: 0.8440 (tp40) REVERT: E 105 LEU cc_start: 0.9562 (mt) cc_final: 0.9258 (mt) REVERT: E 113 ARG cc_start: 0.8883 (tpt170) cc_final: 0.8401 (tpp-160) REVERT: E 177 TRP cc_start: 0.9115 (m100) cc_final: 0.8754 (t-100) REVERT: E 187 LEU cc_start: 0.9186 (mm) cc_final: 0.8831 (mm) REVERT: E 195 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7722 (mt-10) REVERT: E 225 LEU cc_start: 0.9300 (tt) cc_final: 0.9021 (tt) REVERT: E 244 PRO cc_start: 0.9434 (Cg_exo) cc_final: 0.9201 (Cg_endo) REVERT: E 281 LYS cc_start: 0.8530 (tttt) cc_final: 0.8051 (tttt) REVERT: E 295 ILE cc_start: 0.9570 (tt) cc_final: 0.9369 (tt) REVERT: E 297 ARG cc_start: 0.9122 (ttt-90) cc_final: 0.8871 (ttt-90) REVERT: E 306 LYS cc_start: 0.9195 (ttmm) cc_final: 0.8613 (tttt) REVERT: E 578 LEU cc_start: 0.9179 (mt) cc_final: 0.8903 (mt) REVERT: E 599 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8511 (tm-30) REVERT: E 610 TYR cc_start: 0.8715 (t80) cc_final: 0.8035 (t80) REVERT: H 83 MET cc_start: 0.8989 (tpp) cc_final: 0.8704 (tpp) REVERT: H 91 CYS cc_start: 0.8048 (m) cc_final: 0.7563 (m) REVERT: H 105 LEU cc_start: 0.9455 (mt) cc_final: 0.9159 (mt) REVERT: H 195 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8054 (mt-10) REVERT: H 225 LEU cc_start: 0.9198 (tt) cc_final: 0.8851 (tt) REVERT: H 264 LYS cc_start: 0.8369 (mmtt) cc_final: 0.8034 (tttp) REVERT: H 273 GLU cc_start: 0.9036 (tt0) cc_final: 0.8475 (tt0) REVERT: H 277 TYR cc_start: 0.8647 (m-80) cc_final: 0.7676 (m-80) REVERT: H 281 LYS cc_start: 0.8662 (tttt) cc_final: 0.8388 (tttt) REVERT: H 295 ILE cc_start: 0.9664 (tt) cc_final: 0.9444 (tt) REVERT: H 296 LEU cc_start: 0.9665 (tp) cc_final: 0.9445 (tp) REVERT: H 317 LYS cc_start: 0.8599 (mtmm) cc_final: 0.8371 (mtmt) REVERT: H 498 GLU cc_start: 0.8637 (mm-30) cc_final: 0.7889 (mm-30) REVERT: H 504 ARG cc_start: 0.9102 (ttm170) cc_final: 0.8641 (ttm170) REVERT: H 510 ARG cc_start: 0.8240 (mtp85) cc_final: 0.7984 (mtp85) REVERT: H 536 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7855 (tm-30) REVERT: H 538 PHE cc_start: 0.9191 (t80) cc_final: 0.8804 (t80) REVERT: H 545 ASN cc_start: 0.8746 (t0) cc_final: 0.8286 (t0) REVERT: H 599 GLN cc_start: 0.9155 (tm-30) cc_final: 0.8643 (tm-30) REVERT: K 63 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8427 (tm-30) REVERT: K 67 PHE cc_start: 0.8884 (t80) cc_final: 0.8335 (t80) REVERT: K 81 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8416 (tp-100) REVERT: K 83 MET cc_start: 0.9191 (tpp) cc_final: 0.7375 (tpp) REVERT: K 91 CYS cc_start: 0.8413 (m) cc_final: 0.8164 (m) REVERT: K 105 LEU cc_start: 0.9524 (mt) cc_final: 0.9199 (mt) REVERT: K 177 TRP cc_start: 0.9174 (m100) cc_final: 0.8932 (m100) REVERT: K 195 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8037 (mt-10) REVERT: K 201 GLN cc_start: 0.8840 (mp10) cc_final: 0.8250 (mp10) REVERT: K 225 LEU cc_start: 0.9465 (tp) cc_final: 0.9129 (tt) REVERT: K 245 GLU cc_start: 0.8294 (mp0) cc_final: 0.7886 (mp0) REVERT: K 297 ARG cc_start: 0.9201 (ttt180) cc_final: 0.8820 (ttt180) REVERT: K 301 LEU cc_start: 0.9172 (tt) cc_final: 0.8864 (tt) REVERT: K 305 GLN cc_start: 0.9344 (tm-30) cc_final: 0.8327 (tm-30) REVERT: K 498 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8422 (mm-30) REVERT: K 501 ARG cc_start: 0.8734 (tmm-80) cc_final: 0.8344 (tmm-80) REVERT: K 504 ARG cc_start: 0.8937 (ttm170) cc_final: 