Starting phenix.real_space_refine on Tue Jul 7 06:41:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p4k_71272/07_2026/9p4k_71272.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p4k_71272/07_2026/9p4k_71272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p4k_71272/07_2026/9p4k_71272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p4k_71272/07_2026/9p4k_71272.map" model { file = "/net/cci-nas-00/data/ceres_data/9p4k_71272/07_2026/9p4k_71272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p4k_71272/07_2026/9p4k_71272.cif" } resolution = 3.07 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= 0.002 sd= 0.030 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: 5 Type Number sf(0) Gaussians P 428 5.49 5 S 80 5.16 5 C 27086 2.51 5 N 7516 2.21 5 O 9437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 44547 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5933 Classifications: {'peptide': 732} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 23, 'TRANS': 708} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 5954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5954 Classifications: {'peptide': 732} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 23, 'TRANS': 708} Chain breaks: 1 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'ARG:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 5927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5927 Classifications: {'peptide': 732} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 23, 'TRANS': 708} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 5, 'ASP:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "D" Number of atoms: 5960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5960 Classifications: {'peptide': 732} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 23, 'TRANS': 708} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 1, 'ARG:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2965 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 355} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2926 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 355} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "G" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2952 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 355} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 2928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2928 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 355} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "O" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 800 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 2 Chain: "P" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 882 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain breaks: 2 Chain: "I" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1389 Classifications: {'RNA': 65} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 7, 'rna3p_pur': 35, 'rna3p_pyr': 22} Link IDs: {'rna2p': 8, 'rna3p': 56} Chain: "M" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 882 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain breaks: 2 Chain: "J" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1389 Classifications: {'RNA': 65} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 6, 'rna3p_pur': 34, 'rna3p_pyr': 23} Link IDs: {'rna2p': 8, 'rna3p': 56} Chain: "K" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1389 Classifications: {'RNA': 65} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 7, 'rna3p_pur': 34, 'rna3p_pyr': 22} Link IDs: {'rna2p': 9, 'rna3p': 55} Chain: "L" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1389 Classifications: {'RNA': 65} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 33, 'rna3p_pyr': 24} Link IDs: {'rna2p': 8, 'rna3p': 56} Chain: "N" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 882 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain breaks: 2 Time building chain proxies: 8.60, per 1000 atoms: 0.19 Number of scatterers: 44547 At special positions: 0 Unit cell: (227.409, 133.133, 184.093, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 428 15.00 O 9437 8.00 N 7516 7.00 C 27086 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: 3.35 Conformation dependent library (CDL) restraints added in 1.3 seconds 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8448 Finding SS restraints... Secondary structure from input PDB file: 207 helices and 40 sheets defined 54.7% alpha, 10.2% beta 89 base pairs and 209 stacking pairs defined. Time for finding SS restraints: 5.95 Creating SS restraints... Processing helix chain 'A' and resid 32 through 51 removed outlier: 3.671A pdb=" N LYS A 36 " --> pdb=" O ASN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 Processing helix chain 'A' and resid 90 through 100 Processing helix chain 'A' and resid 102 through 107 removed outlier: 4.028A pdb=" N LYS A 107 " --> pdb=" O SER A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 118 Processing helix chain 'A' and resid 143 through 154 removed outlier: 4.095A pdb=" N ARG A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 179 Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.901A pdb=" N ASP A 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 224 through 237 Processing helix chain 'A' and resid 259 through 273 Processing helix chain 'A' and resid 292 through 310 removed outlier: 3.903A pdb=" N PHE A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 347 removed outlier: 3.566A pdb=" N LEU A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 381 Processing helix chain 'A' and resid 382 through 388 removed outlier: 3.737A pdb=" N LEU A 388 " --> pdb=" O ASN A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 407 removed outlier: 3.581A pdb=" N LEU A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 415 removed outlier: 3.799A pdb=" N LEU A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 427 through 435 Processing helix chain 'A' and resid 436 through 439 Processing helix chain 'A' and resid 467 through 478 Processing helix chain 'A' and resid 490 through 501 Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.877A pdb=" N LEU A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 548 Processing helix chain 'A' and resid 552 through 566 Processing helix chain 'A' and resid 574 through 586 Processing helix chain 'A' and resid 591 through 599 Processing helix chain 'A' and resid 610 through 636 Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 659 through 667 Processing helix chain 'A' and resid 669 through 682 Processing helix chain 'A' and resid 687 through 691 Processing helix chain 'A' and resid 692 through 695 Processing helix chain 'A' and resid 696 through 713 Processing helix chain 'A' and resid 715 through 727 Processing helix chain 'A' and resid 727 through 744 Processing helix chain 'B' and resid 32 through 51 removed outlier: 3.526A pdb=" N LYS B 36 " --> pdb=" O ASN B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 removed outlier: 3.522A pdb=" N SER B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 100 removed outlier: 3.512A pdb=" N THR B 99 " --> pdb=" O HIS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 removed outlier: 4.206A pdb=" N LYS B 107 " --> pdb=" O SER B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.863A pdb=" N LYS B 117 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 154 Processing helix chain 'B' and resid 169 through 179 Processing helix chain 'B' and resid 188 through 200 Processing helix chain 'B' and resid 206 through 218 removed outlier: 3.856A pdb=" N TYR B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 237 Processing helix chain 'B' and resid 259 through 273 Processing helix chain 'B' and resid 292 through 310 removed outlier: 3.783A pdb=" N PHE B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 346 removed outlier: 3.675A pdb=" N LEU B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 350 removed outlier: 3.864A pdb=" N GLN B 350 " --> pdb=" O GLY B 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 347 through 350' Processing helix chain 'B' and resid 374 through 380 Processing helix chain 'B' and resid 382 through 390 removed outlier: 3.909A pdb=" N PHE B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 407 removed outlier: 3.535A pdb=" N LEU B 403 " --> pdb=" O GLY B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 427 through 435 Processing helix chain 'B' and resid 467 through 478 Processing helix chain 'B' and resid 489 through 501 removed outlier: 4.095A pdb=" N LYS B 493 " --> pdb=" O GLY B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 532 removed outlier: 3.829A pdb=" N LEU B 523 " --> pdb=" O SER B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 548 removed outlier: 3.810A pdb=" N ALA B 546 " --> pdb=" O THR B 542 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 567 Processing helix chain 'B' and resid 574 through 586 Processing helix chain 'B' and resid 591 through 599 Processing helix chain 'B' and resid 610 through 636 Processing helix chain 'B' and resid 640 through 650 Processing helix chain 'B' and resid 659 through 667 Processing helix chain 'B' and resid 669 through 683 Processing helix chain 'B' and resid 687 through 691 Processing helix chain 'B' and resid 696 through 713 Processing helix chain 'B' and resid 715 through 727 Processing helix chain 'B' and resid 727 through 744 removed outlier: 3.561A pdb=" N GLU B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 51 Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 90 through 100 Processing helix chain 'C' and resid 110 through 118 removed outlier: 4.334A pdb=" N ASN C 118 " --> pdb=" O ILE C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 154 Processing helix chain 'C' and resid 169 through 179 Processing helix chain 'C' and resid 188 through 199 removed outlier: 3.771A pdb=" N LEU C 192 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS C 199 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 215 Processing helix chain 'C' and resid 224 through 237 Processing helix chain 'C' and resid 259 through 273 Processing helix chain 'C' and resid 292 through 310 removed outlier: 3.962A pdb=" N PHE C 310 " --> pdb=" O ILE C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 346 removed outlier: 3.691A pdb=" N LEU C 339 " --> pdb=" O SER C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 350 removed outlier: 3.701A pdb=" N GLN C 350 " --> pdb=" O GLY C 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 347 through 350' Processing helix chain 'C' and resid 374 through 380 Processing helix chain 'C' and resid 382 through 390 removed outlier: 3.746A pdb=" N PHE C 389 " --> pdb=" O GLU C 385 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE C 390 " --> pdb=" O ALA C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 407 removed outlier: 3.592A pdb=" N LEU C 403 " --> pdb=" O GLY C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 415 removed outlier: 3.840A pdb=" N LEU C 414 " --> pdb=" O SER C 410 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR C 415 " --> pdb=" O LEU C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 421 removed outlier: 3.609A pdb=" N LEU C 420 " --> pdb=" O ALA C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 Processing helix chain 'C' and resid 467 through 478 Processing helix chain 'C' and resid 489 through 501 Processing helix chain 'C' and resid 519 through 532 removed outlier: 3.821A pdb=" N LEU C 523 " --> pdb=" O SER C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 548 Processing helix chain 'C' and resid 549 through 551 No H-bonds generated for 'chain 'C' and resid 549 through 551' Processing helix chain 'C' and resid 552 through 567 Processing helix chain 'C' and resid 574 through 585 removed outlier: 4.228A pdb=" N PHE C 578 " --> pdb=" O ASN C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 599 removed outlier: 3.666A pdb=" N LEU C 595 " --> pdb=" O GLN C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 636 removed outlier: 3.584A pdb=" N PHE C 636 " --> pdb=" O VAL C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 650 removed outlier: 4.283A pdb=" N VAL C 643 " --> pdb=" O GLU C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 667 Processing helix chain 'C' and resid 669 through 683 Processing helix chain 'C' and resid 696 through 713 Processing helix chain 'C' and resid 715 through 727 Processing helix chain 'C' and resid 727 through 744 Processing helix chain 'D' and resid 32 through 51 removed outlier: 3.732A pdb=" N LYS D 36 " --> pdb=" O ASN D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 85 removed outlier: 3.663A pdb=" N SER D 85 " --> pdb=" O LYS D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.678A pdb=" N LYS D 107 " --> pdb=" O SER D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 143 through 154 removed outlier: 3.559A pdb=" N ARG D 147 " --> pdb=" O ASP D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 179 Processing helix chain 'D' and resid 188 through 201 removed outlier: 4.347A pdb=" N SER D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 224 through 237 Processing helix chain 'D' and resid 259 through 273 Processing helix chain 'D' and resid 292 through 310 removed outlier: 3.664A pdb=" N PHE D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 347 removed outlier: 3.622A pdb=" N LEU D 339 " --> pdb=" O SER D 335 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY D 347 " --> pdb=" O ILE D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 381 Processing helix chain 'D' and resid 382 through 389 removed outlier: 3.595A pdb=" N LEU D 388 " --> pdb=" O ASN D 384 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE D 389 " --> pdb=" O GLU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 407 removed outlier: 3.679A pdb=" N LEU D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 415 removed outlier: 3.708A pdb=" N LEU D 414 " --> pdb=" O SER D 410 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 421 removed outlier: 3.636A pdb=" N LEU D 420 " --> pdb=" O ALA D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 435 Processing helix chain 'D' and resid 467 through 477 Processing helix chain 'D' and resid 490 through 500 Processing helix chain 'D' and resid 501 through 503 No H-bonds generated for 'chain 'D' and resid 501 through 503' Processing helix chain 'D' and resid 508 through 513 removed outlier: 3.887A pdb=" N LEU D 513 " --> pdb=" O MET D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 532 removed outlier: 3.759A pdb=" N LEU D 523 " --> pdb=" O