Starting phenix.real_space_refine on Sun Feb 8 10:29:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p4k_71272/02_2026/9p4k_71272.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p4k_71272/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9p4k_71272/02_2026/9p4k_71272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p4k_71272/02_2026/9p4k_71272.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p4k_71272/02_2026/9p4k_71272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p4k_71272/02_2026/9p4k_71272.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 9.49, per 1000 atoms: 0.21 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: 3.91 Conformation dependent library (CDL) restraints added in 1.6 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: 5.67 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: 11.37 Time building geometry restraints manager: 5.13 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=" 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=" 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=" CA SER E 61 " pdb=" CB SER E 61 " ideal model delta sigma weight residual 1.528 1.470 0.059 1.66e-02 3.63e+03 1.24e+01 bond pdb=" CA GLY E 88 " pdb=" C GLY E 88 " ideal model delta sigma weight residual 1.518 1.489 0.028 1.00e-02 1.00e+04 8.08e+00 bond pdb=" N VAL E 85 " pdb=" CA VAL E 85 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.14e-02 7.69e+03 5.83e+00 ... (remaining 46347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 63343 1.68 - 3.37: 1068 3.37 - 5.05: 144 5.05 - 6.74: 26 6.74 - 8.42: 4 Bond angle restraints: 64585 Sorted by residual: 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=" N ASN E 68 " pdb=" CA ASN E 68 " pdb=" C ASN E 68 " ideal model delta sigma weight residual 113.15 108.06 5.09 1.19e+00 7.06e-01 1.83e+01 angle pdb=" N LEU E 65 " pdb=" CA LEU E 65 " pdb=" C LEU E 65 " ideal model delta sigma weight residual 111.82 107.33 4.49 1.16e+00 7.43e-01 1.50e+01 angle pdb=" N SER E 61 " pdb=" CA SER E 61 " pdb=" C SER E 61 " ideal model delta sigma weight residual 111.82 107.36 4.46 1.16e+00 7.43e-01 1.48e+01 angle pdb=" CA PHE E 71 " pdb=" CB PHE E 71 " pdb=" CG PHE E 71 " ideal model delta sigma weight residual 113.80 117.42 -3.62 1.00e+00 1.00e+00 1.31e+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 - 0.056: 6384 0.056 - 0.111: 949 0.111 - 0.167: 147 0.167 - 0.222: 9 0.222 - 0.278: 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 2.35 -2.62 -0.28 2.00e-01 2.50e+01 1.93e+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 2.35 -2.61 -0.27 2.00e-01 2.50e+01 1.76e+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 2.35 -2.59 -0.24 2.00e-01 2.50e+01 1.45e+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: 12.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.180 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 45.020 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.100 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 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 : 0.002 0.066 46352 Z= 0.123 Angle : 0.522 8.419 64585 Z= 0.286 Chirality : 0.041 0.278 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 covalent geometry : bond 0.00241 (46352) covalent geometry : angle 0.52182 (64585) hydrogen bonds : bond 0.12187 ( 2003) hydrogen bonds : angle 4.94109 ( 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 : 1.507 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: 0.2979 time to fit residues: 420.6259 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 : 1.425 ------------------------------------------------------------------------------- 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: 9.9990 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: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 