0.8212 (ttt180) REVERT: K 524 PHE cc_start: 0.8724 (m-10) cc_final: 0.8489 (m-10) REVERT: K 528 PHE cc_start: 0.8679 (t80) cc_final: 0.8080 (t80) REVERT: K 536 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7923 (tm-30) REVERT: K 574 GLU cc_start: 0.9143 (tm-30) cc_final: 0.8733 (tm-30) REVERT: K 599 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8702 (tm-30) REVERT: F 83 MET cc_start: 0.9177 (tpt) cc_final: 0.8093 (tpp) REVERT: F 85 GLN cc_start: 0.9046 (tp40) cc_final: 0.8571 (tp40) REVERT: F 105 LEU cc_start: 0.9624 (mt) cc_final: 0.9306 (mt) REVERT: F 177 TRP cc_start: 0.9127 (m100) cc_final: 0.8789 (t-100) REVERT: F 187 LEU cc_start: 0.9191 (mm) cc_final: 0.8848 (mm) REVERT: F 195 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7612 (mt-10) REVERT: F 225 LEU cc_start: 0.9349 (tt) cc_final: 0.8926 (tt) REVERT: F 244 PRO cc_start: 0.9416 (Cg_exo) cc_final: 0.9205 (Cg_endo) REVERT: F 255 GLU cc_start: 0.9214 (pp20) cc_final: 0.8787 (pp20) REVERT: F 281 LYS cc_start: 0.8528 (tttt) cc_final: 0.8034 (tttt) REVERT: F 306 LYS cc_start: 0.8976 (ttpt) cc_final: 0.8545 (ttpt) REVERT: F 536 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7681 (tm-30) REVERT: F 546 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8400 (tm-30) REVERT: F 578 LEU cc_start: 0.9246 (mt) cc_final: 0.8874 (mt) REVERT: F 599 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8527 (tm-30) REVERT: F 610 TYR cc_start: 0.8791 (t80) cc_final: 0.8198 (t80) REVERT: F 617 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.7990 (mtm-85) REVERT: I 83 MET cc_start: 0.8998 (tpp) cc_final: 0.8667 (tpp) REVERT: I 91 CYS cc_start: 0.8161 (m) cc_final: 0.7557 (m) REVERT: I 105 LEU cc_start: 0.9479 (mt) cc_final: 0.9129 (mt) REVERT: I 195 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8027 (mt-10) REVERT: I 264 LYS cc_start: 0.8325 (mmtt) cc_final: 0.8047 (mtpp) REVERT: I 273 GLU cc_start: 0.8948 (tt0) cc_final: 0.8495 (tt0) REVERT: I 277 TYR cc_start: 0.8625 (m-80) cc_final: 0.7666 (m-80) REVERT: I 281 LYS cc_start: 0.8658 (tttt) cc_final: 0.8389 (tttt) REVERT: I 296 LEU cc_start: 0.9552 (tp) cc_final: 0.9349 (tp) REVERT: I 309 GLN cc_start: 0.9326 (tt0) cc_final: 0.8479 (pt0) REVERT: I 317 LYS cc_start: 0.8627 (mtmm) cc_final: 0.8338 (mtmt) REVERT: I 498 GLU cc_start: 0.8630 (mm-30) cc_final: 0.7882 (mm-30) REVERT: I 510 ARG cc_start: 0.8257 (mtp85) cc_final: 0.8022 (mtp85) REVERT: I 536 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7988 (tm-30) REVERT: I 538 PHE cc_start: 0.9217 (t80) cc_final: 0.8930 (t80) REVERT: I 599 GLN cc_start: 0.9196 (tm-30) cc_final: 0.8705 (tm-30) REVERT: L 67 PHE cc_start: 0.8877 (t80) cc_final: 0.8435 (t80) REVERT: L 105 LEU cc_start: 0.9566 (mt) cc_final: 0.9221 (mt) REVERT: L 117 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7809 (mm-30) REVERT: L 177 TRP cc_start: 0.9314 (m100) cc_final: 0.8884 (m100) REVERT: L 201 GLN cc_start: 0.8865 (mp10) cc_final: 0.8335 (mp10) REVERT: L 225 LEU cc_start: 0.9466 (tp) cc_final: 0.9124 (tt) REVERT: L 245 GLU cc_start: 0.8261 (mp0) cc_final: 0.7861 (mp0) REVERT: L 268 LEU cc_start: 0.9288 (pt) cc_final: 0.9079 (pt) REVERT: L 281 LYS cc_start: 0.8331 (tttt) cc_final: 0.7837 (tttt) REVERT: L 301 LEU cc_start: 0.9093 (tt) cc_final: 0.8871 (tt) REVERT: L 305 GLN cc_start: 0.9267 (tm-30) cc_final: 0.7928 (tm-30) REVERT: L 491 LEU cc_start: 