SER D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 548 Processing helix chain 'D' and resid 552 through 567 Processing helix chain 'D' and resid 574 through 586 Processing helix chain 'D' and resid 591 through 599 Processing helix chain 'D' and resid 610 through 636 removed outlier: 3.628A pdb=" N PHE D 636 " --> pdb=" O VAL D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 651 Processing helix chain 'D' and resid 659 through 667 Processing helix chain 'D' and resid 669 through 682 Processing helix chain 'D' and resid 684 through 688 removed outlier: 3.540A pdb=" N GLU D 688 " --> pdb=" O PHE D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 713 Processing helix chain 'D' and resid 715 through 727 Processing helix chain 'D' and resid 727 through 744 removed outlier: 3.648A pdb=" N GLU D 744 " --> pdb=" O SER D 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 17 Processing helix chain 'E' and resid 24 through 29 Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 58 through 71 removed outlier: 3.581A pdb=" N HIS E 62 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 95 Processing helix chain 'E' and resid 96 through 100 removed outlier: 3.916A pdb=" N TYR E 99 " --> pdb=" O PRO E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 125 Processing helix chain 'E' and resid 126 through 128 No H-bonds generated for 'chain 'E' and resid 126 through 128' Processing helix chain 'E' and resid 140 through 147 removed outlier: 3.768A pdb=" N SER E 147 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 192 removed outlier: 3.581A pdb=" N ASN E 174 " --> pdb=" O PRO E 170 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LYS E 179 " --> pdb=" O ILE E 175 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N MET E 180 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 227 removed outlier: 4.041A pdb=" N ILE E 219 " --> pdb=" O SER E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 238 removed outlier: 3.926A pdb=" N TYR E 238 " --> pdb=" O GLN E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 283 Processing helix chain 'E' and resid 286 through 294 removed outlier: 3.700A pdb=" N ILE E 290 " --> pdb=" O PRO E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 304 Processing helix chain 'E' and resid 312 through 344 removed outlier: 3.764A pdb=" N LEU E 322 " --> pdb=" O TYR E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 372 Processing helix chain 'F' and resid 10 through 17 removed outlier: 3.601A pdb=" N LYS F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 37 through 39 No H-bonds generated for 'chain 'F' and resid 37 through 39' Processing helix chain 'F' and resid 58 through 71 removed outlier: 3.520A pdb=" N HIS F 62 " --> pdb=" O SER F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 95 Processing helix chain 'F' and resid 96 through 100 removed outlier: 3.878A pdb=" N TYR F 99 " --> pdb=" O PRO F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 125 Processing helix chain 'F' and resid 140 through 147 removed outlier: 3.983A pdb=" N SER F 147 " --> pdb=" O ALA F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 177 Processing helix chain 'F' and resid 178 through 190 Processing helix chain 'F' and resid 215 through 227 removed outlier: 3.970A pdb=" N ILE F 219 " --> pdb=" O SER F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 283 Processing helix chain 'F' and resid 287 through 292 removed outlier: 3.837A pdb=" N CYS F 291 " --> pdb=" O TYR F 287 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 287 through 292' Processing helix chain 'F' and resid 302 through 307 removed outlier: 3.920A pdb=" N LYS F 305 " --> pdb=" O LYS F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 344 removed outlier: 4.363A pdb=" N LYS F 316 " --> pdb=" O GLU F 312 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU F 322 " --> pdb=" O TYR F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 372 Processing helix chain 'G' and resid 10 through 17 Processing helix chain 'G' and resid 23 through 29 removed outlier: 4.242A pdb=" N ILE G 27 " --> pdb=" O PHE G 23 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE G 28 " --> pdb=" O LYS G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 58 through 71 removed outlier: 3.755A pdb=" N HIS G 62 " --> pdb=" O SER G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 75 removed outlier: 3.661A pdb=" N ILE G 75 " --> pdb=" O LEU G 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 72 through 75' Processing helix chain 'G' and resid 89 through 95 Processing helix chain 'G' and resid 96 through 100 removed outlier: 3.932A pdb=" N TYR G 99 " --> pdb=" O PRO G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 115 Processing helix chain 'G' and resid 116 through 125 Processing helix chain 'G' and resid 140 through 146 Processing helix chain 'G' and resid 168 through 192 removed outlier: 4.773A pdb=" N LYS G 179 " --> pdb=" O ILE G 175 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N MET G 180 " --> pdb=" O VAL G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 227 removed outlier: 4.041A pdb=" N ILE G 219 " --> pdb=" O SER G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 238 removed outlier: 3.726A pdb=" N TYR G 238 " --> pdb=" O GLN G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 283 Processing helix chain 'G' and resid 286 through 294 removed outlier: 3.778A pdb=" N ILE G 290 " --> pdb=" O PRO G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 303 removed outlier: 3.562A pdb=" N LYS G 302 " --> pdb=" O LEU G 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 344 removed outlier: 3.988A pdb=" N LEU G 322 " --> pdb=" O TYR G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 347 through 372 Processing helix chain 'H' and resid 10 through 17 Processing helix chain 'H' and resid 23 through 29 Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 58 through 71 removed outlier: 3.644A pdb=" N HIS H 62 " --> pdb=" O SER H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 95 Processing helix chain 'H' and resid 96 through 100 removed outlier: 3.994A pdb=" N TYR H 99 " --> pdb=" O PRO H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 125 Processing helix chain 'H' and resid 140 through 147 removed outlier: 3.897A pdb=" N SER H 147 " --> pdb=" O ALA H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 192 removed outlier: 4.762A pdb=" N LYS H 179 " --> pdb=" O ILE H 175 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N MET H 180 " --> pdb=" O VAL H 176 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS H 190 " --> pdb=" O ASP H 186 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS H 191 " --> pdb=" O PHE H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 227 removed outlier: 3.934A pdb=" N ILE H 219 " --> pdb=" O SER H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 238 removed outlier: 3.707A pdb=" N TYR H 238 " --> pdb=" O GLN H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 272 through 283 Processing helix chain 'H' and resid 286 through 294 removed outlier: 3.796A pdb=" N ILE H 290 " --> pdb=" O PRO H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 344 removed outlier: 3.744A pdb=" N LEU H 322 " --> pdb=" O TYR H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 347 through 372 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 19 removed outlier: 7.168A pdb=" N ASP A 15 " --> pdb=" O ASN A 10 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE A 3 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASP A 75 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A 5 " --> pdb=" O THR A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 160 removed outlier: 6.901A pdb=" N ILE A 25 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU A 353 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N CYS A 27 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL A 352 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 422 through 425 removed outlier: 6.456A pdb=" N ILE A 394 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE A 448 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE A 396 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ASP A 450 " --> pdb=" O PHE A 396 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N TYR A 537 " --> pdb=" O PHE A 445 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE A 447 " --> pdb=" O TYR A 537 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N MET A 539 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LYS A 449 " --> pdb=" O MET A 539 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 457 Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 509 Processing sheet with id=AA6, first strand: chain 'A' and resid 568 through 570 Processing sheet with id=AA7, first strand: chain 'B' and resid 14 through 19 removed outlier: 7.014A pdb=" N ASP B 15 " --> pdb=" O ASN B 10 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE B 3 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ASP B 75 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 5 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU B 11 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 11.487A pdb=" N VAL B 67 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 156 through 160 removed outlier: 6.688A pdb=" N VAL B 282 " --> pdb=" O PHE B 330 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N SER B 332 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE B 284 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL B 352 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 422 through 425 removed outlier: 6.075A pdb=" N VAL B 395 " --> pdb=" O TYR B 424 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE B 394 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE B 448 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N PHE B 396 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ASP B 450 " --> pdb=" O PHE B 396 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N TYR B 537 " --> pdb=" O PHE B 445 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE B 447 " --> pdb=" O TYR B 537 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N MET B 539 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LYS B 449 " --> pdb=" O MET B 539 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 455 through 458 removed outlier: 3.871A pdb=" N SER B 458 " --> pdb=" O LYS B 463 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS B 463 " --> pdb=" O SER B 458 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 568 through 570 Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 19 removed outlier: 7.056A pdb=" N ASP C 15 " --> pdb=" O ASN C 10 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE C 3 " --> pdb=" O ASP C 75 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ASP C 75 " --> pdb=" O ILE C 3 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 156 through 160 removed outlier: 6.746A pdb=" N VAL C 282 " --> pdb=" O PHE C 330 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N SER C 332 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE C 284 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL C 352 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 422 through 425 removed outlier: 6.507A pdb=" N ILE C 394 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE C 448 " --> pdb=" O ILE C 394 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE C 396 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ASP C 450 " --> pdb=" O PHE C 396 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N TYR C 537 " --> pdb=" O PHE C 445 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE C 447 " --> pdb=" O TYR C 537 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N MET C 539 " --> pdb=" O ILE C 447 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LYS C 449 " --> pdb=" O MET C 539 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 455 through 458 removed outlier: 4.092A pdb=" N LYS C 463 " --> pdb=" O SER C 458 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 508 through 509 Processing sheet with id=AB8, first strand: chain 'C' and resid 569 through 570 Processing sheet with id=AB9, first strand: chain 'D' and resid 14 through 20 removed outlier: 6.666A pdb=" N ASP D 16 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS D 9 " --> pdb=" O ASP D 16 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE D 18 " --> pdb=" O ARG D 7 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARG D 7 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ARG D 20 " --> pdb=" O SER D 5 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER D 5 " --> pdb=" O ARG D 20 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILE D 3 " --> pdb=" O ASP D 75 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASP D 75 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER D 5 " --> pdb=" O THR D 73 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 156 through 160 removed outlier: 4.405A pdb=" N VAL D 352 " --> pdb=" O ILE D 368 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 422 through 425 removed outlier: 7.810A pdb=" N TYR D 537 " --> pdb=" O PHE D 445 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE D 447 " --> pdb=" O TYR D 537 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N MET D 539 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LYS D 449 " --> pdb=" O MET D 539 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 455 through 457 Processing sheet with id=AC4, first strand: chain 'D' and resid 568 through 570 Processing sheet with id=AC5, first strand: chain 'E' and resid 41 through 45 Processing sheet with id=AC6, first strand: chain 'E' and resid 194 through 198 Processing sheet with id=AC7, first strand: chain 'E' and resid 132 through 134 removed outlier: 3.813A pdb=" N ILE E 134 " --> pdb=" O GLN E 138 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 244 through 247 Processing sheet with id=AC9, first strand: chain 'F' and resid 41 through 45 Processing sheet with id=AD1, first strand: chain 'F' and resid 194 through 198 Processing sheet with id=AD2, first strand: chain 'F' and resid 132 through 134 removed outlier: 6.895A pdb=" N GLN F 138 " --> pdb=" O LEU F 133 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 150 through 151 Processing sheet with id=AD4, first strand: chain 'F' and resid 244 through 247 Processing sheet with id=AD5, first strand: chain 'G' and resid 41 through 46 Processing sheet with id=AD6, first strand: chain 'G' and resid 194 through 198 Processing sheet with id=AD7, first strand: chain 'G' and resid 132 through 134 removed outlier: 6.940A pdb=" N GLN G 138 " --> pdb=" O LEU G 133 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 244 through 247 Processing sheet with id=AD9, first strand: chain 'H' and resid 41 through 45 removed outlier: 3.541A pdb=" N ALA H 53 " --> pdb=" O ARG H 42 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 194 through 198 Processing sheet with id=AE2, first strand: chain 'H' and resid 132 through 134 removed outlier: 7.802A pdb=" N GLN H 138 " --> pdb=" O LEU H 133 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 150 through 151 Processing sheet with id=AE4, first strand: chain 'H' and resid 244 through 247 1781 hydrogen bonds defined for protein. 