350 GLN B 26 ASN B 65 ASN B 341 GLN B 384 ASN C 170 ASN ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN D 95 HIS ** D 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 ASN E 68 ASN E 113 ASN E 272 ASN F 26 ASN F 38 ASN G 289 ASN H 258 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.172784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.129890 restraints weight = 59176.083| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.80 r_work: 0.3369 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 46352 Z= 0.323 Angle : 0.639 8.608 64585 Z= 0.338 Chirality : 0.046 0.247 7494 Planarity : 0.004 0.040 6606 Dihedral : 21.421 177.159 10624 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.61 % Favored : 94.30 % Rotamer: Outliers : 1.99 % Allowed : 6.13 % Favored : 91.88 % 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: 0.47 (0.13), residues: 4368 helix: 1.24 (0.11), residues: 2252 sheet: 0.83 (0.23), residues: 552 loop : -1.25 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 673 TYR 0.032 0.003 TYR C 457 PHE 0.053 0.003 PHE B 355 TRP 0.010 0.002 TRP B 559 HIS 0.009 0.002 HIS H 97 Details of bonding type rmsd covalent geometry : bond 0.00766 (46352) covalent geometry : angle 0.63856 (64585) hydrogen bonds : bond 0.04983 ( 2003) hydrogen bonds : angle 4.31404 ( 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 953 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 874 time to evaluate : 1.533 Fit side-chains REVERT: A 37 SER cc_start: 0.8424 (m) cc_final: 0.8090 (p) REVERT: A 81 LYS cc_start: 0.8597 (ttpt) cc_final: 0.8243 (ttmm) REVERT: A 87 LYS cc_start: 0.8084 (mmtp) cc_final: 0.7754 (mmtp) REVERT: A 94 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7724 (mtmm) REVERT: A 102 LYS cc_start: 0.8179 (tttt) cc_final: 0.7822 (tttm) REVERT: A 141 VAL cc_start: 0.8265 (m) cc_final: 0.7994 (t) REVERT: A 286 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7768 (mm-30) REVERT: A 302 ASN cc_start: 0.8526 (m-40) cc_final: 0.8308 (m-40) REVERT: A 305 LYS cc_start: 0.8544 (mtpp) cc_final: 0.8211 (mtpp) REVERT: A 350 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8411 (pp30) REVERT: A 529 LYS cc_start: 0.8474 (mmmt) cc_final: 0.8210 (mtpp) REVERT: A 548 ILE cc_start: 0.8033 (pt) cc_final: 0.7821 (pt) REVERT: A 551 GLN cc_start: 0.8453 (mp10) cc_final: 0.7956 (mp10) REVERT: A 582 MET cc_start: 0.5678 (mmp) cc_final: 0.5409 (mmp) REVERT: A 629 LYS cc_start: 0.7605 (tmtt) cc_final: 0.7347 (pttt) REVERT: A 641 GLU cc_start: 0.7524 (tp30) cc_final: 0.7241 (tp30) REVERT: A 726 ILE cc_start: 0.8706 (mm) cc_final: 0.8472 (mt) REVERT: B 21 ASP cc_start: 0.7709 (p0) cc_final: 0.7281 (p0) REVERT: B 25 ILE cc_start: 0.8630 (mm) cc_final: 0.8386 (mm) REVERT: B 94 LYS cc_start: 0.8219 (mmmm) cc_final: 0.7605 (mmmm) REVERT: B 123 SER cc_start: 0.8311 (m) cc_final: 0.8005 (p) REVERT: B 276 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7298 (mm-30) REVERT: B 277 PHE cc_start: 0.8127 (p90) cc_final: 0.7712 (p90) REVERT: B 286 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7244 (mm-30) REVERT: B 305 LYS cc_start: 0.8625 (mtpt) cc_final: 0.8277 (mtmm) REVERT: B 398 GLU cc_start: 0.7819 (tt0) cc_final: 0.7607 (tt0) REVERT: B 402 GLU cc_start: 0.7835 (mp0) cc_final: 0.7332 (mp0) REVERT: B 452 ASP cc_start: 0.7964 (t0) cc_final: 0.7602 (t0) REVERT: B 532 ARG cc_start: 0.8386 (tpp80) cc_final: 0.8138 (ttp80) REVERT: B 673 ARG cc_start: 0.7508 (mtm-85) cc_final: 0.6809 (mtm-85) REVERT: B 707 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7542 (mm-30) REVERT: B 708 LYS cc_start: 0.8520 (ttmm) cc_final: 0.8160 (ttmm) REVERT: B 713 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7631 (mm-30) REVERT: B 718 