0.9070 (pt) cc_final: 0.8719 (pt) REVERT: L 498 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8523 (mm-30) REVERT: L 501 ARG cc_start: 0.8701 (tmm-80) cc_final: 0.8368 (tmm-80) REVERT: L 504 ARG cc_start: 0.8949 (ttm170) cc_final: 0.8222 (ttt180) REVERT: L 538 PHE cc_start: 0.9044 (t80) cc_final: 0.8749 (t80) REVERT: L 599 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8641 (tm-30) outliers start: 8 outliers final: 0 residues processed: 2099 average time/residue: 0.2371 time to fit residues: 815.9938 Evaluate side-chains 1955 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1955 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 174 optimal weight: 10.0000 chunk 462 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 330 optimal weight: 10.0000 chunk 25 optimal weight: 0.1980 chunk 320 optimal weight: 20.0000 chunk 224 optimal weight: 0.9980 chunk 341 optimal weight: 10.0000 chunk 273 optimal weight: 7.9990 chunk 259 optimal weight: 8.9990 chunk 336 optimal weight: 0.8980 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 265 HIS A 305 GLN A 309 GLN A 632 GLN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN C 632 GLN D 137 GLN D 632 GLN G 137 GLN ** G 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 632 GLN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 GLN ** J 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 632 GLN E 137 GLN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS E 632 GLN ** H 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 HIS H 632 GLN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 632 GLN F 137 GLN F 265 HIS F 305 GLN F 632 GLN I 305 GLN I 632 GLN ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN L 632 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.160259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.134618 restraints weight = 67393.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.138922 restraints weight = 36418.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.141821 restraints weight = 23165.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.143753 restraints weight = 16487.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.145121 restraints weight = 12880.396| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39672 Z= 0.135 Angle : 0.701 9.016 53820 Z= 0.344 Chirality : 0.043 0.169 6168 Planarity : 0.005 0.089 6888 Dihedral : 5.144 31.809 5424 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.22 % Allowed : 0.63 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.12), residues: 4740 helix: -0.95 (0.10), residues: 2400 sheet: -1.73 (0.40), residues: 120 loop : -1.47 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 617 TYR 0.017 0.002 TYR A 165 PHE 0.022 0.002 PHE B 538 TRP 0.058 0.002 TRP F 118 HIS 0.004 0.001 HIS B 493 Details of bonding type rmsd covalent geometry : bond 0.00315 (39672) covalent geometry : angle 0.70081 (53820) hydrogen bonds : bond 0.03419 ( 1410) hydrogen bonds : angle 4.52041 ( 3909) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2108 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 2099 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8175 (tm-30) REVERT: A 83 MET cc_start: 0.9198 (mmp) cc_final: 0.8796 (mmp) REVERT: A 85 GLN cc_start: 0.8636 (tp40) cc_final: 0.8408 (tp40) REVERT: A 94 ARG cc_start: 0.8586 (mtt-85) cc_final: 0.8359 (ttm-80) REVERT: A 105 LEU cc_start: 0.9623 (mt) cc_final: 0.9314 (mt) REVERT: A 163 TYR cc_start: 0.8380 (m-80) cc_final: 0.7782 (m-80) REVERT: A 177 TRP cc_start: 0.9166 (m100) cc_final: 0.8749 (t-100) REVERT: A 187 LEU cc_start: 0.9148 (mm) cc_final: 0.8815 (mm) REVERT: A 195 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8068 (mt-10) REVERT: A 225 LEU cc_start: 0.9295 (tt) cc_final: 0.8937 (tt) REVERT: A 244 PRO cc_start: 0.9410 (Cg_exo) cc_final: 0.8637 (Cg_endo) REVERT: A 245 GLU cc_start: 0.8342 (mp0) cc_final: 0.7888 (mp0) REVERT: A 255 GLU cc_start: 0.9228 (pp20) cc_final: 0.8802 (pp20) REVERT: A 267 ARG cc_start: 0.8770 (tmm-80) cc_final: 0.8555 (tmm-80) REVERT: A 281 LYS cc_start: 0.8587 (tttt) cc_final: 0.8137 (tttt) REVERT: A 295 ILE cc_start: 0.9589 (tt) cc_final: 0.9338 (tt) REVERT: A 297 ARG cc_start: 0.9127 (ttt-90) cc_final: 0.8908 (ttt-90) REVERT: A 306 LYS cc_start: 0.8942 (tttt) cc_final: 0.8608 (ttmm) REVERT: A 314 PHE cc_start: 0.8908 (t80) cc_final: 0.8590 (t80) REVERT: A 491 LEU cc_start: 0.8881 (pt) cc_final: 0.8651 (pt) REVERT: A 523 SER cc_start: 0.8489 (p) cc_final: 0.8099 (p) REVERT: A 524 PHE cc_start: 0.8883 (m-80) cc_final: 0.8650 (m-80) REVERT: A 536 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 574 GLU cc_start: 0.9407 (tm-30) cc_final: 0.8975 (tm-30) REVERT: A 578 LEU cc_start: 0.9116 (mt) cc_final: 0.8776 (mt) REVERT: A 599 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8542 (tm-30) REVERT: A 610 TYR cc_start: 0.8854 (t80) cc_final: 0.8123 (t80) REVERT: A 625 ARG cc_start: 0.6869 (tmt170) cc_final: 0.5270 (ttt180) REVERT: B 91 CYS cc_start: 0.7807 (m) cc_final: 0.7271 (m) REVERT: B 105 LEU cc_start: 0.9436 (mt) cc_final: 0.9066 (mt) REVERT: B 151 GLN cc_start: 0.8846 (tt0) cc_final: 0.8521 (tt0) REVERT: B 195 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8072 (mt-10) REVERT: B 264 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7962 (tttp) REVERT: B 277 TYR cc_start: 0.8603 (m-80) cc_final: 0.7813 (m-80) REVERT: B 281 LYS cc_start: 0.8667 (tttt) cc_final: 0.8412 (tttt) REVERT: B 296 LEU cc_start: 0.9553 (tp) cc_final: 0.9305 (tp) REVERT: B 317 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8383 (mtmt) REVERT: B 498 GLU cc_start: 0.8565 (mm-30) cc_final: 0.7801 (mm-30) REVERT: B 510 ARG cc_start: 0.8270 (mtp85) cc_final: 0.8007 (mtp85) REVERT: B 536 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8017 (tm-30) REVERT: B 538 PHE cc_start: 0.9162 (t80) cc_final: 0.8675 (t80) REVERT: B 599 GLN cc_start: 0.9171 (tm-30) cc_final: 0.8677 (tm-30) REVERT: C 63 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8351 (tm-30) REVERT: C 81 GLN cc_start: 0.8697 (tp-100) cc_final: 0.8466 (tp-100) REVERT: C 83 MET cc_start: 0.9137 (tpp) cc_final: 0.7419 (tpp) REVERT: C 91 CYS cc_start: 0.8274 (m) cc_final: 0.8000 (m) REVERT: C 105 LEU cc_start: 0.9546 (mt) cc_final: 0.9206 (mt) REVERT: C 137 GLN cc_start: 0.3228 (OUTLIER) cc_final: 0.2817 (pm20) REVERT: C 177 TRP cc_start: 0.9154 (m100) cc_final: 0.8900 (m100) REVERT: C 195 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7959 (mt-10) REVERT: C 201 GLN cc_start: 0.8924 (mp10) cc_final: 0.8424 (mp10) REVERT: C 225 LEU cc_start: 0.9426 (tp) cc_final: 0.9038 (tt) REVERT: C 245 GLU cc_start: 0.8223 (mp0) cc_final: 0.7823 (mp0) REVERT: C 301 LEU cc_start: 0.9125 (tt) cc_final: 0.8845 (tt) REVERT: C 309 GLN