5145 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 222 hydrogen bonds 420 hydrogen bond angles 0 basepair planarities 89 basepair parallelities 209 stacking parallelities Total time for adding SS restraints: 9.09 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8721 1.33 - 1.45: 12846 1.45 - 1.57: 23812 1.57 - 1.69: 841 1.69 - 1.81: 132 Bond restraints: 46352 Sorted by residual: bond pdb=" C3' DA O 65 " pdb=" C2' DA O 65 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.63e+01 bond pdb=" CA SER E 89 " pdb=" CB SER E 89 " ideal model delta sigma weight residual 1.533 1.467 0.066 1.65e-02 3.67e+03 1.60e+01 bond pdb=" C3' DA O 2 " pdb=" C2' DA O 2 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.40e+01 bond pdb=" CA SER E 73 " pdb=" CB SER E 73 " ideal model delta sigma weight residual 1.530 1.468 0.062 1.69e-02 3.50e+03 1.34e+01 bond pdb=" C3' DG P 66 " pdb=" C2' DG P 66 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.30e+01 ... (remaining 46347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 62970 1.68 - 3.37: 1437 3.37 - 5.05: 147 5.05 - 6.74: 27 6.74 - 8.42: 4 Bond angle restraints: 64585 Sorted by residual: angle pdb=" O4' DT P 74 " pdb=" C4' DT P 74 " pdb=" C3' DT P 74 " ideal model delta sigma weight residual 106.00 102.73 3.27 6.00e-01 2.78e+00 2.98e+01 angle pdb=" O4' DT N 74 " pdb=" C4' DT N 74 " pdb=" C3' DT N 74 " ideal model delta sigma weight residual 106.00 102.89 3.11 6.00e-01 2.78e+00 2.68e+01 angle pdb=" N GLY E 87 " pdb=" CA GLY E 87 " pdb=" C GLY E 87 " ideal model delta sigma weight residual 115.00 107.99 7.01 1.44e+00 4.82e-01 2.37e+01 angle pdb=" O4' DA N 15 " pdb=" C4' DA N 15 " pdb=" C3' DA N 15 " ideal model delta sigma weight residual 106.00 103.11 2.89 6.00e-01 2.78e+00 2.32e+01 angle pdb=" O4' DA P 15 " pdb=" C4' DA P 15 " pdb=" C3' DA P 15 " ideal model delta sigma weight residual 106.00 103.18 2.82 6.00e-01 2.78e+00 2.21e+01 ... (remaining 64580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 26264 35.50 - 71.00: 1415 71.00 - 106.50: 101 106.50 - 141.99: 6 141.99 - 177.49: 10 Dihedral angle restraints: 27796 sinusoidal: 14744 harmonic: 13052 Sorted by residual: dihedral pdb=" O4' U J 45 " pdb=" C1' U J 45 " pdb=" N1 U J 45 " pdb=" C2 U J 45 " ideal model delta sinusoidal sigma weight residual 200.00 44.90 155.10 1 1.50e+01 4.44e-03 8.14e+01 dihedral pdb=" O4' U L 45 " pdb=" C1' U L 45 " pdb=" N1 U L 45 " pdb=" C2 U L 45 " ideal model delta sinusoidal sigma weight residual 200.00 45.29 154.71 1 1.50e+01 4.44e-03 8.12e+01 dihedral pdb=" O4' U K 45 " pdb=" C1' U K 45 " pdb=" N1 U K 45 " pdb=" C2 U K 45 " ideal model delta sinusoidal sigma weight residual 200.00 46.83 153.17 1 1.50e+01 4.44e-03 8.07e+01 ... (remaining 27793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 6380 0.058 - 0.115: 967 0.115 - 0.173: 132 0.173 - 0.230: 10 0.230 - 0.288: 5 Chirality restraints: 7494 Sorted by residual: chirality pdb=" P DA M 2 " pdb=" OP1 DA M 2 " pdb=" OP2 DA M 2 " pdb=" O5' DA M 2 " both_signs ideal model delta sigma weight residual True 2.34 -2.62 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" P DA M 15 " pdb=" OP1 DA M 15 " pdb=" OP2 DA M 15 " pdb=" O5' DA M 15 " both_signs ideal model delta sigma weight residual True 2.34 -2.61 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" P DA M 3 " pdb=" OP1 DA M 3 " pdb=" OP2 DA M 3 " pdb=" O5' DA M 3 " both_signs ideal model delta sigma weight residual True 2.34 -2.59 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 7491 not shown) Planarity restraints: 6606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A I 76 " 0.029 2.00e-02 2.50e+03 2.14e-02 1.26e+01 pdb=" N9 A I 76 " -0.058 2.00e-02 2.50e+03 pdb=" C8 A I 76 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A I 76 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A I 76 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A I 76 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A I 76 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A I 76 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A I 76 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A I 76 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A I 76 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 68 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C ASN E 68 " -0.052 2.00e-02 2.50e+03 pdb=" O ASN E 68 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG E 69 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 332 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C TYR H 332 " 0.051 2.00e-02 2.50e+03 pdb=" O TYR H 332 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU H 333 " -0.017 2.00e-02 2.50e+03 ... (remaining 6603 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 7344 2.77 - 3.30: 41674 3.30 - 3.83: 78264 3.83 - 4.37: 90737 4.37 - 4.90: 149518 Nonbonded interactions: 367537 Sorted by model distance: nonbonded pdb=" O ASP F 142 " pdb=" ND2 ASN F 146 " model vdw 2.232 3.120 nonbonded pdb=" OD2 ASP D 24 " pdb=" OH TYR D 307 " model vdw 2.247 3.040 nonbonded pdb=" O PRO H 76 " pdb=" NH1 ARG H 178 " model vdw 2.257 3.120 nonbonded pdb=" O TYR H 332 " pdb=" OG SER H 335 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASN D 65 " pdb=" OG SER H 79 " model vdw 2.258 3.040 ... (remaining 367532 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 or (resid 109 through 110 and (name N or \ name CA or name C or name O or name CB )) or resid 111 through 115 or (resid 11 \ 6 through 117 and (name N or name CA or name C or name O or name CB )) or resid \ 118 through 196 or (resid 197 and (name N or name CA or name C or name O or name \ CB )) or resid 198 through 225 or (resid 226 and (name N or name CA or name C o \ r name O or name CB )) or resid 227 through 657 or (resid 658 and (name N or nam \ e CA or name C or name O or name CB )) or resid 659 through 750)) selection = (chain 'B' and (resid 2 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 through 109 or (resid 110 and (name N or \ name CA or name C or name O or name CB )) or resid 111 through 115 or (resid 11 \ 6 through 117 and (name N or name CA or name C or name O or name CB )) or resid \ 118 through 164 or (resid 165 through 167 and (name N or name CA or name C or na \ me O or name CB )) or resid 168 through 202 or (resid 203 through 204 and (name \ N or name CA or name C or name O or name CB )) or resid 205 through 225 or (resi \ d 226 and (name N or name CA or name C or name O or name CB )) or resid 227 thro \ ugh 478 or (resid 479 and (name N or name CA or name C or name O or name CB )) o \ r resid 480 through 657 or (resid 658 and (name N or name CA or name C or name O \ or name CB )) or resid 659 through 750)) selection = (chain 'C' and (resid 2 through 108 or (resid 109 through 110 and (name N or nam \ e CA or name C or name O or name CB )) or resid 111 through 164 or (resid 165 th \ rough 167 and (name N or name CA or name C or name O or name CB )) or resid 168 \ through 196 or (resid 197 and (name N or name CA or name C or name O or name CB \ )) or resid 198 through 225 or (resid 226 and (name N or name CA or name C or na \ me O or name CB )) or resid 227 through 459 or (resid 460 and (name N or name CA \ or name C or name O or name CB )) or resid 461 through 478 or (resid 479 and (n \ ame N or name CA or name C or name O or name CB )) or resid 480 through 750)) selection = (chain 'D' and (resid 2 through 108 or (resid 109 through 110 and (name N or nam \ e CA or name C or name O or name CB )) or resid 111 through 115 or (resid 116 th \ rough 117 and (name N or name CA or name C or name O or name CB )) or resid 118 \ through 164 or (resid 165 through 167 and (name N or name CA or name C or name O \ or name CB )) or resid 168 through 196 or (resid 197 and (name N or name CA or \ name C or name O or name CB )) or resid 198 through 202 or (resid 203 through 20 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 205 through \ 459 or (resid 460 and (name N or name CA or name C or name O or name CB )) or re \ sid 461 through 478 or (resid 479 and (name N or name CA or name C or name O or \ name CB )) or resid 480 through 505 or (resid 506 through 507 and (name N or nam \ e CA or name C or name O or name CB )) or resid 508 through 657 or (resid 658 an \ d (name N or name CA or name C or name O or name CB )) or resid 659 through 750) \ ) } ncs_group { reference = (chain 'E' and (resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )) or resid 55 through 154 or (resid 155 through 156 and ( \ name N or name CA or name C or name O or name CB )) or resid 157 through 208 or \ (resid 209 and (name N or name CA or name C or name O or name CB )) or resid 210 \ through 299 or (resid 300 through 302 and (name N or name CA or name C or name \ O or name CB )) or resid 303 through 304 or (resid 305 through 307 and (name N o \ r name CA or name C or name O or name CB )) or resid 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 311 or (res \ id 312 and (name N or name CA or name C or name O or name CB )) or resid 313 thr \ ough 318 or (resid 319 and (name N or name CA or name C or name O or name CB )) \ or resid 320 through 372)) selection = (chain 'F' and (resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )) or resid 55 through 304 or (resid 305 through 307 and ( \ name N or name CA or name C or name O or name CB )) or resid 308 through 318 or \ (resid 319 and (name N or name CA or name C or name O or name CB )) or resid 320 \ through 371 or (resid 372 and (name N or name CA or name C or name O or name CB \ )))) selection = (chain 'G' and (resid 7 through 208 or (resid 209 and (name N or name CA or name \ C or name O or name CB )) or resid 210 through 299 or (resid 300 through 302 an \ d (name N or name CA or name C or name O or name CB )) or resid 303 through 304 \ or (resid 305 through 307 and (name N or name CA or name C or name O or name CB \ )) or resid 308 or (resid 309 and (name N or name CA or name C or name O or name \ CB )) or resid 310 through 311 or (resid 312 and (name N or name CA or name C o \ r name O or name CB )) or resid 313 through 318 or (resid 319 and (name N or nam \ e CA or name C or name O or name CB )) or resid 320 through 372)) selection = (chain 'H' and (resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )) or resid 55 through 208 or (resid 209 and (name N or na \ me CA or name C or name O or name CB )) or resid 210 through 300 or (resid 301 t \ hrough 302 and (name N or name CA or name C or name O or name CB )) or resid 303 \ through 311 or (resid 312 and (name N or name CA or name C or name O or name CB \ )) or resid 313 through 371 or (resid 372 and (name N or name CA or name C or n \ ame O or name CB )))) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'M' and (resid 1 through 27 or resid 61 through 75)) selection = (chain 'N' and (resid 1 through 27 or resid 61 through 75)) selection = chain 'O' selection = (chain 'P' and (resid 1 through 27 or resid 61 through 75)) } 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 individual isotropic 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: 17.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.320 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 41.390 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.170 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:1.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 : 0.003 0.066 46352 Z= 0.243 Angle : 0.559 8.419 64585 Z= 0.412 Chirality : 0.042 0.288 7494 Planarity : 0.003 0.056 6606 Dihedral : 18.036 177.492 19348 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.88 % Favored : 95.05 % Rotamer: Outliers : 0.13 % Allowed : 0.23 % Favored : 99.65 % 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: 1.05 (0.13), residues: 4368 helix: 1.85 (0.12), residues: 2225 sheet: 1.20 (0.23), residues: 562 loop : -1.23 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 178 TYR 0.013 0.001 TYR C 633 PHE 0.022 0.001 PHE B 355 TRP 0.007 0.001 TRP B 169 HIS 0.005 0.001 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.24 (46352) covalent geometry : angle 0.55906 / 0.41 (64585) hydrogen bonds : bond 0.12187 / 7.82 ( 2003) hydrogen bonds : angle 4.94109 / 3.44 ( 5565) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 884 time to evaluate : 1.376 Fit side-chains revert: symmetry clash REVERT: A 37 SER cc_start: 0.8278 (m) cc_final: 0.7722 (p) REVERT: A 67 VAL cc_start: 0.8624 (t) cc_final: 0.8385 (t) REVERT: A 81 LYS cc_start: 0.8650 (ttpt) cc_final: 0.8244 (ttmm) REVERT: A 102 LYS cc_start: 0.8024 (tttt) cc_final: 0.7783 (tttp) REVERT: A 264 THR cc_start: 0.7757 (m) cc_final: 0.7519 (p) REVERT: A 286 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7129 (mm-30) REVERT: A 305 LYS cc_start: 0.8226 (mtpp) cc_final: 0.7938 (mtpp) REVERT: A 309 LYS cc_start: 0.8364 (ttmt) cc_final: 0.8144 (ttmt) REVERT: A 419 SER cc_start: 0.8600 (t) cc_final: 0.8377 (m) REVERT: A 435 ASN cc_start: 0.8259 (t0) cc_final: 0.7895 (t0) REVERT: A 467 ARG cc_start: 0.8320 (mmm-85) cc_final: 0.8012 (mmt-90) REVERT: A 472 LYS cc_start: 0.7948 (ttmm) cc_final: 0.7730 (ttmm) REVERT: A 529 LYS cc_start: 0.8456 (mmmt) cc_final: 0.8162 (mtpp) REVERT: A 534 LEU cc_start: 0.8590 (mm) cc_final: 0.8280 (mt) REVERT: A 548 ILE cc_start: 0.7795 (pt) cc_final: 0.7573 (pt) REVERT: A 629 LYS cc_start: 0.7390 (tmtt) cc_final: 0.7187 (pttt) REVERT: A 725 PHE cc_start: 0.8633 (t80) cc_final: 0.8421 (t80) REVERT: B 21 ASP cc_start: 0.7561 (p0) cc_final: 0.7026 (p0) REVERT: B 25 ILE cc_start: 0.8467 (mm) cc_final: 0.8247 (mm) REVERT: B 94 LYS cc_start: 0.8112 (mmmm) cc_final: 0.7338 (mmmm) REVERT: B 98 ASN cc_start: 0.7145 (m-40) cc_final: 0.6637 (m-40) REVERT: B 100 LEU cc_start: 0.8413 (mp) cc_final: 0.8194 (mt) REVERT: B 123 SER cc_start: 0.8363 (m) cc_final: 0.8022 (p) REVERT: B 277 PHE cc_start: 0.7823 (p90) cc_final: 0.7437 (p90) REVERT: B 286 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7072 (mm-30) REVERT: B 305 LYS cc_start: 0.8290 (mtpt) cc_final: 0.7933 (mtmm) REVERT: B 452 ASP cc_start: 0.7968 (t0) cc_final: 0.7572 (t0) REVERT: B 472 LYS cc_start: 0.7709 (tppt) cc_final: 0.7384 (tppt) REVERT: B 532 ARG cc_start: 0.8137 (tpp80) cc_final: 0.7856 (tpp80) REVERT: B 641 GLU cc_start: 0.7505 (tp30) cc_final: 0.7271 (tp30) REVERT: B 707 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7384 (mm-30) REVERT: B 708 LYS cc_start: 0.8316 (ttmm) cc_final: 0.7978 (ttmm) REVERT: B 713 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7453 (mm-30) REVERT: C 148 SER cc_start: 0.8350 (t) cc_final: 0.8055 (m) REVERT: C 154 TYR cc_start: 0.8074 (m-10) cc_final: 0.7812 (m-10) REVERT: C 331 TYR cc_start: 0.8040 (m-10) cc_final: 0.7449 (m-80) REVERT: C 413 ASN cc_start: 0.8489 (t0) cc_final: 0.8150 (t0) REVERT: C 725 PHE cc_start: 0.8551 (t80) cc_final: 0.8342 (t80) REVERT: C 735 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7557 (mm-30) REVERT: D 9 LYS cc_start: 0.8729 (mtpt) cc_final: 0.8517 (mtmt) REVERT: D 53 LYS cc_start: 0.8422 (mttm) cc_final: 0.8151 (mttt) REVERT: D 94 LYS cc_start: 0.8314 (mmmm) cc_final: 0.7894 (mtmt) REVERT: D 303 LEU cc_start: 0.8542 (tt) cc_final: 0.8234 (tp) REVERT: D 311 LYS cc_start: 0.8054 (tppt) cc_final: 0.7849 (ttmt) REVERT: D 331 TYR cc_start: 0.8073 (m-10) cc_final: 0.7542 (m-80) REVERT: D 348 LYS cc_start: 0.8609 (ptmt) cc_final: 0.8357 (pttm) REVERT: D 472 LYS cc_start: 0.7670 (tppt) cc_final: 0.7469 (tppt) REVERT: D 532 ARG cc_start: 0.8296 (tpp80) cc_final: 0.8044 (mmm-85) REVERT: D 544 GLU cc_start: 0.7783 (mp0) cc_final: 0.7390 (mp0) REVERT: D 551 GLN cc_start: 0.8401 (mp10) cc_final: 0.7905 (mp10) REVERT: D 552 SER cc_start: 0.8226 (t) cc_final: 0.8016 (p) REVERT: D 568 MET cc_start: 0.5107 (mpp) cc_final: 0.4242 (mmt) REVERT: D 665 LYS cc_start: 0.8421 (mmmm) cc_final: 0.8168 (mmmm) REVERT: D 694 THR cc_start: 0.8279 (m) cc_final: 0.8011 (p) REVERT: D 707 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7501 (mm-30) REVERT: D 713 GLU cc_start: 0.7877 (mp0) cc_final: 0.7141 (mp0) REVERT: E 16 LYS cc_start: 0.7648 (mttm) cc_final: 0.7417 (mtpp) REVERT: E 40 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7365 (mt-10) REVERT: E 46 SER cc_start: 0.8488 (m) cc_final: 0.7919 (t) REVERT: E 86 ARG cc_start: 0.8256 (ttt90) cc_final: 0.8035 (ttt90) REVERT: E 116 SER cc_start: 0.8485 (m) cc_final: 0.7949 (p) REVERT: E 253 GLU cc_start: 0.8037 (tt0) cc_final: 0.7727 (tt0) REVERT: E 255 LYS cc_start: 0.8371 (mttm) cc_final: 0.8025 (mttm) REVERT: F 24 LYS cc_start: 0.8226 (ttpp) cc_final: 0.7996 (ttpp) REVERT: F 40 GLU cc_start: 0.7703 (tt0) cc_final: 0.7481 (tt0) REVERT: F 56 ASN cc_start: 0.7819 (t0) cc_final: 0.7565 (m-40) REVERT: F 86 ARG cc_start: 0.8233 (ttm110) cc_final: 0.7936 (ttm110) REVERT: F 137 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7688 (mt-10) REVERT: F 232 ASN cc_start: 0.8239 (m110) cc_final: 0.8015 (m-40) REVERT: F 237 LYS cc_start: 0.8410 (ptpt) cc_final: 0.8079 (ptmt) REVERT: F 255 LYS cc_start: 0.8172 (mtpp) cc_final: 0.7867 (mtpp) REVERT: G 15 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6846 (mm-30) REVERT: G 25 GLU cc_start: 0.7388 (pm20) cc_final: 0.7174 (pm20) REVERT: G 41 VAL cc_start: 0.8403 (t) cc_final: 0.8164 (p) REVERT: G 107 ASP cc_start: 0.7382 (t0) cc_final: 0.6996 (t0) REVERT: G 147 SER cc_start: 0.8717 (m) cc_final: 0.8316 (t) REVERT: G 200 ASP cc_start: 0.7699 (p0) cc_final: 0.7398 (p0) REVERT: G 201 ASP cc_start: 0.7787 (m-30) cc_final: 0.7136 (m-30) REVERT: G 213 LEU cc_start: 0.8057 (mt) cc_final: 0.7841 (mt) REVERT: G 216 ASP cc_start: 0.8055 (m-30) cc_final: 0.7670 (m-30) REVERT: G 220 ASP cc_start: 0.7835 (m-30) cc_final: 0.7484 (m-30) REVERT: G 224 SER cc_start: 0.8238 (t) cc_final: 0.7869 (p) REVERT: G 238 TYR cc_start: 0.7990 (t80) cc_final: 0.7338 (t80) REVERT: H 8 LEU cc_start: 0.8501 (mt) cc_final: 0.8218 (mm) REVERT: H 40 GLU cc_start: 0.7739 (tt0) cc_final: 0.7517 (tt0) REVERT: H 95 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7688 (tm-30) REVERT: H 213 LEU cc_start: 0.8140 (mt) cc_final: 0.7836 (mt) REVERT: H 224 SER cc_start: 0.8546 (t) cc_final: 0.8325 (p) REVERT: H 237 LYS cc_start: 0.8226 (mtmt) cc_final: 0.7996 (mtmt) REVERT: H 238 TYR cc_start: 0.8090 (t80) cc_final: 0.7695 (t80) REVERT: H 243 LYS cc_start: 0.8371 (mtmm) cc_final: 0.8013 (mttm) REVERT: H 255 LYS cc_start: 0.8360 (mmtt) cc_final: 0.8079 (mmtt) REVERT: H 294 TYR cc_start: 0.7647 (m-10) cc_final: 0.7410 (m-10) outliers start: 5 outliers final: 2 residues processed: 885 average time/residue: 0.2759 time to fit residues: 391.4030 Evaluate side-chains 785 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 783 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 21 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 432 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.8980 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 50.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 470 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 ASN B 26 ASN B 65 ASN B 384 ASN C 231 ASN D 88 ASN D 95 HIS ** D 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 ASN E 68 ASN E 113 ASN F 26 ASN F 38 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.174017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.130896 restraints weight = 59224.143| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.99 r_work: 0.3378 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 46352 Z= 0.315 Angle : 0.636 7.918 64585 Z= 0.351 Chirality : 0.047 0.249 7494 Planarity : 0.004 0.050 6606 Dihedral : 21.567 174.544 10624 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.49 % Favored : 94.39 % Rotamer: Outliers : 1.71 % Allowed : 6.18 % Favored : 92.11 % 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: 0.61 (0.13), residues: 4368 helix: 1.37 (0.11), residues: 2252 sheet: 0.92 (0.23), residues: 552 loop : -1.23 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 673 TYR 0.033 0.002 TYR C 457 PHE 0.045 0.003 PHE B 355 TRP 0.010 0.002 TRP C 559 HIS 0.007 0.002 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00739 / 0.32 (46352) covalent geometry : angle 0.63605 / 0.35 (64585) hydrogen bonds : bond 0.04863 / 3.19 ( 2003) hydrogen bonds : angle 4.29758 / 3.00 ( 5565) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 847 time to evaluate : 1.468 Fit side-chains REVERT: A 37 SER cc_start: 0.8424 (m) cc_final: 0.8005 (p) REVERT: A 81 LYS cc_start: 0.8583 (ttpt) cc_final: 0.8210 (ttmm) REVERT: A 102 LYS cc_start: 0.8128 (tttt) cc_final: 0.7852 (tttp) REVERT: A 264 THR cc_start: 0.7667 (m) cc_final: 0.7385 (p) REVERT: A 286 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7713 (mm-30) REVERT: A 305 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8149 (mtpp) REVERT: A 419 SER cc_start: 0.8674 (t) cc_final: 0.8465 (m) REVERT: A 529 LYS cc_start: 0.8452 (mmmt) cc_final: 0.8140 (mtpp) REVERT: A 551 GLN cc_start: 0.8445 (mp10) cc_final: 0.7881 (mp10) REVERT: A 582 MET cc_start: 0.5682 (mmp) cc_final: 0.5430 (mmp) REVERT: A 629 LYS cc_start: 0.7545 (tmtt) cc_final: 0.7282 (pttt) REVERT: A 641 GLU cc_start: 0.7525 (tp30) cc_final: 0.7311 (tp30) REVERT: A 726 ILE cc_start: 0.8687 (mm) cc_final: 0.8459 (mt) REVERT: B 21 ASP cc_start: 0.7725 (p0) cc_final: 0.7274 (p0) REVERT: B 25 ILE cc_start: 0.8620 (mm) cc_final: 0.8379 (mm) REVERT: B 94 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7516 (mmmm) REVERT: B 123 SER cc_start: 0.8367 (m) cc_final: 0.7970 (p) REVERT: B 276 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7331 (mm-30) REVERT: B 277 PHE cc_start: 0.8092 (p90) cc_final: 0.7671 (p90) REVERT: B 286 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7246 (mm-30) REVERT: B 305 LYS cc_start: 0.8558 (mtpt) cc_final: 0.8188 (mtmm) REVERT: B 368 ILE cc_start: 0.8387 (mm) cc_final: 0.8155 (mt) REVERT: B 402 GLU cc_start: 0.7855 (mp0) cc_final: 0.7534 (mp0) REVERT: B 452 ASP cc_start: 0.8019 (t0) cc_final: 0.7630 (t0) REVERT: B 532 ARG cc_start: 0.8368 (tpp80) cc_final: 0.8108 (ttp80) REVERT: B 673 ARG cc_start: 0.7303 (mtm-85) cc_final: 0.6527 (mtm-85) REVERT: B 707 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7522 (mm-30) REVERT: B 708 LYS cc_start: 0.8486 (ttmm) cc_final: 0.8119 (ttmm) REVERT: B 713 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7594 (mm-30) REVERT: B 718 ARG cc_start: 0.8346 (mmt90) cc_final: 0.8003 (mmt90) REVERT: C 148 SER cc_start: 0.8434 (t) cc_final: 0.8211 (m) REVERT: C 157 LEU cc_start: 0.8621 (mt) cc_final: 0.8415 (mp) REVERT: C 277 PHE cc_start: 0.7969 (p90) cc_final: 0.7670 (p90) REVERT: C 331 TYR cc_start: 0.8323 (m-10) cc_final: 0.7981 (m-10) REVERT: C 350 GLN cc_start: 0.8661 (pp30) cc_final: 0.8446 (pp30) REVERT: C 364 ARG cc_start: 0.8127 (ttp-170) cc_final: 0.7829 (mtp180) REVERT: C 385 GLU cc_start: 0.8151 (mp0) cc_final: 0.7869 (mp0) REVERT: C 413 ASN cc_start: 0.8599 (t0) cc_final: 0.8291 (t0) REVERT: C 532 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8049 (mmm-85) REVERT: D 94 LYS cc_start: 0.8230 (mmmm) cc_final: 0.7841 (mtmt) REVERT: D 152 THR cc_start: 0.8757 (t) cc_final: 0.8324 (p) REVERT: D 311 LYS cc_start: 0.8044 (tppt) cc_final: 0.7826 (ttmt) REVERT: D 331 TYR cc_start: 0.8354 (m-10) cc_final: 0.7953 (m-10) REVERT: D 348 LYS cc_start: 0.8642 (ptmt) cc_final: 0.8414 (pttm) REVERT: D 398 GLU cc_start: 0.7530 (tp30) cc_final: 0.7222 (tp30) REVERT: D 532 ARG cc_start: 0.8409 (tpp80) cc_final: 0.8110 (mmm-85) REVERT: D 551 GLN cc_start: 0.8414 (mp10) cc_final: 0.8004 (mp10) REVERT: D 552 SER cc_start: 0.8337 (t) cc_final: 0.8057 (p) REVERT: D 568 MET cc_start: 0.5361 (mpp) cc_final: 0.4448 (mmt) REVERT: D 686 PHE cc_start: 0.7810 (p90) cc_final: 0.7458 (p90) REVERT: D 707 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7609 (mm-30) REVERT: D 708 LYS cc_start: 0.8461 (ttmm) cc_final: 0.8221 (ttmm) REVERT: D 713 GLU cc_start: 0.8070 (mp0) cc_final: 0.7361 (mp0) REVERT: E 16 LYS cc_start: 0.7964 (mttm) cc_final: 0.7694 (mtpp) REVERT: E 24 LYS cc_start: 0.8468 (ttpp) cc_final: 0.8064 (ttmm) REVERT: E 45 SER cc_start: 0.8700 (m) cc_final: 0.8465 (t) REVERT: E 105 ARG cc_start: 0.8614 (ttt-90) cc_final: 0.8365 (ttt180) REVERT: E 200 ASP cc_start: 0.8113 (p0) cc_final: 0.7911 (p0) REVERT: E 201 ASP cc_start: 0.7781 (t0) cc_final: 0.7557 (t0) REVERT: E 253 GLU cc_start: 0.8293 (tt0) cc_final: 0.7851 (tt0) REVERT: E 255 LYS cc_start: 0.8486 (mttm) cc_final: 0.8145 (mttm) REVERT: E 332 TYR cc_start: 0.8108 (t80) cc_final: 0.7869 (t80) REVERT: F 86 ARG cc_start: 0.8161 (ttm110) cc_final: 0.7869 (ttm110) REVERT: F 107 ASP cc_start: 0.7531 (t0) cc_final: 0.7273 (t0) REVERT: F 216 ASP cc_start: 0.8059 (m-30) cc_final: 0.7743 (m-30) REVERT: F 237 LYS cc_start: 0.8587 (ptpt) cc_final: 0.8139 (ptmt) REVERT: F 255 LYS cc_start: 0.8362 (mtpp) cc_final: 0.8136 (mtpp) REVERT: G 15 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6935 (mm-30) REVERT: G 21 GLU cc_start: 0.7771 (pm20) cc_final: 0.7235 (pm20) REVERT: G 24 LYS cc_start: 0.8394 (ttpp) cc_final: 0.8061 (ttmm) REVERT: G 41 VAL cc_start: 0.8536 (t) cc_final: 0.8307 (p) REVERT: G 95 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7963 (tm-30) REVERT: G 105 ARG cc_start: 0.8691 (ttt-90) cc_final: 0.8457 (ttt180) REVERT: G 107 ASP cc_start: 0.7659 (t0) cc_final: 0.7158 (t0) REVERT: G 196 SER cc_start: 0.8455 (t) cc_final: 0.8056 (p) REVERT: G 200 ASP cc_start: 0.7806 (p0) cc_final: 0.7530 (p0) REVERT: G 201 ASP cc_start: 0.7938 (m-30) cc_final: 0.7545 (m-30) REVERT: G 213 LEU cc_start: 0.8380 (mt) cc_final: 0.8103 (mt) REVERT: G 216 ASP cc_start: 0.8190 (m-30) cc_final: 0.7824 (m-30) REVERT: G 220 ASP cc_start: 0.8038 (m-30) cc_final: 0.7710 (m-30) REVERT: G 224 SER cc_start: 0.8776 (t) cc_final: 0.8264 (m) REVERT: G 255 LYS cc_start: 0.8586 (pttt) cc_final: 0.8192 (pttt) REVERT: G 323 ILE cc_start: 0.8375 (mm) cc_final: 0.8124 (mm) REVERT: H 95 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7836 (tm-30) REVERT: H 130 ASP cc_start: 0.7834 (t0) cc_final: 0.7500 (t0) REVERT: H 213 LEU cc_start: 0.8355 (mt) cc_final: 0.8109 (mt) REVERT: H 224 SER cc_start: 0.8688 (t) cc_final: 0.8394 (p) REVERT: H 243 LYS cc_start: 0.8482 (mtmm) cc_final: 0.8174 (mttm) REVERT: H 244 GLU cc_start: 0.7658 (tp30) cc_final: 0.7145 (tp30) outliers start: 68 outliers final: 42 residues processed: 869 average time/residue: 0.2692 time to fit residues: 374.8251 Evaluate side-chains 832 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 789 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 532 ARG Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 315 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 199 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 317 optimal weight: 0.7980 chunk 358 optimal weight: 0.8980 chunk 363 optimal weight: 2.9990 chunk 378 optimal weight: 0.0170 chunk 417 optimal weight: 0.5980 chunk 213 optimal weight: 0.4980 chunk 127 optimal weight: 0.5980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 ASN C 170 ASN D 65 ASN D 384 ASN E 56 ASN E 353 GLN F 38 ASN G 146 ASN H 206 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.176065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.133347 restraints weight = 59178.431| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.95 r_work: 0.3421 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 46352 Z= 0.133 Angle : 0.493 7.563 64585 Z= 0.281 Chirality : 0.040 0.248 7494 Planarity : 0.003 0.036 6606 Dihedral : 21.435 173.687 10624 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.51 % Favored : 95.38 % Rotamer: Outliers : 1.58 % Allowed : 8.45 % Favored : 89.97 % 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: 0.80 (0.13), residues: 4368 helix: 1.58 (0.11), residues: 2256 sheet: 0.85 (0.23), residues: 550 loop : -1.17 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 664 TYR 0.017 0.001 TYR H 332 PHE 0.014 0.001 PHE B 355 TRP 0.008 0.001 TRP C 697 HIS 0.005 0.001 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (46352) covalent geometry : angle 0.49258 / 0.28 (64585) hydrogen bonds : bond 0.03867 / 2.55 ( 2003) hydrogen bonds : angle 4.08555 / 2.84 ( 5565) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 809 time to evaluate : 1.476 Fit side-chains revert: symmetry clash REVERT: A 37 SER cc_start: 0.8384 (m) cc_final: 0.7972 (p) REVERT: A 81 LYS cc_start: 0.8561 (ttpt) cc_final: 0.8201 (ttmm) REVERT: A 87 LYS cc_start: 0.8036 (mmtp) cc_final: 0.7806 (mmtp) REVERT: A 102 LYS cc_start: 0.8150 (tttt) cc_final: 