ARG cc_start: 0.8337 (mmt90) cc_final: 0.8044 (mmt90) REVERT: C 37 SER cc_start: 0.8417 (m) cc_final: 0.8194 (p) REVERT: C 142 ASP cc_start: 0.7437 (p0) cc_final: 0.7201 (p0) REVERT: C 148 SER cc_start: 0.8501 (t) cc_final: 0.8117 (m) REVERT: C 331 TYR cc_start: 0.8346 (m-10) cc_final: 0.8022 (m-10) REVERT: C 364 ARG cc_start: 0.8168 (ttp-170) cc_final: 0.7896 (mtp180) REVERT: C 532 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8042 (mmm-85) REVERT: D 94 LYS cc_start: 0.8247 (mmmm) cc_final: 0.7912 (mtmt) REVERT: D 99 THR cc_start: 0.8576 (p) cc_final: 0.8309 (t) REVERT: D 140 SER cc_start: 0.8738 (m) cc_final: 0.8238 (p) REVERT: D 152 THR cc_start: 0.8753 (t) cc_final: 0.8350 (p) REVERT: D 331 TYR cc_start: 0.8331 (m-10) cc_final: 0.7923 (m-80) REVERT: D 348 LYS cc_start: 0.8636 (ptmt) cc_final: 0.8427 (pttm) REVERT: D 502 GLN cc_start: 0.6714 (mm-40) cc_final: 0.6151 (tm-30) REVERT: D 551 GLN cc_start: 0.8374 (mp10) cc_final: 0.7999 (mp10) REVERT: D 552 SER cc_start: 0.8369 (t) cc_final: 0.8133 (p) REVERT: D 568 MET cc_start: 0.5409 (mpp) cc_final: 0.4544 (mmt) REVERT: D 686 PHE cc_start: 0.7851 (p90) cc_final: 0.7476 (p90) REVERT: D 707 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7622 (mm-30) REVERT: D 708 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8216 (ttmm) REVERT: D 713 GLU cc_start: 0.8068 (mp0) cc_final: 0.7447 (mp0) REVERT: D 735 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7696 (mm-30) REVERT: E 24 LYS cc_start: 0.8490 (ttpp) cc_final: 0.8137 (ttmm) REVERT: E 45 SER cc_start: 0.8757 (m) cc_final: 0.8533 (t) REVERT: E 86 ARG cc_start: 0.8207 (ttt90) cc_final: 0.7988 (ttt90) REVERT: E 205 SER cc_start: 0.8679 (t) cc_final: 0.8474 (t) REVERT: E 253 GLU cc_start: 0.8239 (tt0) cc_final: 0.7826 (tt0) REVERT: E 255 LYS cc_start: 0.8492 (mttm) cc_final: 0.8157 (mttm) REVERT: F 10 ASP cc_start: 0.8036 (p0) cc_final: 0.7785 (p0) REVERT: F 86 ARG cc_start: 0.8150 (ttm110) cc_final: 0.7855 (ttm110) REVERT: F 107 ASP cc_start: 0.7528 (t0) cc_final: 0.7273 (t0) REVERT: F 151 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7316 (mt-10) REVERT: F 196 SER cc_start: 0.8443 (t) cc_final: 0.8099 (p) REVERT: F 216 ASP cc_start: 0.8048 (m-30) cc_final: 0.7714 (m-30) REVERT: F 232 ASN cc_start: 0.8485 (m110) cc_final: 0.8274 (m-40) REVERT: F 237 LYS cc_start: 0.8579 (ptpt) cc_final: 0.8138 (ptmt) REVERT: F 255 LYS cc_start: 0.8340 (mtpp) cc_final: 0.8110 (mtpp) REVERT: G 15 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6985 (mm-30) REVERT: G 21 GLU cc_start: 0.7728 (pm20) cc_final: 0.7290 (pm20) REVERT: G 24 LYS cc_start: 0.8379 (ttpp) cc_final: 0.8058 (ttmm) REVERT: G 41 VAL cc_start: 0.8553 (t) cc_final: 0.8330 (p) REVERT: G 95 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8000 (tm-30) REVERT: G 107 ASP cc_start: 0.7637 (t0) cc_final: 0.7288 (t0) REVERT: G 196 SER cc_start: 0.8410 (t) cc_final: 0.8072 (p) REVERT: G 200 ASP cc_start: 0.7829 (p0) cc_final: 0.7570 (p0) REVERT: G 201 ASP cc_start: 0.7940 (m-30) cc_final: 0.7634 (m-30) REVERT: G 213 LEU cc_start: 0.8430 (mt) cc_final: 0.8172 (mt) REVERT: G 216 ASP cc_start: 0.8176 (m-30) cc_final: 0.7915 (m-30) REVERT: G 220 ASP cc_start: 0.7979 (m-30) cc_final: 0.7631 (m-30) REVERT: G 224 SER cc_start: 0.8798 (t) cc_final: 0.8235 (m) REVERT: G 255 LYS cc_start: 0.8566 (pttt) cc_final: 0.8184 (pttt) REVERT: H 95 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7818 (tm-30) REVERT: H 130 ASP cc_start: 0.7771 (t0) cc_final: 0.7474 (t0) REVERT: H 213 LEU cc_start: 0.8419 (mt) cc_final: 0.8167 (mt) REVERT: H 224 SER cc_start: 0.8719 (t) cc_final: 0.8397 (p) REVERT: H 243 LYS cc_start: 0.8463 (mtmm) cc_final: 0.8175 (mttm) REVERT: H 244 GLU cc_start: 0.7553 (tp30) cc_final: 0.7084 (tp30) REVERT: H 