cc_start: 0.9177 (mt0) cc_final: 0.8643 (mt0) REVERT: C 491 LEU cc_start: 0.9186 (pt) cc_final: 0.8875 (pt) REVERT: C 498 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8343 (mm-30) REVERT: C 501 ARG cc_start: 0.8745 (tmm-80) cc_final: 0.8323 (tmm-80) REVERT: C 504 ARG cc_start: 0.8947 (ttm170) cc_final: 0.8266 (ttt180) REVERT: C 536 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7820 (tm-30) REVERT: C 574 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8650 (tm-30) REVERT: C 597 TYR cc_start: 0.9279 (m-80) cc_final: 0.8983 (m-80) REVERT: C 599 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8675 (tm-30) REVERT: D 63 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8246 (tm-30) REVERT: D 85 GLN cc_start: 0.8801 (tp40) cc_final: 0.8345 (tp40) REVERT: D 105 LEU cc_start: 0.9547 (mt) cc_final: 0.9290 (mt) REVERT: D 177 TRP cc_start: 0.9101 (m100) cc_final: 0.8727 (t-100) REVERT: D 187 LEU cc_start: 0.9185 (mm) cc_final: 0.8834 (mm) REVERT: D 195 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7747 (mt-10) REVERT: D 201 GLN cc_start: 0.8322 (mt0) cc_final: 0.7934 (mm110) REVERT: D 225 LEU cc_start: 0.9276 (tt) cc_final: 0.8987 (tt) REVERT: D 244 PRO cc_start: 0.9436 (Cg_exo) cc_final: 0.8538 (Cg_endo) REVERT: D 245 GLU cc_start: 0.8343 (mp0) cc_final: 0.7849 (mp0) REVERT: D 281 LYS cc_start: 0.8435 (tttt) cc_final: 0.8096 (tttt) REVERT: D 491 LEU cc_start: 0.8981 (pt) cc_final: 0.8768 (pt) REVERT: D 523 SER cc_start: 0.8644 (p) cc_final: 0.8134 (p) REVERT: D 536 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7564 (tm-30) REVERT: D 578 LEU cc_start: 0.9120 (mt) cc_final: 0.8850 (mt) REVERT: D 595 GLU cc_start: 0.7555 (pt0) cc_final: 0.7351 (pt0) REVERT: D 599 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8524 (tm-30) REVERT: D 610 TYR cc_start: 0.8715 (t80) cc_final: 0.8022 (t80) REVERT: D 625 ARG cc_start: 0.6334 (tmt170) cc_final: 0.4861 (ttt180) REVERT: G 83 MET cc_start: 0.9028 (tpp) cc_final: 0.8652 (tpp) REVERT: G 91 CYS cc_start: 0.7597 (m) cc_final: 0.6858 (m) REVERT: G 105 LEU cc_start: 0.9472 (mt) cc_final: 0.9144 (mt) REVERT: G 195 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8045 (mt-10) REVERT: G 209 ARG cc_start: 0.8372 (tpt90) cc_final: 0.7952 (tpt90) REVERT: G 264 LYS cc_start: 0.8291 (mmtt) cc_final: 0.7958 (tttp) REVERT: G 273 GLU cc_start: 0.9006 (tt0) cc_final: 0.8549 (tt0) REVERT: G 277 TYR cc_start: 0.8576 (m-80) cc_final: 0.7713 (m-80) REVERT: G 281 LYS cc_start: 0.8641 (tttt) cc_final: 0.8398 (tttt) REVERT: G 317 LYS cc_start: 0.8717 (mtmm) cc_final: 0.8464 (mtmt) REVERT: G 498 GLU cc_start: 0.8570 (mm-30) cc_final: 0.7863 (mm-30) REVERT: G 510 ARG cc_start: 0.8319 (mtp85) cc_final: 0.8050 (mtp85) REVERT: G 528 PHE cc_start: 0.8570 (t80) cc_final: 0.7936 (t80) REVERT: G 536 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8057 (tm-30) REVERT: G 538 PHE cc_start: 0.9286 (t80) cc_final: 0.8808 (t80) REVERT: G 546 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8202 (tm-30) REVERT: G 550 THR cc_start: 0.8737 (p) cc_final: 0.7855 (p) REVERT: G 599 GLN cc_start: 0.9193 (tm-30) cc_final: 0.8699 (tm-30) REVERT: J 63 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8313 (tm-30) REVERT: J 81 GLN cc_start: 0.8734 (tp-100) cc_final: 0.8445 (tp-100) REVERT: J 85 GLN cc_start: 0.8981 (tp-100) cc_final: 0.8582 (tp-100) REVERT: J 91 CYS