0.7880 (tttp) REVERT: A 264 THR cc_start: 0.7660 (m) cc_final: 0.7376 (p) REVERT: A 286 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7664 (mm-30) REVERT: A 302 ASN cc_start: 0.8453 (m-40) cc_final: 0.8077 (m-40) REVERT: A 305 LYS cc_start: 0.8493 (mtpp) cc_final: 0.8184 (mtpp) REVERT: A 419 SER cc_start: 0.8681 (t) cc_final: 0.8445 (m) REVERT: A 529 LYS cc_start: 0.8466 (mmmt) cc_final: 0.8174 (mtpp) REVERT: A 551 GLN cc_start: 0.8422 (mp10) cc_final: 0.7885 (mp10) REVERT: A 582 MET cc_start: 0.5707 (mmp) cc_final: 0.5431 (mmp) REVERT: A 629 LYS cc_start: 0.7543 (tmtt) cc_final: 0.7272 (pttt) REVERT: A 726 ILE cc_start: 0.8705 (mm) cc_final: 0.8459 (mt) REVERT: B 21 ASP cc_start: 0.7753 (p0) cc_final: 0.7324 (p0) REVERT: B 94 LYS cc_start: 0.8224 (mmmm) cc_final: 0.7592 (mmmm) REVERT: B 123 SER cc_start: 0.8383 (m) cc_final: 0.8048 (p) REVERT: B 276 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7282 (mm-30) REVERT: B 286 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7285 (mm-30) REVERT: B 305 LYS cc_start: 0.8571 (mtpt) cc_final: 0.8314 (mtmm) REVERT: B 402 GLU cc_start: 0.7838 (mp0) cc_final: 0.7534 (mp0) REVERT: B 452 ASP cc_start: 0.7929 (t0) cc_final: 0.7532 (t0) REVERT: B 532 ARG cc_start: 0.8340 (tpp80) cc_final: 0.8070 (ttp80) REVERT: B 707 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7479 (mm-30) REVERT: B 708 LYS cc_start: 0.8499 (ttmm) cc_final: 0.8182 (ttmm) REVERT: B 713 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7568 (mm-30) REVERT: B 718 ARG cc_start: 0.8313 (mmt90) cc_final: 0.7976 (mmt90) REVERT: C 148 SER cc_start: 0.8430 (t) cc_final: 0.8082 (m) REVERT: C 277 PHE cc_start: 0.7884 (p90) cc_final: 0.7546 (p90) REVERT: C 331 TYR cc_start: 0.8253 (m-10) cc_final: 0.7833 (m-80) REVERT: C 413 ASN cc_start: 0.8581 (t0) cc_final: 0.8269 (t0) REVERT: D 94 LYS cc_start: 0.8232 (mmmm) cc_final: 0.7854 (mtmt) REVERT: D 152 THR cc_start: 0.8743 (t) cc_final: 0.8316 (p) REVERT: D 311 LYS cc_start: 0.8045 (tppt) cc_final: 0.7818 (ttmt) REVERT: D 331 TYR cc_start: 0.8418 (m-10) cc_final: 0.7992 (m-80) REVERT: D 348 LYS cc_start: 0.8627 (ptmt) cc_final: 0.8424 (pttm) REVERT: D 551 GLN cc_start: 0.8376 (mp10) cc_final: 0.8002 (mp10) REVERT: D 552 SER cc_start: 0.8374 (t) cc_final: 0.8069 (p) REVERT: D 568 MET cc_start: 0.5173 (mpp) cc_final: 0.4265 (mmt) REVERT: D 686 PHE cc_start: 0.7776 (p90) cc_final: 0.7426 (p90) REVERT: D 694 THR cc_start: 0.8255 (m) cc_final: 0.8002 (p) REVERT: D 707 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7587 (mm-30) REVERT: D 708 LYS cc_start: 0.8407 (ttmm) cc_final: 0.8202 (ttmm) REVERT: D 713 GLU cc_start: 0.8057 (mp0) cc_final: 0.7377 (mp0) REVERT: D 735 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7718 (mm-30) REVERT: E 24 LYS cc_start: 0.8437 (ttpp) cc_final: 0.8097 (ttmm) REVERT: E 200 ASP cc_start: 0.8159 (p0) cc_final: 0.7939 (p0) REVERT: E 201 ASP cc_start: 0.7743 (t0) cc_final: 0.7528 (t0) REVERT: E 253 GLU cc_start: 0.8263 (tt0) cc_final: 0.7842 (tt0) REVERT: E 255 LYS cc_start: 0.8479 (mttm) cc_final: 0.8123 (mttm) REVERT: E 332 TYR cc_start: 0.8005 (t80) cc_final: 0.7759 (t80) REVERT: F 56 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7616 (m-40) REVERT: F 86 ARG cc_start: 0.8104 (ttm110) cc_final: 0.7823 (ttm110) REVERT: F 107 ASP cc_start: 0.7536 (t0) cc_final: 0.7190 (t0) REVERT: F 216 ASP cc_start: 0.8016 (m-30) cc_final: 0.7719 (m-30) REVERT: F 237 LYS cc_start: 0.8545 (ptpt) cc_final: 0.8114 (ptmt) REVERT: F 255 LYS cc_start: 0.8332 (mtpp) cc_final: 0.8095 (mtpp) REVERT: G 15 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6959 (mm-30) REVERT: G 21 GLU cc_start: 0.7687 (pm20) cc_final: 0.7223 (pm20) REVERT: G 24 LYS cc_start: 0.8348 (ttpp) cc_final: 0.8011 (ttmm) REVERT: G 41 VAL cc_start: 0.8504 (t) cc_final: 0.8286 (p) REVERT: G 95 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7924 (tm-30) REVERT: G 105 ARG cc_start: 0.8646 (ttt-90) cc_final: 0.8435 (ttt180) REVERT: G 107 ASP cc_start: 0.7511 (t0) cc_final: 0.7065 (t0) REVERT: G 200 ASP cc_start: 0.7801 (p0) cc_final: 0.7503 (p0) REVERT: G 201 ASP cc_start: 0.7929 (m-30) cc_final: 0.7527 (m-30) REVERT: G 213 LEU cc_start: 0.8392 (mt) cc_final: 0.8116 (mt) REVERT: G 216 ASP cc_start: 0.8187 (m-30) cc_final: 0.7783 (m-30) REVERT: G 220 ASP cc_start: 0.8020 (m-30) cc_final: 0.7651 (m-30) REVERT: G 224 SER cc_start: 0.8751 (t) cc_final: 0.8281 (p) REVERT: G 255 LYS cc_start: 0.8544 (pttt) cc_final: 0.8206 (pttt) REVERT: G 323 ILE cc_start: 0.8346 (mm) cc_final: 0.8095 (mm) REVERT: H 95 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7824 (tm-30) REVERT: H 213 LEU cc_start: 0.8360 (mt) cc_final: 0.8105 (mt) REVERT: H 224 SER cc_start: 0.8660 (t) cc_final: 0.8411 (p) REVERT: H 243 LYS cc_start: 0.8436 (mtmm) cc_final: 0.8116 (mttm) REVERT: H 244 GLU cc_start: 0.7604 (tp30) cc_final: 0.7096 (tp30) outliers start: 63 outliers final: 40 residues processed: 827 average time/residue: 0.2619 time to fit residues: 345.9618 Evaluate side-chains 832 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 791 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 68 ASN Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 56 ASN Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 322 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 274 optimal weight: 20.0000 chunk 110 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 299 optimal weight: 2.9990 chunk 386 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 23 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 ASN C 65 ASN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 ASN F 38 ASN F 292 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.175595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.132990 restraints weight = 59262.022| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.94 r_work: 0.3399 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 46352 Z= 0.154 Angle : 0.499 8.171 64585 Z= 0.281 Chirality : 0.041 0.275 7494 Planarity : 0.003 0.032 6606 Dihedral : 21.281 173.394 10622 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.97 % Favored : 94.92 % Rotamer: Outliers : 1.78 % Allowed : 9.60 % Favored : 88.61 % 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: 0.83 (0.13), residues: 4368 helix: 1.65 (0.11), residues: 2251 sheet: 0.79 (0.23), residues: 562 loop : -1.19 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 532 TYR 0.017 0.001 TYR D 307 PHE 0.027 0.001 PHE B 355 TRP 0.007 0.001 TRP C 697 HIS 0.005 0.001 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (46352) covalent geometry : angle 0.49915 / 0.28 (64585) hydrogen bonds : bond 0.03772 / 2.50 ( 2003) hydrogen bonds : angle 3.97698 / 2.77 ( 5565) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 802 time to evaluate : 1.022 Fit side-chains REVERT: A 37 SER cc_start: 0.8376 (m) cc_final: 0.7988 (p) REVERT: A 81 LYS cc_start: 0.8555 (ttpt) cc_final: 0.8204 (ttmm) REVERT: A 87 LYS cc_start: 0.8044 (mmtp) cc_final: 0.7800 (mmtp) REVERT: A 102 LYS cc_start: 0.8141 (tttt) cc_final: 0.7840 (tttp) REVERT: A 124 PHE cc_start: 0.8563 (m-80) cc_final: 0.8189 (m-10) REVERT: A 286 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7689 (mm-30) REVERT: A 305 LYS cc_start: 0.8519 (mtpp) cc_final: 0.8192 (mtpp) REVERT: A 419 SER cc_start: 0.8676 (t) cc_final: 0.8458 (m) REVERT: A 529 LYS cc_start: 0.8476 (mmmt) cc_final: 0.8182 (mtpp) REVERT: A 551 GLN cc_start: 0.8430 (mp10) cc_final: 0.7896 (mp10) REVERT: A 582 MET cc_start: 0.5702 (mmp) cc_final: 0.5448 (mmp) REVERT: A 629 LYS cc_start: 0.7556 (tmtt) cc_final: 0.7269 (pttt) REVERT: A 726 ILE cc_start: 0.8710 (mm) cc_final: 0.8475 (mt) REVERT: B 21 ASP cc_start: 0.7741 (p0) cc_final: 0.7313 (p0) REVERT: B 94 LYS cc_start: 0.8260 (mmmm) cc_final: 0.7638 (mmmm) REVERT: B 123 SER cc_start: 0.8377 (m) cc_final: 0.8054 (p) REVERT: B 137 VAL cc_start: 0.8624 (p) cc_final: 0.8357 (t) REVERT: B 276 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7265 (mm-30) REVERT: B 277 PHE cc_start: 0.8009 (p90) cc_final: 0.7576 (p90) REVERT: B 286 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7306 (mm-30) REVERT: B 305 LYS cc_start: 0.8573 (mtpt) cc_final: 0.8313 (mtmm) REVERT: B 402 GLU cc_start: 0.7818 (mp0) cc_final: 0.7527 (mp0) REVERT: B 452 ASP cc_start: 0.7881 (t0) cc_final: 0.7531 (t0) REVERT: B 472 LYS cc_start: 0.7886 (tppt) cc_final: 0.7472 (tppt) REVERT: B 532 ARG cc_start: 0.8323 (tpp80) cc_final: 0.8047 (ttp80) REVERT: B 673 ARG cc_start: 0.7379 (mtm-85) cc_final: 0.6704 (mtm-85) REVERT: B 707 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7516 (mm-30) REVERT: B 708 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8186 (ttmm) REVERT: B 713 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7508 (mm-30) REVERT: B 718 ARG cc_start: 0.8333 (mmt90) cc_final: 0.7930 (mmt90) REVERT: C 142 ASP cc_start: 0.7380 (p0) cc_final: 0.7042 (p0) REVERT: C 148 SER cc_start: 0.8441 (t) cc_final: 0.8092 (m) REVERT: C 331 TYR cc_start: 0.8257 (m-10) cc_final: 0.7897 (m-80) REVERT: C 364 ARG cc_start: 0.8097 (ttp-170) cc_final: 0.7830 (mtp180) REVERT: C 413 ASN cc_start: 0.8593 (t0) cc_final: 0.8284 (t0) REVERT: C 663 LEU cc_start: 0.6940 (mt) cc_final: 0.6628 (mp) REVERT: D 94 LYS cc_start: 0.8244 (mmmm) cc_final: 0.7875 (mtmt) REVERT: D 99 THR cc_start: 0.8567 (p) cc_final: 0.8267 (t) REVERT: D 152 THR cc_start: 0.8751 (t) cc_final: 0.8326 (p) REVERT: D 311 LYS cc_start: 0.8045 (tppt) cc_final: 0.7823 (ttmt) REVERT: D 331 TYR cc_start: 0.8452 (m-10) cc_final: 0.7996 (m-80) REVERT: D 469 LEU cc_start: 0.7867 (tt) cc_final: 0.7554 (tp) REVERT: D 483 TYR cc_start: 0.8191 (p90) cc_final: 0.7948 (p90) REVERT: D 551 GLN cc_start: 0.8378 (mp10) cc_final: 0.8027 (mp10) REVERT: D 552 SER cc_start: 0.8394 (t) cc_final: 0.8104 (p) REVERT: D 686 PHE cc_start: 0.7802 (p90) cc_final: 0.7462 (p90) REVERT: D 694 THR cc_start: 0.8297 (m) cc_final: 0.8050 (p) REVERT: D 707 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7603 (mm-30) REVERT: D 708 LYS cc_start: 0.8453 (ttmm) cc_final: 0.8224 (ttmm) REVERT: D 713 GLU cc_start: 0.8060 (mp0) cc_final: 0.7436 (mp0) REVERT: D 735 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7678 (mm-30) REVERT: E 24 LYS cc_start: 0.8435 (ttpp) cc_final: 0.8063 (ttmm) REVERT: E 27 ILE cc_start: 0.8057 (mt) cc_final: 0.7787 (tt) REVERT: E 86 ARG cc_start: 0.8172 (ttt90) cc_final: 0.7959 (ttt90) REVERT: E 200 ASP cc_start: 0.8135 (p0) cc_final: 0.7912 (p0) REVERT: E 201 ASP cc_start: 0.7728 (t0) cc_final: 0.7450 (t0) REVERT: E 253 GLU cc_start: 0.8271 (tt0) cc_final: 0.7819 (tt0) REVERT: E 255 LYS cc_start: 0.8474 (mttm) cc_final: 0.8117 (mttm) REVERT: E 332 TYR cc_start: 0.7977 (t80) cc_final: 0.7735 (t80) REVERT: E 367 LYS cc_start: 0.7715 (mtpp) cc_final: 0.7360 (mttm) REVERT: F 56 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7623 (m-40) REVERT: F 86 ARG cc_start: 0.8050 (ttm110) cc_final: 0.7772 (ttm110) REVERT: F 107 ASP cc_start: 0.7482 (t0) cc_final: 0.7181 (t0) REVERT: F 201 ASP cc_start: 0.7993 (m-30) cc_final: 0.7660 (m-30) REVERT: F 216 ASP cc_start: 0.8050 (m-30) cc_final: 0.7777 (m-30) REVERT: F 237 LYS cc_start: 0.8556 (ptpt) cc_final: 0.8130 (ptmt) REVERT: F 255 LYS cc_start: 0.8339 (mtpp) cc_final: 0.8109 (mtpp) REVERT: G 15 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6960 (mm-30) REVERT: G 21 GLU cc_start: 0.7661 (pm20) cc_final: 0.7325 (pm20) REVERT: G 24 LYS cc_start: 0.8351 (ttpp) cc_final: 0.7979 (ttmm) REVERT: G 41 VAL cc_start: 0.8542 (t) cc_final: 0.8309 (p) REVERT: G 95 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7940 (tm-30) REVERT: G 105 ARG cc_start: 0.8649 (ttt-90) cc_final: 0.8424 (ttt180) REVERT: G 107 ASP cc_start: 0.7542 (t0) cc_final: 0.7165 (t0) REVERT: G 181 ASP cc_start: 0.8511 (m-30) cc_final: 0.8271 (m-30) REVERT: G 200 ASP cc_start: 0.7803 (p0) cc_final: 0.7545 (p0) REVERT: G 201 ASP cc_start: 0.7900 (m-30) cc_final: 0.7569 (m-30) REVERT: G 213 LEU cc_start: 0.8410 (mt) cc_final: 0.8132 (mt) REVERT: G 216 ASP cc_start: 0.8180 (m-30) cc_final: 0.7814 (m-30) REVERT: G 220 ASP cc_start: 0.8062 (m-30) cc_final: 0.7709 (m-30) REVERT: G 224 SER cc_start: 0.8750 (t) cc_final: 0.8277 (p) REVERT: G 255 LYS cc_start: 0.8526 (pttt) cc_final: 0.8215 (pttt) REVERT: G 323 ILE cc_start: 0.8345 (mm) cc_final: 0.8100 (mm) REVERT: H 95 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7823 (tm-30) REVERT: H 213 LEU cc_start: 0.8373 (mt) cc_final: 0.8132 (mt) REVERT: H 224 SER cc_start: 0.8657 (t) cc_final: 0.8409 (p) REVERT: H 238 TYR cc_start: 0.8240 (t80) cc_final: 0.7807 (t80) REVERT: H 243 LYS cc_start: 0.8449 (mtmm) cc_final: 0.8190 (mttm) REVERT: H 244 GLU cc_start: 0.7631 (tp30) cc_final: 0.7271 (tt0) outliers start: 71 outliers final: 49 residues processed: 826 average time/residue: 0.2670 time to fit residues: 352.1048 Evaluate side-chains 828 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 778 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 711 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 68 ASN Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 56 ASN Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 322 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 167 optimal weight: 6.9990 chunk 348 optimal weight: 0.9990 chunk 319 optimal weight: 0.0470 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 410 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 234 optimal weight: 0.7980 chunk 184 optimal weight: 0.9990 chunk 352 optimal weight: 2.