326 LEU cc_start: 0.8698 (mm) cc_final: 0.8388 (mt) outliers start: 79 outliers final: 47 residues processed: 902 average time/residue: 0.3014 time to fit residues: 432.1788 Evaluate side-chains 863 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 814 time to evaluate : 1.493 ------------------------------------------------------------------------------- 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 350 GLN Chi-restraints excluded: chain A residue 380 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 464 PHE Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain C residue 67 VAL 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 453 THR Chi-restraints excluded: chain C residue 532 ARG Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 40 LEU 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 440 LYS Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain F residue 25 GLU 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 39 LYS 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 G residue 336 LEU Chi-restraints excluded: chain G residue 368 ILE Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 216 ASP 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: 0.8980 chunk 79 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 317 optimal weight: 0.8980 chunk 358 optimal weight: 2.9990 chunk 363 optimal weight: 0.8980 chunk 378 optimal weight: 0.7980 chunk 417 optimal weight: 0.5980 chunk 213 optimal weight: 0.0170 chunk 127 optimal weight: 0.6980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 350 GLN A 558 ASN B 65 ASN C 231 ASN D 65 ASN D 88 ASN G 26 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.175126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.132662 restraints weight = 59107.681| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.94 r_work: 0.3396 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 46352 Z= 0.136 Angle : 0.499 7.599 64585 Z= 0.270 Chirality : 0.039 0.184 7494 Planarity : 0.003 0.034 6606 Dihedral : 21.218 174.342 10622 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.58 % Favored : 95.31 % Rotamer: Outliers : 1.84 % Allowed : 9.33 % Favored : 88.84 % 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: 0.74 (0.13), residues: 4368 helix: 1.54 (0.11), residues: 2256 sheet: 0.84 (0.23), residues: 550 loop : -1.22 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 532 TYR 0.017 0.001 TYR H 332 PHE 0.019 0.001 PHE C 464 TRP 0.008 0.001 TRP D 697 HIS 0.006 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00304 (46352) covalent geometry : angle 0.49923 (64585) hydrogen bonds : bond 0.03666 ( 2003) hydrogen bonds : angle 4.02385 ( 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 906 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 833 time to evaluate : 1.476 Fit side-chains REVERT: A 37 SER cc_start: 0.8375 (m) cc_final: 0.7979 (p) REVERT: A 81 LYS cc_start: 0.8549 (ttpt) cc_final: 0.8191 (ttmm) REVERT: A 87 LYS cc_start: 0.8040 (mmtp) cc_final: 0.7712 (mmtp) REVERT: A 102 LYS cc_start: 0.8165 (tttt) cc_final: 0.7934 (tttt) REVERT: A 286 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7725 (mm-30) REVERT: A 305 LYS cc_start: 0.8540 (mtpp) cc_final: 0.8218 (mtpp) REVERT: A 529 LYS cc_start: 0.8456 (mmmt) cc_final: 0.8171 (mtpp) REVERT: A 551 GLN cc_start: 0.8443 (mp10) cc_final: 0.7929 (mp10) REVERT: A 582 MET cc_start: 0.5684 (mmp) cc_final: 0.5448 (mmp) REVERT: A 629 LYS cc_start: 0.7587 (tmtt) cc_final: 0.7317 (pttt) REVERT: A 641 GLU cc_start: 0.7534 (tp30) cc_final: 0.7177 (tp30) REVERT: A 726 ILE cc_start: 0.8694 (mm) cc_final: 0.8433 (mt) REVERT: B 21 ASP cc_start: 0.7711 (p0) cc_final: 0.7301 (p0) REVERT: B 63 ASN cc_start: 0.8768 (m-40) cc_final: 0.8538 (m-40) REVERT: B 94 LYS