cc_start: 0.8301 (m) cc_final: 0.7988 (m) REVERT: J 105 LEU cc_start: 0.9530 (mt) cc_final: 0.9199 (mt) REVERT: J 145 SER cc_start: 0.8922 (t) cc_final: 0.8465 (p) REVERT: J 177 TRP cc_start: 0.9168 (m100) cc_final: 0.8917 (m100) REVERT: J 195 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7978 (mt-10) REVERT: J 201 GLN cc_start: 0.8875 (mp10) cc_final: 0.8284 (mp10) REVERT: J 225 LEU cc_start: 0.9461 (tp) cc_final: 0.9097 (tt) REVERT: J 245 GLU cc_start: 0.8238 (mp0) cc_final: 0.7844 (mp0) REVERT: J 297 ARG cc_start: 0.9248 (ttp80) cc_final: 0.8806 (ttt-90) REVERT: J 301 LEU cc_start: 0.9161 (tt) cc_final: 0.8889 (tt) REVERT: J 309 GLN cc_start: 0.9205 (mt0) cc_final: 0.8645 (mt0) REVERT: J 498 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8366 (mm-30) REVERT: J 501 ARG cc_start: 0.8795 (tmm-80) cc_final: 0.8389 (tmm-80) REVERT: J 504 ARG cc_start: 0.8963 (ttm170) cc_final: 0.8285 (ttt180) REVERT: J 536 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7889 (tm-30) REVERT: J 599 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8665 (tm-30) REVERT: E 85 GLN cc_start: 0.8818 (tp40) cc_final: 0.8373 (tp40) REVERT: E 105 LEU cc_start: 0.9524 (mt) cc_final: 0.9291 (mt) REVERT: E 113 ARG cc_start: 0.8785 (tpt170) cc_final: 0.8273 (tpp-160) REVERT: E 177 TRP cc_start: 0.9098 (m100) cc_final: 0.8685 (t-100) REVERT: E 187 LEU cc_start: 0.9170 (mm) cc_final: 0.8826 (mm) REVERT: E 195 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7914 (mt-10) REVERT: E 225 LEU cc_start: 0.9294 (tt) cc_final: 0.8993 (tt) REVERT: E 244 PRO cc_start: 0.9414 (Cg_exo) cc_final: 0.8556 (Cg_endo) REVERT: E 245 GLU cc_start: 0.8375 (mp0) cc_final: 0.7884 (mp0) REVERT: E 281 LYS cc_start: 0.8310 (tttt) cc_final: 0.8035 (tttt) REVERT: E 295 ILE cc_start: 0.9563 (tt) cc_final: 0.9360 (tt) REVERT: E 297 ARG cc_start: 0.9120 (ttt-90) cc_final: 0.8846 (ttt-90) REVERT: E 306 LYS cc_start: 0.9216 (ttmm) cc_final: 0.8737 (tttt) REVERT: E 491 LEU cc_start: 0.8958 (pt) cc_final: 0.8757 (pt) REVERT: E 578 LEU cc_start: 0.9127 (mt) cc_final: 0.8861 (mt) REVERT: E 599 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8557 (tm-30) REVERT: E 610 TYR cc_start: 0.8653 (t80) cc_final: 0.7932 (t80) REVERT: H 83 MET cc_start: 0.8965 (tpp) cc_final: 0.8704 (tpp) REVERT: H 91 CYS cc_start: 0.7610 (m) cc_final: 0.6807 (m) REVERT: H 105 LEU cc_start: 0.9439 (mt) cc_final: 0.9095 (mt) REVERT: H 151 GLN cc_start: 0.8928 (tt0) cc_final: 0.8608 (tt0) REVERT: H 195 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8047 (mt-10) REVERT: H 264 LYS cc_start: 0.8286 (mmtt) cc_final: 0.7960 (tttp) REVERT: H 273 GLU cc_start: 0.9043 (tt0) cc_final: 0.8582 (tt0) REVERT: H 277 TYR cc_start: 0.8574 (m-80) cc_final: 0.7654 (m-80) REVERT: H 281 LYS cc_start: 0.8640 (tttt) cc_final: 0.8387 (tttt) REVERT: H 295 ILE cc_start: 0.9636 (tt) cc_final: 0.9407 (tt) REVERT: H 296 LEU cc_start: 0.9655 (tp) cc_final: 0.9419 (tp) REVERT: H 309 GLN cc_start: 0.9408 (pt0) cc_final: 0.9183 (pt0) REVERT: H 317 LYS cc_start: 0.8668 (mtmm) cc_final: 0.8376 (mtmt) REVERT: H 498 GLU cc_start: 0.8589 (mm-30) cc_final: 0.7876 (mm-30) REVERT: H 510 ARG cc_start: 0.8163 (mtp85) cc_final: 0.7924 (mtp85) REVERT: H 528 PHE cc_start: 0.8613 (t80) cc_final: 0.7998 (t80) REVERT: H 536 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7911 (tm-30) REVERT: H 599 