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 558 ASN C 65 ASN D 38 ASN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 ASN F 38 ASN F 292 ASN G 26 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.175507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.132941 restraints weight = 58858.075| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.79 r_work: 0.3413 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 46352 Z= 0.148 Angle : 0.490 9.245 64585 Z= 0.276 Chirality : 0.040 0.258 7494 Planarity : 0.003 0.032 6606 Dihedral : 21.232 172.980 10622 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.78 % Favored : 95.10 % Rotamer: Outliers : 1.84 % Allowed : 10.53 % Favored : 87.63 % 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: 0.85 (0.13), residues: 4368 helix: 1.68 (0.11), residues: 2251 sheet: 0.76 (0.23), residues: 562 loop : -1.19 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 66 TYR 0.017 0.001 TYR B 97 PHE 0.022 0.001 PHE B 355 TRP 0.008 0.001 TRP C 697 HIS 0.005 0.001 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (46352) covalent geometry : angle 0.48996 / 0.28 (64585) hydrogen bonds : bond 0.03671 / 2.43 ( 2003) hydrogen bonds : angle 3.95177 / 2.75 ( 5565) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 796 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 37 SER cc_start: 0.8361 (m) cc_final: 0.7970 (p) REVERT: A 81 LYS cc_start: 0.8557 (ttpt) cc_final: 0.8209 (ttmm) REVERT: A 102 LYS cc_start: 0.8160 (tttt) cc_final: 0.7869 (tttp) REVERT: A 124 PHE cc_start: 0.8593 (m-80) cc_final: 0.8121 (m-10) REVERT: A 141 VAL cc_start: 0.8198 (m) cc_final: 0.7898 (t) REVERT: A 286 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7684 (mm-30) REVERT: A 302 ASN cc_start: 0.8460 (m-40) cc_final: 0.8073 (m-40) REVERT: A 305 LYS cc_start: 0.8530 (mtpp) cc_final: 0.8199 (mtpp) REVERT: A 419 SER cc_start: 0.8664 (t) cc_final: 0.8454 (m) REVERT: A 529 LYS cc_start: 0.8457 (mmmt) cc_final: 0.8176 (mtpp) REVERT: A 551 GLN cc_start: 0.8423 (mp10) cc_final: 0.7912 (mp10) REVERT: A 582 MET cc_start: 0.5640 (mmp) cc_final: 0.5405 (mmp) REVERT: A 629 LYS cc_start: 0.7561 (tmtt) cc_final: 0.7288 (pttt) REVERT: A 726 ILE cc_start: 0.8707 (mm) cc_final: 0.8465 (mt) REVERT: B 21 ASP cc_start: 0.7722 (p0) cc_final: 0.7317 (p0) REVERT: B 94 LYS cc_start: 0.8259 (mmmm) cc_final: 0.7665 (mmmm) REVERT: B 123 SER cc_start: 0.8359 (m) cc_final: 0.8071 (p) REVERT: B 137 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8340 (t) REVERT: B 276 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7235 (mm-30) REVERT: B 277 PHE cc_start: 0.8020 (p90) cc_final: 0.7614 (p90) REVERT: B 286 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7189 (mm-30) REVERT: B 452 ASP cc_start: 0.7832 (t0) cc_final: 0.7513 (t0) REVERT: B 472 LYS cc_start: 0.7902 (tppt) cc_final: 0.7485 (tppt) REVERT: B 532 ARG cc_start: 0.8330 (tpp80) cc_final: 0.8058 (ttp80) REVERT: B 641 GLU cc_start: 0.7438 (tp30) cc_final: 0.7232 (tp30) REVERT: B 673 ARG cc_start: 0.7398 (mtm-85) cc_final: 0.6693 (mtm-85) REVERT: B 707 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7516 (mm-30) REVERT: B 708 LYS cc_start: 0.8518 (ttmm) cc_final: 0.8169 (ttmm) REVERT: B 713 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7509 (mm-30) REVERT: B 718 ARG cc_start: 0.8313 (mmt90) cc_final: 0.7926 (mmt90) REVERT: C 142 ASP cc_start: 0.7374 (p0) cc_final: 0.7050 (p0) REVERT: C 148 SER cc_start: 0.8448 (t) cc_final: 0.8101 (m) REVERT: C 331 TYR cc_start: 0.8242 (m-10) cc_final: 0.7833 (m-80) REVERT: C 413 ASN cc_start: 0.8581 (t0) cc_final: 0.8285 (t0) REVERT: C 663 LEU cc_start: 0.6963 (mt) cc_final: 0.6546 (mp) REVERT: D 94 LYS cc_start: 0.8232 (mmmm) cc_final: 0.7811 (mtmm) REVERT: D 99 THR cc_start: 0.8560 (p) cc_final: 0.8269 (t) REVERT: D 152 THR cc_start: 0.8748 (t) cc_final: 0.8324 (p) REVERT: D 303 LEU cc_start: 0.8411 (tt) cc_final: 0.8202 (tp) REVERT: D 311 LYS cc_start: 0.8036 (tppt) cc_final: 0.7823 (ttmt) REVERT: D 331 TYR cc_start: 0.8448 (m-10) cc_final: 0.8024 (m-80) REVERT: D 469 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7610 (tp) REVERT: D 502 GLN cc_start: 0.6662 (mm-40) cc_final: 0.6103 (tm-30) REVERT: D 551 GLN cc_start: 0.8345 (mp10) cc_final: 0.8011 (mp10) REVERT: D 686 PHE cc_start: 0.7810 (p90) cc_final: 0.7495 (p90) REVERT: D 694 THR cc_start: 0.8315 (m) cc_final: 0.8058 (p) REVERT: D 707 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7582 (mm-30) REVERT: D 708 LYS cc_start: 0.8451 (ttmm) cc_final: 0.8222 (ttmm) REVERT: D 713 GLU cc_start: 0.8056 (mp0) cc_final: 0.7474 (mp0) REVERT: D 735 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7630 (mm-30) REVERT: E 24 LYS cc_start: 0.8405 (ttpp) cc_final: 0.7917 (ttmm) REVERT: E 27 ILE cc_start: 0.8059 (mt) cc_final: 0.7801 (tt) REVERT: E 66 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7173 (mtt180) REVERT: E 86 ARG cc_start: 0.8137 (ttt90) cc_final: 0.7932 (ttt90) REVERT: E 201 ASP cc_start: 0.7669 (t0) cc_final: 0.7429 (t0) REVERT: E 253 GLU cc_start: 0.8221 (tt0) cc_final: 0.7779 (tt0) REVERT: E 255 LYS cc_start: 0.8475 (mttm) cc_final: 0.8119 (mttm) REVERT: E 332 TYR cc_start: 0.7979 (t80) cc_final: 0.7746 (t80) REVERT: E 367 LYS cc_start: 0.7702 (mtpp) cc_final: 0.7353 (mttm) REVERT: F 56 ASN cc_start: 0.7884 (OUTLIER) cc_final: 0.7614 (m-40) REVERT: F 86 ARG cc_start: 0.8042 (ttm110) cc_final: 0.7791 (ttm110) REVERT: F 107 ASP cc_start: 0.7455 (t0) cc_final: 0.7154 (t0) REVERT: F 201 ASP cc_start: 0.7948 (m-30) cc_final: 0.7626 (m-30) REVERT: F 216 ASP cc_start: 0.8003 (m-30) cc_final: 0.7766 (m-30) REVERT: F 237 LYS cc_start: 0.8546 (ptpt) cc_final: 0.8119 (ptmt) REVERT: F 255 LYS cc_start: 0.8315 (mtpp) cc_final: 0.8081 (mtpp) REVERT: G 15 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6968 (mm-30) REVERT: G 21 GLU cc_start: 0.7628 (pm20) cc_final: 0.7299 (pm20) REVERT: G 24 LYS cc_start: 0.8336 (ttpp) cc_final: 0.7960 (ttmm) REVERT: G 41 VAL cc_start: 0.8547 (t) cc_final: 0.8308 (p) REVERT: G 95 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7923 (tm-30) REVERT: G 107 ASP cc_start: 0.7489 (t0) cc_final: 0.7224 (t0) REVERT: G 201 ASP cc_start: 0.7867 (m-30) cc_final: 0.7583 (m-30) REVERT: G 213 LEU cc_start: 0.8405 (mt) cc_final: 0.8138 (mt) REVERT: G 216 ASP cc_start: 0.8156 (m-30) cc_final: 0.7814 (m-30) REVERT: G 220 ASP cc_start: 0.8029 (m-30) cc_final: 0.7686 (m-30) REVERT: G 224 SER cc_start: 0.8747 (t) cc_final: 0.8268 (p) REVERT: G 255 LYS cc_start: 0.8521 (pttt) cc_final: 0.8208 (pttt) REVERT: G 323 ILE cc_start: 0.8345 (mm) cc_final: 0.8101 (mm) REVERT: H 95 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7798 (tm-30) REVERT: H 213 LEU cc_start: 0.8387 (mt) cc_final: 0.8125 (mt) REVERT: H 224 SER cc_start: 0.8658 (t) cc_final: 0.8402 (p) REVERT: H 243 LYS cc_start: 0.8432 (mtmm) cc_final: 0.8189 (mttm) REVERT: H 244 GLU cc_start: 0.7564 (tp30) cc_final: 0.7236 (tt0) outliers start: 73 outliers final: 52 residues processed: 823 average time/residue: 0.2562 time to fit residues: 337.2836 Evaluate side-chains 837 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 781 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 68 ASN Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 56 ASN Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 322 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 10 optimal weight: 0.7980 chunk 208 optimal weight: 0.9980 chunk 303 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 216 optimal weight: 0.1980 chunk 430 optimal weight: 3.9990 chunk 356 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 375 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 474 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 ASN C 65 ASN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.175511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132907 restraints weight = 59159.898| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.92 r_work: 0.3404 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 46352 Z= 0.134 Angle : 0.480 8.349 64585 Z= 0.272 Chirality : 0.040 0.260 7494 Planarity : 0.003 0.040 6606 Dihedral : 21.188 172.636 10622 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.95 % Favored : 94.94 % Rotamer: Outliers : 2.09 % Allowed : 10.68 % Favored : 87.23 % 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: 0.89 (0.13), residues: 4368 helix: 1.72 (0.11), residues: 2251 sheet: 0.73 (0.23), residues: 562 loop : -1.17 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 86 TYR 0.015 0.001 TYR H 332 PHE 0.022 0.001 PHE D 725 TRP 0.008 0.001 TRP C 697 HIS 0.005 0.001 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (46352) covalent geometry : angle 0.48011 / 0.27 (64585) hydrogen bonds : bond 0.03557 / 2.36 ( 2003) hydrogen bonds : angle 3.90281 / 2.72 ( 5565) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 795 time to evaluate : 1.227 Fit side-chains revert: symmetry clash REVERT: A 37 SER cc_start: 0.8371 (m) cc_final: 0.7973 (p) REVERT: A 81 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8208 (ttmm) REVERT: A 102 LYS cc_start: 0.8139 (tttt) cc_final: 0.7846 (tttp) REVERT: A 286 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7706 (mm-30) REVERT: A 305 LYS cc_start: 0.8541 (mtpp) cc_final: 0.8218 (mtpp) REVERT: A 419 SER cc_start: 0.8670 (t) cc_final: 0.8462 (m) REVERT: A 529 LYS cc_start: 0.8465 (mmmt) cc_final: 0.8174 (mtpp) REVERT: A 551 GLN cc_start: 0.8423 (mp10) cc_final: 0.7903 (mp10) REVERT: A 582 MET cc_start: 0.5680 (mmp) cc_final: 0.5445 (mmp) REVERT: A 629 LYS cc_start: 0.7564 (tmtt) cc_final: 0.7284 (pttt) REVERT: A 726 ILE cc_start: 0.8697 (mm) cc_final: 0.8447 (mt) REVERT: B 21 ASP cc_start: 0.7742 (p0) cc_final: 0.7333 (p0) REVERT: B 94 LYS cc_start: 0.8257 (mmmm) cc_final: 0.7658 (mmmm) REVERT: B 123 SER cc_start: 0.8365 (m) cc_final: 0.8074 (p) REVERT: B 137 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8325 (t) REVERT: B 276 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7228 (mm-30) REVERT: B 277 PHE cc_start: 0.8009 (p90) cc_final: 0.7582 (p90) REVERT: B 452 ASP cc_start: 0.7846 (t0) cc_final: 0.7509 (t0) REVERT: B 472 LYS cc_start: 0.7907 (tppt) cc_final: 0.7483 (tppt) REVERT: B 532 ARG cc_start: 0.8331 (tpp80) cc_final: 0.8058 (ttp80) REVERT: B 641 GLU cc_start: 0.7508 (tp30) cc_final: 0.7262 (tp30) REVERT: B 673 ARG cc_start: 0.7431 (mtm-85) cc_final: 0.6680 (mtm-85) REVERT: B 707 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7517 (mm-30) REVERT: B 708 LYS cc_start: 0.8536 (ttmm) cc_final: 0.8186 (ttmm) REVERT: B 713 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7527 (mm-30) REVERT: B 718 ARG cc_start: 0.8328 (mmt90) cc_final: 0.7935 (mmt90) REVERT: C 142 ASP cc_start: 0.7420 (p0) cc_final: 0.7111 (p0) REVERT: C 148 SER cc_start: 0.8439 (t) cc_final: 0.8107 (m) REVERT: C 331 TYR cc_start: 0.8240 (m-10) cc_final: 0.7866 (m-80) REVERT: C 413 ASN cc_start: 0.8582 (t0) cc_final: 0.8272 (t0) REVERT: C 663 LEU cc_start: 0.6943 (mt) cc_final: 0.6577 (mp) REVERT: D 94 LYS cc_start: 0.8235 (mmmm) cc_final: 0.7816 (mtmm) REVERT: D 99 THR cc_start: 0.8549 (p) cc_final: 0.8274 (t) REVERT: D 152 THR cc_start: 0.8758 (t) cc_final: 0.8330 (p) REVERT: D 303 LEU cc_start: 0.8430 (tt) cc_final: 0.8216 (tp) REVERT: D 311 LYS cc_start: 0.8031 (tppt) cc_final: 0.7813 (ttmt) REVERT: D 331 TYR cc_start: 0.8445 (m-10) cc_final: 0.8088 (m-80) REVERT: D 469 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7617 (tp) REVERT: D 502 GLN cc_start: 0.6686 (mm-40) cc_final: 0.6137 (tm-30) REVERT: D 551 GLN cc_start: 0.8378 (mp10) cc_final: 0.8025 (mp10) REVERT: D 686 PHE cc_start: 0.7804 (p90) cc_final: 0.7479 (p90) REVERT: D 694 THR cc_start: 0.8324 (m) cc_final: 0.8065 (p) REVERT: D 707 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7584 (mm-30) REVERT: D 708 LYS cc_start: 0.8456 (ttmm) cc_final: 0.8225 (ttmm) REVERT: D 713 GLU cc_start: 0.8066 (mp0) cc_final: 0.7469 (mp0) REVERT: D 735 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7671 (mm-30) REVERT: E 24 LYS cc_start: 0.8403 (ttpp) cc_final: 0.7920 (ttmm) REVERT: E 27 ILE cc_start: 0.8062 (mt) cc_final: 0.7813 (tt) REVERT: E 66 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7151 (mtt180) REVERT: E 86 ARG cc_start: 0.8145 (ttt90) cc_final: 0.7938 (ttt90) REVERT: E 201 ASP cc_start: 0.7686 (t0) cc_final: 0.7436 (t0) REVERT: E 253 GLU cc_start: 0.8262 (tt0) cc_final: 0.7805 (tt0) REVERT: E 255 LYS cc_start: 0.8497 (mttm) cc_final: 0.8137 (mttm) REVERT: E 332 TYR cc_start: 0.7955 (t80) cc_final: 0.7728 (t80) REVERT: E 367 LYS cc_start: 0.7716 (mtpp) cc_final: 0.7363 (mttm) REVERT: F 56 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7634 (m-40) REVERT: F 86 ARG cc_start: 0.8063 (ttm110) cc_final: 0.7813 (ttm110) REVERT: F 107 ASP cc_start: 0.7471 (t0) cc_final: 0.7157 (t0) REVERT: F 201 ASP cc_start: 0.7981 (m-30) cc_final: 0.7654 (m-30) REVERT: F 237 LYS cc_start: 0.8568 (ptpt) cc_final: 0.8147 (ptmt) REVERT: F 242 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7950 (mt-10) REVERT: F 255 LYS cc_start: 0.8330 (mtpp) cc_final: 0.8103 (mtpp) REVERT: G 15 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6974 (mm-30) REVERT: G 21 GLU cc_start: 0.7644 (pm20) cc_final: 0.7290 (pm20) REVERT: G 24 LYS cc_start: 0.8349 (ttpp) cc_final: 0.7976 (ttmm) REVERT: G 41 VAL cc_start: 0.8548 (t) cc_final: 0.8299 (p) REVERT: G 95 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7927 (tm-30) REVERT: G 200 ASP cc_start: 0.7947 (p0) cc_final: 0.7708 (p0) REVERT: G 201 ASP cc_start: 0.7928 (m-30) cc_final: 0.7582 (m-30) REVERT: G 213 LEU cc_start: 0.8409 (mt) cc_final: 0.8143 (mt) REVERT: G 216 ASP cc_start: 0.8187 (m-30) cc_final: 0.7828 (m-30) REVERT: G 220 ASP cc_start: 0.8029 (m-30) cc_final: 0.7692 (m-30) REVERT: G 224 SER cc_start: 0.8746 (t) cc_final: 0.8270 (p) REVERT: G 255 LYS cc_start: 0.8539 (pttt) cc_final: 0.8191 (pttt) REVERT: G 323 ILE cc_start: 0.8372 (mm) cc_final: 0.8129 (mm) REVERT: H 95 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7805 (tm-30) REVERT: H 213 LEU cc_start: 0.8385 (mt) cc_final: 0.8125 (mt) REVERT: H 224 SER cc_start: 0.8656 (t) cc_final: 0.8401 (p) REVERT: H 243 LYS cc_start: 0.8436 (mtmm) cc_final: 0.8187 (mttm) REVERT: H 244 GLU cc_start: 0.7591 (tp30) cc_final: 0.7259 (tt0) outliers start: 83 outliers final: 63 residues processed: 828 average time/residue: 0.2396 time to fit residues: 317.5988 Evaluate side-chains 843 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 776 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 540 THR Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain D residue 711 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 68 ASN Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 56 ASN Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 322 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 386 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 337 optimal weight: 0.8980 chunk 255 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 308 optimal weight: 0.5980 chunk 460 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 280 optimal weight: 4.9990 chunk 367 optimal weight: 1.9990 chunk 361 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 ASN C 65 ASN E 56 ASN G 146 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.173753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131358 restraints weight = 58869.921| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.91 r_work: 0.3372 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 46352 Z= 0.194 Angle : 0.516 8.027 64585 Z= 0.288 Chirality : 0.042 0.261 7494 Planarity : 0.003 0.033 6606 Dihedral : 21.157 172.481 10622 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.92 % Favored : 94.99 % Rotamer: Outliers : 2.24 % Allowed : 11.04 % Favored : 86.73 % 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: 0.75 (0.13), residues: 4368 helix: 1.54 (0.11), residues: 2280 sheet: 0.66 (0.23), residues: 552 loop : -1.16 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 673 TYR 0.021 0.002 TYR B 457 PHE 0.035 0.002 PHE B 355 TRP 0.008 0.001 TRP D 697 HIS 0.005 0.001 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (46352) covalent geometry : angle 0.51615 / 0.29 (64585) hydrogen bonds : bond 0.03870 / 2.57 ( 2003) hydrogen bonds : angle 3.95100 / 2.76 ( 5565) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 814 time to evaluate : 0.990 Fit side-chains REVERT: A 37 SER cc_start: 0.8387 (m) cc_final: 0.8020 (p) REVERT: A 81 LYS cc_start: 0.8568 (ttpt) cc_final: 0.8216 (ttmm) REVERT: A 102 LYS cc_start: 0.8130 (tttt) cc_final: 0.7861 (tttp) REVERT: A 124 PHE cc_start: 0.8572 (m-80) cc_final: 0.8186 (m-10) REVERT: A 141 VAL cc_start: 0.8282 (m) cc_final: 0.8006 (t) REVERT: A 286 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7740 (mm-30) REVERT: A 302 ASN cc_start: 0.8501 (m-40) cc_final: 0.8290 (m-40) REVERT: A 305 LYS cc_start: 0.8556 (mtpp) cc_final: 0.8232 (mtpp) REVERT: A 529 LYS cc_start: 0.8476 (mmmt) cc_final: 0.8180 (mtpp) REVERT: A 551 GLN cc_start: 0.8429 (mp10) cc_final: 0.7922 (mp10) REVERT: A 582 MET cc_start: 0.5684 (mmp) cc_final: 0.5464 (mmp) REVERT: A 629 LYS cc_start: 0.7586 (tmtt) cc_final: 0.7302 (pttt) REVERT: A 726 ILE cc_start: 0.8712 (mm) cc_final: 0.8469 (mt) REVERT: B 21 ASP cc_start: 0.7735 (p0) cc_final: 0.7346 (p0) REVERT: B 94 LYS cc_start: 0.8261 (mmmm) cc_final: 0.7675 (mmmm) REVERT: B 123 SER cc_start: 0.8360 (m) cc_final: 0.8058 (p) REVERT: B 137 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8366 (t) REVERT: B 277 PHE cc_start: 0.8070 (p90) cc_final: 0.7674 (p90) REVERT: B 413 ASN cc_start: 0.8514 (t0) cc_final: 0.8219 (t0) REVERT: B 452 ASP cc_start: 0.7868 (t0) cc_final: 0.7491 (t0) REVERT: B 472 LYS cc_start: 0.7890 (tppt) cc_final: 0.7466 (tppt) REVERT: B 532 ARG cc_start: 0.8372 (tpp80) cc_final: 0.8096 (ttp80) REVERT: B 673 ARG cc_start: 0.7522 (mtm-85) cc_final: 0.6747 (mtm-85) REVERT: B 707 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7579 (mm-30) REVERT: B 708 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8208 (ttmm) REVERT: B 713 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7537 (mm-30) REVERT: B 718 ARG cc_start: 0.8331 (mmt90) cc_final: 0.7928 (mmt90) REVERT: C 142 ASP cc_start: 0.7427 (p0) cc_final: 0.7205 (p0) REVERT: C 148 SER cc_start: 0.8437 (t) cc_final: 0.8101 (m) REVERT: C 331 TYR cc_start: 0.8292 (m-10) cc_final: 0.7956 (m-10) REVERT: C 364 ARG cc_start: 0.8104 (ttp-170) cc_final: 0.7855 (mtp180) REVERT: C 413 ASN cc_start: 0.8590 (t0) cc_final: 0.8296 (t0) REVERT: C 663 LEU cc_start: 0.6954 (mt) cc_final: 0.6582 (mp) REVERT: D 94 LYS cc_start: 0.8240 (mmmm) cc_final: 0.7702 (mmmm) REVERT: D 99 THR cc_start: 0.8557 (p) cc_final: 0.8262 (t) REVERT: D 152 THR cc_start: 0.8756 (t) cc_final: 0.8332 (p) REVERT: D 311 LYS cc_start: 0.8061 (tppt) cc_final: 0.7835 (ttmt) REVERT: D 331 TYR cc_start: 0.8448 (m-10) cc_final: 0.8072 (m-80) REVERT: D 502 GLN cc_start: 0.6805 (mm-40) cc_final: 0.6262 (tm-30) REVERT: D 551 GLN cc_start: 0.8409 (mp10) cc_final: 0.8047 (mp10) REVERT: D 686 PHE cc_start: 0.7809 (p90) cc_final: 0.7491 (p90) REVERT: D 694 THR cc_start: 0.8346 (m) cc_final: 0.8093 (p) REVERT: D 707 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7614 (mm-30) REVERT: D 708 LYS cc_start: 0.8485 (ttmm) cc_final: 0.8240 (ttmm) REVERT: D 713 GLU cc_start: 0.8083 (mp0) cc_final: 0.7490 (mp0) REVERT: D 735 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7633 (mm-30) REVERT: E 24 LYS cc_start: 0.8422 (ttpp) cc_final: 0.7978 (ttmm) REVERT: E 66 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7219 (mtt180) REVERT: E 86 ARG cc_start: 0.8175 (ttt90) cc_final: 0.7960 (ttt90) REVERT: E 200 ASP cc_start: 0.8132 (p0) cc_final: 0.7918 (p0) REVERT: E 201 ASP cc_start: 0.7735 (t0) cc_final: 0.7444 (t0) REVERT: E 253 GLU cc_start: 0.8272 (tt0) cc_final: 0.7816 (tt0) REVERT: E 255 LYS cc_start: 0.8537 (mttm) cc_final: 0.8169 (mttm) REVERT: F 56 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7648 (m-40) REVERT: F 86 ARG cc_start: 0.8101 (ttm110) cc_final: 0.7840 (ttm110) REVERT: F 107 ASP cc_start: 0.7520 (t0) cc_final: 0.7216 (t0) REVERT: F 201 ASP cc_start: 0.7983 (m-30) cc_final: 0.7664 (m-30) REVERT: F 237 LYS cc_start: 0.8600 (ptpt) cc_final: 0.8183 (ptmt) REVERT: F 242 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7958 (mt-10) REVERT: F 255 LYS cc_start: 0.8351 (mtpp) cc_final: 0.8116 (mtpp) REVERT: G 15 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6995 (mm-30) REVERT: G 24 LYS cc_start: 0.8333 (ttpp) cc_final: 0.8024 (ttmm) REVERT: G 95 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7954 (tm-30) REVERT: G 200 ASP cc_start: 0.7922 (p0) cc_final: 0.7674 (p0) REVERT: G 201 ASP cc_start: 0.7885 (m-30) cc_final: 0.7673 (m-30) REVERT: G 213 LEU cc_start: 0.8422 (mt) cc_final: 0.8164 (mt) REVERT: G 216 ASP cc_start: 0.8174 (m-30) cc_final: 0.7905 (m-30) REVERT: G 220 ASP cc_start: 0.8059 (m-30) cc_final: 0.7745 (m-30) REVERT: G 224 SER cc_start: 0.8762 (t) cc_final: 0.8265 (p) REVERT: G 255 LYS cc_start: 0.8531 (pttt) cc_final: 0.8160 (pttt) REVERT: G 323 ILE cc_start: 0.8413 (mm) cc_final: 0.8164 (mm) REVERT: H 49 LYS cc_start: 0.8297 (ptpt) cc_final: 0.8038 (pttt) REVERT: H 95 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7837 (tm-30) REVERT: H 213 LEU cc_start: 0.8385 (mt) cc_final: 0.8138 (mt) REVERT: H 224 SER cc_start: 0.8684 (t) cc_final: 0.8405 (p) REVERT: H 243 LYS cc_start: 0.8457 (mtmm) cc_final: 0.8221 (mttm) REVERT: H 244 GLU cc_start: 0.7607 (tp30) cc_final: 0.7266 (tt0) outliers start: 89 outliers final: 68 residues processed: 849 average time/residue: 0.2206 time to fit residues: 301.1859 Evaluate side-chains 869 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 798 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 540 THR Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain D residue 711 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 68 ASN Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 56 ASN Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 322 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 54 optimal weight: 0.8980 chunk 252 optimal weight: 0.2980 chunk 99 optimal weight: 0.7980 chunk 451 optimal weight: 20.0000 chunk 38 optimal weight: 0.2980 chunk 325 optimal weight: 0.9980 chunk 432 optimal weight: 0.9980 chunk 233 optimal weight: 0.2980 chunk 102 optimal weight: 4.9990 chunk 37 optimal weight: 0.4980 chunk 208 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 HIS B 65 ASN C 65 ASN E 56 ASN H 279 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.175363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.133045 restraints weight = 59126.144| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.92 r_work: 0.3418 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 46352 Z= 0.117 Angle : 0.484 8.004 64585 Z= 0.272 Chirality : 0.040 0.262 7494 Planarity : 0.003 0.060 6606 Dihedral : 21.135 172.022 10622 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.67 % Favored : 95.24 % Rotamer: Outliers : 1.78 % Allowed : 11.76 % Favored : 86.45 % 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: 0.90 (0.13), residues: 4368 helix: 1.73 (0.11), residues: 2251 sheet: 0.70 (0.23), residues: 562 loop : -1.15 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 673 TYR 0.016 0.001 TYR H 332 PHE 0.023 0.001 PHE D 725 TRP 0.013 0.001 TRP D 169 HIS 0.005 0.001 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (46352) covalent geometry : angle 0.48447 / 0.27 (64585) hydrogen bonds : bond 0.03446 / 2.29 ( 2003) hydrogen bonds : angle 3.88803 / 2.71 ( 5565) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 789 time to evaluate : 1.100 Fit side-chains REVERT: A 37 SER cc_start: 0.8364 (m) cc_final: 0.7970 (p) REVERT: A 81 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8210 (ttmm) REVERT: A 102 LYS cc_start: 0.8157 (tttt) cc_final: 0.7790 (tttm) REVERT: A 124 PHE cc_start: 0.8515 (m-80) cc_final: 0.8065 (m-10) REVERT: A 141 VAL cc_start: 0.8286 (m) cc_final: 0.7996 (t) REVERT: A 286 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7715 (mm-30) REVERT: A 302 ASN cc_start: 0.8490 (m-40) cc_final: 0.8096 (m-40) REVERT: A 305 LYS cc_start: 0.8535 (mtpp) cc_final: 0.8208 (mtpp) REVERT: A 529 LYS cc_start: 0.8455 (mmmt) cc_final: 0.8156 (mtpp) REVERT: A 551 GLN cc_start: 0.8417 (mp10) cc_final: 0.7892 (mp10) REVERT: A 582 MET cc_start: 0.5707 (mmp) cc_final: 0.5491 (mmp) REVERT: A 629 LYS cc_start: 0.7579 (tmtt) cc_final: 0.7307 (pttt) REVERT: A 726 ILE cc_start: 0.8693 (mm) cc_final: 0.8437 (mt) REVERT: B 21 ASP cc_start: 0.7732 (p0) cc_final: 0.7319 (p0) REVERT: B 94 LYS cc_start: 0.8260 (mmmm) cc_final: 0.8037 (mmmm) REVERT: B 123 SER cc_start: 0.8358 (m) cc_final: 0.8062 (p) REVERT: B 137 VAL cc_start: 0.8573 (p) cc_final: 0.8317 (t) REVERT: B 277 PHE cc_start: 0.8009 (p90) cc_final: 0.7623 (p90) REVERT: B 286 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7318 (mm-30) REVERT: B 413 ASN cc_start: 0.8491 (t0) cc_final: 0.8198 (t0) REVERT: B 452 ASP cc_start: 0.7827 (t0) cc_final: 0.7431 (t0) REVERT: B 472 LYS cc_start: 0.7881 (tppt) cc_final: 0.7454 (tppt) REVERT: B 532 ARG cc_start: 0.8327 (tpp80) cc_final: 0.8040 (ttp80) REVERT: B 641 GLU cc_start: 0.7493 (tp30) cc_final: 0.7129 (tp30) REVERT: B 673 ARG cc_start: 0.7439 (mtm-85) cc_final: 0.6675 (mtm-85) REVERT: B 707 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7568 (mm-30) REVERT: B 708 LYS cc_start: 0.8541 (ttmm) cc_final: 0.8191 (ttmm) REVERT: B 713 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7557 (mm-30) REVERT: B 718 ARG cc_start: 0.8325 (mmt90) cc_final: 0.7936 (mmt90) REVERT: C 142 ASP cc_start: 0.7434 (p0) cc_final: 0.7210 (p0) REVERT: C 148 SER cc_start: 0.8427 (t) cc_final: 0.8108 (m) REVERT: C 331 TYR cc_start: 0.8232 (m-10) cc_final: 0.7870 (m-80) REVERT: C 413 ASN cc_start: 0.8563 (t0) cc_final: 0.8252 (t0) REVERT: C 663 LEU cc_start: 0.6923 (mt) cc_final: 0.6531 (mp) REVERT: D 94 LYS cc_start: 0.8230 (mmmm) cc_final: 0.7892 (mtmt) REVERT: D 99 THR cc_start: 0.8532 (p) cc_final: 0.8251 (t) REVERT: D 152 THR cc_start: 0.8759 (t) cc_final: 0.8327 (p) REVERT: D 311 LYS cc_start: 0.8034 (tppt) cc_final: 0.7805 (ttmt) REVERT: D 331 TYR cc_start: 0.8459 (m-10) cc_final: 0.8090 (m-80) REVERT: D 502 GLN cc_start: 0.6788 (mm-40) cc_final: 0.6262 (tm-30) REVERT: D 551 GLN cc_start: 0.8386 (mp10) cc_final: 0.8040 (mp10) REVERT: D 686 PHE cc_start: 0.7746 (p90) cc_final: 0.7495 (p90) REVERT: D 694 THR cc_start: 0.8350 (m) cc_final: 0.8090 (p) REVERT: D 707 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7587 (mm-30) REVERT: D 708 LYS cc_start: 0.8447 (ttmm) cc_final: 0.8210 (ttmm) REVERT: D 713 GLU cc_start: 0.8071 (mp0) cc_final: 0.7492 (mp0) REVERT: D 735 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7631 (mm-30) REVERT: E 24 LYS cc_start: 0.8444 (ttpp) cc_final: 0.8134 (ttmm) REVERT: E 66 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7189 (mtt180) REVERT: E 86 ARG cc_start: 0.8149 (ttt90) cc_final: 0.7937 (ttt90) REVERT: E 201 ASP cc_start: 0.7722 (t0) cc_final: 0.7430 (t0) REVERT: E 253 GLU cc_start: 0.8249 (tt0) cc_final: 0.7802 (tt0) REVERT: E 255 LYS cc_start: 0.8521 (mttm) cc_final: 0.8145 (mttm) REVERT: E 332 TYR cc_start: 0.7958 (t80) cc_final: 0.7723 (t80) REVERT: E 367 LYS cc_start: 0.7709 (mtpp) cc_final: 0.7350 (mttm) REVERT: F 56 ASN cc_start: 0.7871 (OUTLIER) cc_final: 0.7606 (m-40) REVERT: F 86 ARG cc_start: 0.8100 (ttm110) cc_final: 0.7835 (ttm110) REVERT: F 201 ASP cc_start: 0.7912 (m-30) cc_final: 0.7566 (m-30) REVERT: F 237 LYS cc_start: 0.8590 (ptpt) cc_final: 0.8237 (ptmt) REVERT: F 242 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7935 (mt-10) REVERT: F 255 LYS cc_start: 0.8333 (mtpp) cc_final: 0.8103 (mtpp) REVERT: F 367 LYS cc_start: 0.7578 (mtpp) cc_final: 0.7144 (mttm) REVERT: G 15 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6986 (mm-30) REVERT: G 21 GLU cc_start: 0.7621 (pm20) cc_final: 0.7282 (pm20) REVERT: G 24 LYS cc_start: 0.8327 (ttpp) cc_final: 0.7969 (ttmm) REVERT: G 95 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7909 (tm-30) REVERT: G 213 LEU cc_start: 0.8408 (mt) cc_final: 0.8145 (mt) REVERT: G 216 ASP cc_start: 0.8169 (m-30) cc_final: 0.7824 (m-30) REVERT: G 220 ASP cc_start: 0.8039 (m-30) cc_final: 0.7713 (m-30) REVERT: G 224 SER cc_start: 0.8744 (t) cc_final: 0.8273 (p) REVERT: G 255 LYS cc_start: 0.8502 (pttt) cc_final: 0.8142 (pttt) REVERT: G 323 ILE cc_start: 0.8377 (mm) cc_final: 0.8125 (mm) REVERT: H 49 LYS cc_start: 0.8243 (ptpt) cc_final: 0.7984 (pttt) REVERT: H 95 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7806 (tm-30) REVERT: H 213 LEU cc_start: 0.8378 (mt) cc_final: 0.8120 (mt) REVERT: H 224 SER cc_start: 0.8661 (t) cc_final: 0.8405 (p) REVERT: H 243 LYS cc_start: 0.8428 (mtmm) cc_final: 0.8187 (mttm) REVERT: H 244 GLU cc_start: 0.7578 (tp30) cc_final: 0.7231 (tt0) outliers start: 71 outliers final: 61 residues processed: 817 average time/residue: 0.2211 time to fit residues: 289.7579 Evaluate side-chains 840 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 777 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 540 THR Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 68 ASN Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 56 ASN Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 322 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 212 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 435 optimal weight: 2.9990 chunk 410 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 467 optimal weight: 10.0000 chunk 154 optimal weight: 0.7980 chunk 297 optimal weight: 2.9990 chunk 59 optimal weight: 40.0000 chunk 145 optimal weight: 5.9990 chunk 259 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN C 65 ASN D 351 GLN E 56 ASN E 272 ASN G 26 ASN G 289 ASN G 362 GLN H 279 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.172745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.130007 restraints weight = 58746.951| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.93 r_work: 0.3370 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 46352 Z= 0.253 Angle : 0.560 13.454 64585 Z= 0.308 Chirality : 0.044 0.325 7494 Planarity : 0.003 0.038 6606 Dihedral : 21.126 