cc_start: 0.8199 (mmmm) cc_final: 0.7589 (mmmm) REVERT: B 123 SER cc_start: 0.8377 (m) cc_final: 0.8064 (p) REVERT: B 137 VAL cc_start: 0.8648 (p) cc_final: 0.8399 (t) REVERT: B 277 PHE cc_start: 0.8051 (p90) cc_final: 0.7713 (p90) REVERT: B 286 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7277 (mm-30) REVERT: B 398 GLU cc_start: 0.7804 (tt0) cc_final: 0.7599 (tt0) REVERT: B 402 GLU cc_start: 0.7830 (mp0) cc_final: 0.7302 (mp0) REVERT: B 452 ASP cc_start: 0.7892 (t0) cc_final: 0.7532 (t0) REVERT: B 532 ARG cc_start: 0.8350 (tpp80) cc_final: 0.8073 (ttp80) REVERT: B 673 ARG cc_start: 0.7446 (mtm-85) cc_final: 0.6702 (mtm-85) REVERT: B 707 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7551 (mm-30) REVERT: B 708 LYS cc_start: 0.8539 (ttmm) cc_final: 0.8204 (ttmm) REVERT: B 713 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7576 (mm-30) REVERT: B 718 ARG cc_start: 0.8312 (mmt90) cc_final: 0.8008 (mmt90) REVERT: C 148 SER cc_start: 0.8445 (t) cc_final: 0.8103 (m) REVERT: C 154 TYR cc_start: 0.8220 (m-10) cc_final: 0.7985 (m-10) REVERT: C 331 TYR cc_start: 0.8233 (m-10) cc_final: 0.7812 (m-80) REVERT: C 364 ARG cc_start: 0.8085 (ttp-170) cc_final: 0.7809 (mtp180) REVERT: C 413 ASN cc_start: 0.8600 (t0) cc_final: 0.8299 (t0) REVERT: C 425 ASP cc_start: 0.7803 (t0) cc_final: 0.7541 (t0) REVERT: C 532 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8024 (mmm-85) REVERT: D 94 LYS cc_start: 0.8221 (mmmm) cc_final: 0.7884 (mtmt) REVERT: D 99 THR cc_start: 0.8548 (p) cc_final: 0.8283 (t) REVERT: D 152 THR cc_start: 0.8755 (t) cc_final: 0.8323 (p) REVERT: D 286 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7290 (mp0) REVERT: D 331 TYR cc_start: 0.8459 (m-10) cc_final: 0.8087 (m-80) REVERT: D 551 GLN cc_start: 0.8387 (mp10) cc_final: 0.8049 (mp10) REVERT: D 552 SER cc_start: 0.8391 (t) cc_final: 0.8129 (p) REVERT: D 629 LYS cc_start: 0.6479 (mtmt) cc_final: 0.5929 (mtmt) REVERT: D 641 GLU cc_start: 0.7051 (tp30) cc_final: 0.6780 (tp30) REVERT: D 686 PHE cc_start: 0.7765 (p90) cc_final: 0.7447 (p90) REVERT: D 694 THR cc_start: 0.8286 (m) cc_final: 0.8048 (p) REVERT: D 707 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7601 (mm-30) REVERT: D 708 LYS cc_start: 0.8451 (ttmm) cc_final: 0.8241 (ttmm) REVERT: D 713 GLU cc_start: 0.8047 (mp0) cc_final: 0.7401 (mp0) REVERT: D 735 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7740 (mm-30) REVERT: E 24 LYS cc_start: 0.8510 (ttpp) cc_final: 0.8051 (ttmm) REVERT: E 86 ARG cc_start: 0.8143 (ttt90) cc_final: 0.7916 (ttt90) REVERT: E 205 SER cc_start: 0.8720 (t) cc_final: 0.8500 (t) REVERT: E 253 GLU cc_start: 0.8302 (tt0) cc_final: 0.7830 (tt0) REVERT: E 255 LYS cc_start: 0.8521 (mttm) cc_final: 0.8159 (mttm) REVERT: E 332 TYR cc_start: 0.7972 (t80) cc_final: 0.7764 (t80) REVERT: F 56 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7647 (m-40) REVERT: F 86 ARG cc_start: 0.8093 (ttm110) cc_final: 0.7812 (ttm110) REVERT: F 107 ASP cc_start: 0.7552 (t0) cc_final: 0.7201 (t0) REVERT: F 201 ASP cc_start: 0.7913 (m-30) cc_final: 0.7515 (m-30) REVERT: F 216 ASP cc_start: 0.8066 (m-30) cc_final: 0.7798 (m-30) REVERT: F 237 LYS cc_start: 0.8501 (ptpt) cc_final: 0.8082 (ptmt) REVERT: F 255 LYS cc_start: 0.8335 (mtpp) cc_final: 0.8104 (mtpp) REVERT: G 15 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6940 (mm-30) REVERT: G 24 LYS cc_start: 0.8347 (ttpp) cc_final: 0.8029 (ttmm) REVERT: G 41 VAL cc_start: 0.8526 (t) cc_final: 0.8316 (p) REVERT: G 95 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7950 (tm-30) REVERT: G 107 ASP cc_start: 0.7529 (t0) cc_final: 0.7153 (t0) REVERT: G 200 ASP cc_start: 0.7832 (p0) cc_final: 0.7546 (p0) REVERT: G 201 ASP cc_start: 0.7942 (m-30) cc_final: 0.7644 (m-30) REVERT: G 213 LEU cc_start: 