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8699 (tm-30) REVERT: K 63 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8357 (tm-30) REVERT: K 91 CYS cc_start: 0.8061 (m) cc_final: 0.7791 (m) REVERT: K 105 LEU cc_start: 0.9522 (mt) cc_final: 0.9186 (mt) REVERT: K 177 TRP cc_start: 0.9168 (m100) cc_final: 0.8893 (m100) REVERT: K 201 GLN cc_start: 0.8911 (mp10) cc_final: 0.8400 (mp10) REVERT: K 225 LEU cc_start: 0.9478 (tp) cc_final: 0.9135 (tt) REVERT: K 245 GLU cc_start: 0.8262 (mp0) cc_final: 0.7869 (mp0) REVERT: K 295 ILE cc_start: 0.9579 (tt) cc_final: 0.9366 (tt) REVERT: K 297 ARG cc_start: 0.9274 (ttt180) cc_final: 0.8944 (ttt180) REVERT: K 301 LEU cc_start: 0.9171 (tt) cc_final: 0.8854 (tt) REVERT: K 305 GLN cc_start: 0.9315 (tm-30) cc_final: 0.8323 (tm-30) REVERT: K 498 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8422 (mm-30) REVERT: K 536 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7787 (tm-30) REVERT: K 599 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8664 (tm-30) REVERT: F 83 MET cc_start: 0.9139 (tpt) cc_final: 0.8142 (tpp) REVERT: F 85 GLN cc_start: 0.8996 (tp40) cc_final: 0.8545 (tp40) REVERT: F 105 LEU cc_start: 0.9630 (mt) cc_final: 0.9325 (mt) REVERT: F 137 GLN cc_start: 0.3819 (OUTLIER) cc_final: 0.3386 (pm20) REVERT: F 177 TRP cc_start: 0.9084 (m100) cc_final: 0.8743 (t-100) REVERT: F 187 LEU cc_start: 0.9170 (mm) cc_final: 0.8860 (mm) REVERT: F 195 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7764 (mt-10) REVERT: F 225 LEU cc_start: 0.9350 (tt) cc_final: 0.8895 (tt) REVERT: F 244 PRO cc_start: 0.9428 (Cg_exo) cc_final: 0.8570 (Cg_endo) REVERT: F 245 GLU cc_start: 0.8375 (mp0) cc_final: 0.7873 (mp0) REVERT: F 281 LYS cc_start: 0.8469 (tttt) cc_final: 0.8102 (tttt) REVERT: F 295 ILE cc_start: 0.9562 (tt) cc_final: 0.9343 (tt) REVERT: F 306 LYS cc_start: 0.8937 (ttpt) cc_final: 0.8723 (ttpt) REVERT: F 491 LEU cc_start: 0.9064 (pt) cc_final: 0.8863 (pt) REVERT: F 536 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7720 (tm-30) REVERT: F 546 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8335 (tm-30) REVERT: F 578 LEU cc_start: 0.9206 (mt) cc_final: 0.8841 (mt) REVERT: F 599 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8530 (tm-30) REVERT: F 610 TYR cc_start: 0.8908 (t80) cc_final: 0.8342 (t80) REVERT: I 83 MET cc_start: 0.9000 (tpp) cc_final: 0.8653 (tpp) REVERT: I 91 CYS cc_start: 0.7662 (m) cc_final: 0.7098 (m) REVERT: I 105 LEU cc_start: 0.9478 (mt) cc_final: 0.9158 (mt) REVERT: I 195 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8064 (mt-10) REVERT: I 264 LYS cc_start: 0.8311 (mmtt) cc_final: 0.8029 (mtpp) REVERT: I 273 GLU cc_start: 0.8995 (tt0) cc_final: 0.8555 (tt0) REVERT: I 277 TYR cc_start: 0.8537 (m-80) cc_final: 0.7729 (m-80) REVERT: I 281 LYS cc_start: 0.8634 (tttt) cc_final: 0.8381 (tttt) REVERT: I 296 LEU cc_start: 0.9590 (tp) cc_final: 0.9360 (tp) REVERT: I 309 GLN cc_start: 0.9374 (tt0) cc_final: 0.8477 (pt0) REVERT: I 317 LYS cc_start: 0.8599 (mtmm) cc_final: 0.8322 (mtmt) REVERT: I 498 GLU cc_start: 0.8572 (mm-30) cc_final: 0.7879 (mm-30) REVERT: I 510 ARG cc_start: 0.8243 (mtp85) cc_final: 0.7991 (mtp85) REVERT: I 536 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7903 (tm-30) REVERT: I 599 GLN cc_start: 0.9175 (tm-30) cc_final: 0.8678 (tm-30) REVERT: L 105 LEU cc_start: 0.9569 (mt) cc_final: 0.9230 (mt) REVERT: L 137 GLN cc_start: 0.3235 (OUTLIER) cc_final: 0.2820 (pm20) REVERT: L 177 TRP cc_start: 0.9300 (m100) cc_final: 0.8866 (m100) REVERT: L 201 GLN cc_start: 0.8869 (mp10) cc_final: 0.8223 (mp10) REVERT: L 225 LEU cc_start: 0.9467 (tp) cc_final: 0.9051 (tt) REVERT: L 245 GLU cc_start: 0.8207 (mp0) cc_final: 0.7811 (mp0) REVERT: L 301 LEU cc_start: 0.9110 (tt) cc_final: 0.8873 (tt) REVERT: L 309 GLN cc_start: 0.9161 (mt0) cc_final: 0.8563 (mt0) REVERT: L 491 LEU cc_start: 0.9048 (pt) cc_final: 0.8632 (pt) REVERT: L 498 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8475 (mm-30) REVERT: L 536 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7826 (tm-30) REVERT: L 599 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8653 (tm-30) outliers start: 9 outliers final: 0 residues processed: 2105 average time/residue: 0.2302 time to fit residues: 798.7782 Evaluate side-chains 1945 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1942 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 164 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 468 optimal weight: 10.0000 chunk 428 optimal weight: 4.9990 chunk 234 optimal weight: 10.0000 chunk 196 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 258 optimal weight: 7.9990 chunk 236 optimal weight: 7.9990 chunk 292 optimal weight: 0.4980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 265 HIS A 632 GLN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN C 632 GLN D 137 GLN D 632 GLN ** G 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 632 GLN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 GLN ** J 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 632 GLN E 137 GLN E 265 HIS E 632 GLN ** H 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 632 GLN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN K 632 GLN F 137 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 HIS F 545 ASN F 632 GLN I 632 GLN ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN L 632 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.159988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.134516 restraints weight = 68079.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.138829 restraints weight = 36555.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.141742 restraints weight = 23054.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.143679 restraints weight = 16362.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.144994 restraints weight = 12734.416| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39672 Z= 0.139 Angle : 0.701 9.406 53820 Z= 0.345 Chirality : 0.043 0.150 6168 Planarity : 0.005 0.083 6888 Dihedral : 5.138 27.069 5424 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.19 % Allowed : 0.75 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.12), residues: 4740 helix: -0.84 (0.10), residues: 2436 sheet: -1.64 (0.41), residues: 120 loop : -1.50 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 617 TYR 0.021 0.002 TYR C 138 PHE 0.029 0.002 PHE K 524 TRP 0.053 0.002 TRP F 118 HIS 0.008 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00323 (39672) covalent geometry : angle 0.70096 (53820) hydrogen bonds : bond 0.03426 ( 1410) hydrogen bonds : angle 4.48104 ( 3909) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12197.72 seconds wall clock time: 209 minutes 22.87 seconds (12562.87 seconds total)