173.564 10622 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.38 % Favored : 94.53 % Rotamer: Outliers : 1.76 % Allowed : 12.39 % Favored : 85.85 % 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: 0.63 (0.13), residues: 4368 helix: 1.43 (0.11), residues: 2276 sheet: 0.59 (0.23), residues: 552 loop : -1.18 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 20 TYR 0.024 0.002 TYR C 457 PHE 0.042 0.002 PHE B 355 TRP 0.010 0.002 TRP D 697 HIS 0.006 0.001 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.25 (46352) covalent geometry : angle 0.55951 / 0.31 (64585) hydrogen bonds : bond 0.04181 / 2.76 ( 2003) hydrogen bonds : angle 4.00633 / 2.79 ( 5565) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 799 time to evaluate : 1.098 Fit side-chains REVERT: A 37 SER cc_start: 0.8403 (m) cc_final: 0.8063 (p) REVERT: A 81 LYS cc_start: 0.8578 (ttpt) cc_final: 0.8228 (ttmm) REVERT: A 124 PHE cc_start: 0.8627 (m-80) cc_final: 0.8180 (m-10) REVERT: A 141 VAL cc_start: 0.8370 (m) cc_final: 0.8125 (t) REVERT: A 286 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7874 (mm-30) REVERT: A 302 ASN cc_start: 0.8525 (m-40) cc_final: 0.8301 (m-40) REVERT: A 305 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8234 (mtpp) REVERT: A 529 LYS cc_start: 0.8482 (mmmt) cc_final: 0.8177 (mtpp) REVERT: A 542 THR cc_start: 0.8432 (m) cc_final: 0.8219 (m) REVERT: A 551 GLN cc_start: 0.8431 (mp10) cc_final: 0.7919 (mp10) REVERT: A 582 MET cc_start: 0.5712 (mmp) cc_final: 0.5499 (mmp) REVERT: A 629 LYS cc_start: 0.7625 (tmtt) cc_final: 0.7344 (pttt) REVERT: A 726 ILE cc_start: 0.8713 (mm) cc_final: 0.8472 (mt) REVERT: B 21 ASP cc_start: 0.7708 (p0) cc_final: 0.7300 (p0) REVERT: B 94 LYS cc_start: 0.8283 (mmmm) cc_final: 0.7713 (mmmm) REVERT: B 123 SER cc_start: 0.8328 (m) cc_final: 0.8031 (p) REVERT: B 277 PHE cc_start: 0.8152 (p90) cc_final: 0.7796 (p90) REVERT: B 413 ASN cc_start: 0.8492 (t0) cc_final: 0.8199 (t0) REVERT: B 452 ASP cc_start: 0.7874 (t0) cc_final: 0.7471 (t0) REVERT: B 472 LYS cc_start: 0.7897 (tppt) cc_final: 0.7477 (tppt) REVERT: B 532 ARG cc_start: 0.8399 (tpp80) cc_final: 0.8122 (ttp80) REVERT: B 673 ARG cc_start: 0.7588 (mtm-85) cc_final: 0.6791 (mtm-85) REVERT: B 707 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7612 (mm-30) REVERT: B 708 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8207 (ttmm) REVERT: B 713 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7641 (mm-30) REVERT: B 718 ARG cc_start: 0.8358 (mmt90) cc_final: 0.7996 (mmt90) REVERT: C 142 ASP cc_start: 0.7466 (p0) cc_final: 0.7255 (p0) REVERT: C 148 SER cc_start: 0.8438 (t) cc_final: 0.8097 (m) REVERT: C 331 TYR cc_start: 0.8318 (m-10) cc_final: 0.8017 (m-10) REVERT: C 413 ASN cc_start: 0.8587 (t0) cc_final: 0.8329 (t0) REVERT: D 94 LYS cc_start: 0.8220 (mmmm) cc_final: 0.7803 (mtmm) REVERT: D 152 THR cc_start: 0.8755 (t) cc_final: 0.8324 (p) REVERT: D 286 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7431 (mp0) REVERT: D 311 LYS cc_start: 0.8074 (tppt) cc_final: 0.7867 (ttmt) REVERT: D 331 TYR cc_start: 0.8490 (m-10) cc_final: 0.8134 (m-80) REVERT: D 502 GLN cc_start: 0.6920 (mm-40) cc_final: 0.6420 (tm-30) REVERT: D 551 GLN cc_start: 0.8443 (mp10) cc_final: 0.8076 (mp10) REVERT: D 694 THR cc_start: 0.8387 (m) cc_final: 0.8118 (p) REVERT: D 707 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7670 (mm-30) REVERT: D 713 GLU cc_start: 0.8115 (mp0) cc_final: 0.7418 (mp0) REVERT: D 735 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7740 (mm-30) REVERT: E 24 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8186 (ttmm) REVERT: E 86 ARG cc_start: 0.8172 (ttt90) cc_final: 0.7956 (ttt90) REVERT: E 180 MET cc_start: 0.8340 (tpp) cc_final: 0.7708 (tpp) REVERT: E 201 ASP cc_start: 0.7692 (t0) cc_final: 0.7437 (t0) REVERT: E 253 GLU cc_start: 0.8286 (tt0) cc_final: 0.7836 (tt0) REVERT: E 255 LYS cc_start: 0.8549 (mttm) cc_final: 0.8179 (mttm) REVERT: F 56 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7643 (m-40) REVERT: F 86 ARG cc_start: 0.8134 (ttm110) cc_final: 0.7871 (ttm110) REVERT: F 130 ASP cc_start: 0.7908 (t0) cc_final: 0.7553 (t0) REVERT: F 181 ASP cc_start: 0.8521 (m-30) cc_final: 0.8258 (m-30) REVERT: F 237 LYS cc_start: 0.8612 (ptpt) cc_final: 0.8221 (ptmt) REVERT: F 242 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7974 (mt-10) REVERT: F 255 LYS cc_start: 0.8379 (mtpp) cc_final: 0.8148 (mtpp) REVERT: G 15 GLU cc_start: 0.7270 (mm-30) cc_final: 0.7012 (mm-30) REVERT: G 21 GLU cc_start: 0.7686 (pm20) cc_final: 0.7362 (pm20) REVERT: G 24 LYS cc_start: 0.8332 (ttpp) cc_final: 0.8006 (ttmm) REVERT: G 95 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7964 (tm-30) REVERT: G 196 SER cc_start: 0.8365 (t) cc_final: 0.8044 (m) REVERT: G 213 LEU cc_start: 0.8437 (mt) cc_final: 0.8182 (mt) REVERT: G 216 ASP cc_start: 0.8167 (m-30) cc_final: 0.7896 (m-30) REVERT: G 220 ASP cc_start: 0.8009 (m-30) cc_final: 0.7707 (m-30) REVERT: G 224 SER cc_start: 0.8788 (t) cc_final: 0.8271 (p) REVERT: G 255 LYS cc_start: 0.8531 (pttt) cc_final: 0.8157 (pttt) REVERT: G 323 ILE cc_start: 0.8428 (mm) cc_final: 0.8191 (mm) REVERT: H 49 LYS cc_start: 0.8329 (ptpt) cc_final: 0.8084 (pttt) REVERT: H 95 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7820 (tm-30) REVERT: H 213 LEU cc_start: 0.8383 (mt) cc_final: 0.8138 (mt) REVERT: H 224 SER cc_start: 0.8718 (t) cc_final: 0.8420 (p) REVERT: H 243 LYS cc_start: 0.8463 (mtmm) cc_final: 0.8238 (mttm) REVERT: H 244 GLU cc_start: 0.7642 (tp30) cc_final: 0.7305 (tt0) REVERT: H 266 LEU cc_start: 0.8268 (mp) cc_final: 0.7976 (mt) outliers start: 70 outliers final: 58 residues processed: 827 average time/residue: 0.1953 time to fit residues: 258.3521 Evaluate side-chains 847 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 788 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 540 THR Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 68 ASN Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 56 ASN Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 322 LEU Chi-restraints excluded: chain H residue 368 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 103 optimal weight: 0.0370 chunk 274 optimal weight: 9.9990 chunk 251 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 255 optimal weight: 0.5980 chunk 219 optimal weight: 1.9990 chunk 434 optimal weight: 0.9990 chunk 353 optimal weight: 0.9990 chunk 277 optimal weight: 20.0000 chunk 252 optimal weight: 0.6980 chunk 238 optimal weight: 10.0000 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 ASN C 65 ASN D 65 ASN E 56 ASN G 362 GLN H 279 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.175117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.132715 restraints weight = 59005.739| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.92 r_work: 0.3394 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 46352 Z= 0.127 Angle : 0.501 11.432 64585 Z= 0.280 Chirality : 0.040 0.292 7494 Planarity : 0.003 0.040 6606 Dihedral : 21.115 172.559 10622 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.95 % Favored : 94.96 % Rotamer: Outliers : 1.46 % Allowed : 13.20 % Favored : 85.34 % 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: 0.79 (0.13), residues: 4368 helix: 1.63 (0.11), residues: 2248 sheet: 0.60 (0.23), residues: 562 loop : -1.16 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 20 TYR 0.017 0.001 TYR H 332 PHE 0.022 0.001 PHE D 725 TRP 0.011 0.001 TRP D 697 HIS 0.006 0.001 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (46352) covalent geometry : angle 0.50135 / 0.28 (64585) hydrogen bonds : bond 0.03556 / 2.36 ( 2003) hydrogen bonds : angle 3.93724 / 2.74 ( 5565) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 791 time to evaluate : 1.013 Fit side-chains REVERT: A 37 SER cc_start: 0.8380 (m) cc_final: 0.7987 (p) REVERT: A 81 LYS cc_start: 0.8538 (ttpt) cc_final: 0.8205 (ttmm) REVERT: A 124 PHE cc_start: 0.8564 (m-80) cc_final: 0.8116 (m-10) REVERT: A 286 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7745 (mm-30) REVERT: A 302 ASN cc_start: 0.8512 (m-40) cc_final: 0.8293 (m-40) REVERT: A 305 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8216 (mtpp) REVERT: A 529 LYS cc_start: 0.8459 (mmmt) cc_final: 0.8158 (mtpp) REVERT: A 551 GLN cc_start: 0.8406 (mp10) cc_final: 0.7865 (mp10) REVERT: A 582 MET cc_start: 0.5717 (mmp) cc_final: 0.5505 (mmp) REVERT: A 629 LYS cc_start: 0.7617 (tmtt) cc_final: 0.7335 (pttt) REVERT: A 726 ILE cc_start: 0.8693 (mm) cc_final: 0.8440 (mt) REVERT: B 21 ASP cc_start: 0.7722 (p0) cc_final: 0.7311 (p0) REVERT: B 94 LYS cc_start: 0.8284 (mmmm) cc_final: 0.7709 (mmmm) REVERT: B 123 SER cc_start: 0.8349 (m) cc_final: 0.8046 (p) REVERT: B 129 LEU cc_start: 0.8694 (tt) cc_final: 0.8464 (tp) REVERT: B 277 PHE cc_start: 0.8086 (p90) cc_final: 0.7694 (p90) REVERT: B 286 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7329 (mm-30) REVERT: B 413 ASN cc_start: 0.8479 (t0) cc_final: 0.8183 (t0) REVERT: B 452 ASP cc_start: 0.7815 (t0) cc_final: 0.7452 (t0) REVERT: B 472 LYS cc_start: 0.7866 (tppt) cc_final: 0.7434 (tppt) REVERT: B 532 ARG cc_start: 0.8344 (tpp80) cc_final: 0.8047 (ttp80) REVERT: B 641 GLU cc_start: 0.7411 (tp30) cc_final: 0.7062 (tp30) REVERT: B 673 ARG cc_start: 0.7507 (mtm-85) cc_final: 0.6720 (mtm-85) REVERT: B 707 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7569 (mm-30) REVERT: B 708 LYS cc_start: 0.8559 (ttmm) cc_final: 0.8213 (ttmm) REVERT: B 713 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7596 (mm-30) REVERT: B 718 ARG cc_start: 0.8338 (mmt90) cc_final: 0.7942 (mmt90) REVERT: C 148 SER cc_start: 0.8424 (t) cc_final: 0.8095 (m) REVERT: C 331 TYR cc_start: 0.8252 (m-10) cc_final: 0.7918 (m-80) REVERT: C 413 ASN cc_start: 0.8578 (t0) cc_final: 0.8266 (t0) REVERT: D 94 LYS cc_start: 0.8211 (mmmm) cc_final: 0.7858 (mtmt) REVERT: D 152 THR cc_start: 0.8754 (t) cc_final: 0.8312 (p) REVERT: D 311 LYS cc_start: 0.8033 (tppt) cc_final: 0.7804 (ttmt) REVERT: D 331 TYR cc_start: 0.8462 (m-10) cc_final: 0.8110 (m-80) REVERT: D 385 GLU cc_start: 0.8217 (mp0) cc_final: 0.7966 (mp0) REVERT: D 502 GLN cc_start: 0.6943 (mm-40) cc_final: 0.6456 (tm-30) REVERT: D 551 GLN cc_start: 0.8425 (mp10) cc_final: 0.8063 (mp10) REVERT: D 694 THR cc_start: 0.8375 (m) cc_final: 0.8109 (p) REVERT: D 707 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7640 (mm-30) REVERT: D 713 GLU cc_start: 0.8095 (mp0) cc_final: 0.7566 (mp0) REVERT: D 735 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7664 (mm-30) REVERT: E 24 LYS cc_start: 0.8463 (ttpp) cc_final: 0.8045 (ttmm) REVERT: E 66 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7218 (mtt180) REVERT: E 86 ARG cc_start: 0.8107 (ttt90) cc_final: 0.7891 (ttt90) REVERT: E 180 MET cc_start: 0.8337 (tpp) cc_final: 0.7726 (tpp) REVERT: E 201 ASP cc_start: 0.7736 (t0) cc_final: 0.7449 (t0) REVERT: E 253 GLU cc_start: 0.8277 (tt0) cc_final: 0.7829 (tt0) REVERT: E 255 LYS cc_start: 0.8538 (mttm) cc_final: 0.8164 (mttm) REVERT: E 367 LYS cc_start: 0.7713 (mtpp) cc_final: 0.7343 (mttp) REVERT: F 56 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7609 (m-40) REVERT: F 86 ARG cc_start: 0.8130 (ttm110) cc_final: 0.7855 (ttm110) REVERT: F 130 ASP cc_start: 0.7870 (t0) cc_final: 0.7538 (t0) REVERT: F 181 ASP cc_start: 0.8511 (m-30) cc_final: 0.8233 (m-30) REVERT: F 237 LYS cc_start: 0.8583 (ptpt) cc_final: 0.8211 (ptmt) REVERT: F 255 LYS cc_start: 0.8365 (mtpp) cc_final: 0.8126 (mtpp) REVERT: G 15 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6963 (mm-30) REVERT: G 21 GLU cc_start: 0.7663 (pm20) cc_final: 0.7352 (pm20) REVERT: G 24 LYS cc_start: 0.8327 (ttpp) cc_final: 0.8024 (ttmm) REVERT: G 95 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7917 (tm-30) REVERT: G 213 LEU cc_start: 0.8396 (mt) cc_final: 0.8153 (mt) REVERT: G 216 ASP cc_start: 0.8182 (m-30) cc_final: 0.7879 (m-30) REVERT: G 220 ASP cc_start: 0.7994 (m-30) cc_final: 0.7692 (m-30) REVERT: G 224 SER cc_start: 0.8770 (t) cc_final: 0.8287 (p) REVERT: G 255 LYS cc_start: 0.8520 (pttt) cc_final: 0.8144 (pttt) REVERT: G 323 ILE cc_start: 0.8393 (mm) cc_final: 0.8146 (mm) REVERT: H 49 LYS cc_start: 0.8263 (ptpt) cc_final: 0.8017 (pttt) REVERT: H 95 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7804 (tm-30) REVERT: H 213 LEU cc_start: 0.8369 (mt) cc_final: 0.8111 (mt) REVERT: H 224 SER cc_start: 0.8665 (t) cc_final: 0.8397 (p) REVERT: H 243 LYS cc_start: 0.8444 (mtmm) cc_final: 0.8210 (mttm) REVERT: H 244 GLU cc_start: 0.7629 (tp30) cc_final: 0.7281 (tt0) outliers start: 58 outliers final: 52 residues processed: 811 average time/residue: 0.1911 time to fit residues: 249.5170 Evaluate side-chains 829 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 775 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 540 THR Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 68 ASN Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 56 ASN Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 309 LYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 322 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 155 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 127 optimal weight: 0.0020 chunk 258 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 450 optimal weight: 9.9990 chunk 411 optimal weight: 0.9990 chunk 383 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 ASN C 65 ASN D 65 ASN E 56 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.174167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.131281 restraints weight = 58927.628| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.82 r_work: 0.3379 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 46352 Z= 0.171 Angle : 0.522 11.302 64585 Z= 0.289 Chirality : 0.041 0.293 7494 Planarity : 0.003 0.038 6606 Dihedral : 21.097 172.705 10622 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.24 % Favored : 94.67 % Rotamer: Outliers : 1.58 % Allowed : 13.00 % Favored : 85.42 % 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: 0.77 (0.13), residues: 4368 helix: 1.61 (0.11), residues: 2248 sheet: 0.58 (0.23), residues: 562 loop : -1.17 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 20 TYR 0.019 0.001 TYR D 64 PHE 0.026 0.001 PHE B 355 TRP 0.008 0.001 TRP D 697 HIS 0.006 0.001 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (46352) covalent geometry : angle 0.52250 / 0.29 (64585) hydrogen bonds : bond 0.03758 / 2.49 ( 2003) hydrogen bonds : angle 3.93834 / 2.74 ( 5565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12261.72 seconds wall clock time: 209 minutes 29.68 seconds (12569.68 seconds total)