0.8422 (mt) cc_final: 0.8161 (mt) REVERT: G 216 ASP cc_start: 0.8199 (m-30) cc_final: 0.7931 (m-30) REVERT: G 220 ASP cc_start: 0.8054 (m-30) cc_final: 0.7765 (m-30) REVERT: G 224 SER cc_start: 0.8775 (t) cc_final: 0.8263 (p) REVERT: G 255 LYS cc_start: 0.8528 (pttt) cc_final: 0.8195 (pttt) REVERT: G 323 ILE cc_start: 0.8403 (mm) cc_final: 0.8147 (mm) REVERT: H 95 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7828 (tm-30) REVERT: H 130 ASP cc_start: 0.7762 (t0) cc_final: 0.7458 (t0) REVERT: H 213 LEU cc_start: 0.8382 (mt) cc_final: 0.8130 (mt) REVERT: H 224 SER cc_start: 0.8664 (t) cc_final: 0.8421 (p) REVERT: H 238 TYR cc_start: 0.8147 (t80) cc_final: 0.7922 (t80) REVERT: H 243 LYS cc_start: 0.8447 (mtmm) cc_final: 0.8210 (mttm) REVERT: H 244 GLU cc_start: 0.7596 (tp30) cc_final: 0.7245 (tt0) outliers start: 73 outliers final: 48 residues processed: 857 average time/residue: 0.2970 time to fit residues: 404.7009 Evaluate side-chains 860 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 810 time to evaluate : 1.529 ------------------------------------------------------------------------------- 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 473 MET Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 534 LEU 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 289 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 532 ARG 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 65 ASN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 422 ASP 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 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 65 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 315 LYS 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: 5.9990 chunk 110 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 96 optimal weight: 0.0970 chunk 299 optimal weight: 2.9990 chunk 386 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 267 HIS A 350 GLN B 65 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 ASN D 38 ASN D 65 ASN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN D 384 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.174436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.131933 restraints weight = 59212.351| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.78 r_work: 0.3398 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 46352 Z= 0.154 Angle : 0.503 8.951 64585 Z= 0.269 Chirality : 0.039 0.261 7494 Planarity : 0.003 0.034 6606 Dihedral : 21.115 175.446 10622 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.90 % Favored : 94.99 % Rotamer: Outliers : 1.94 % Allowed : 10.63 % Favored : 87.43 % 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: 0.76 (0.13), residues: 4368 helix: 1.55 (0.11), residues: 2272 sheet: 0.77 (0.23), residues: 550 loop : -1.20 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 86 TYR 0.016 0.001 TYR H 332 PHE 0.025 0.001 PHE B 355 TRP 0.007 0.001 TRP D 697 HIS 0.006 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00354 (46352) covalent geometry : angle 0.50307 (64585) hydrogen bonds : bond 0.03622 ( 2003) hydrogen bonds : angle 3.94784 ( 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 897 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 820 time to evaluate : 1.508 Fit side-chains REVERT: A 37 SER cc_start: 0.8370 (m) cc_final: 0.7989 (p) REVERT: A 81 LYS cc_start: 0.8552 (ttpt) cc_final: 0.8199 (ttmm) REVERT: A 102 LYS cc_start: 0.8174 (tttt) cc_final: 0.7884 (tttp) REVERT: A 124 PHE cc_start: 0.8564 (m-80) cc_final: 0.8347 (m-80) REVERT: A 141 VAL cc_start: 0.8311 (m) cc_final: 0.8020 (t) REVERT: A 286 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7715 (mm-30) REVERT: A 302 ASN cc_start: 0.8494 (m-40) cc_final: 0.8276 (m-40) REVERT: A 305 LYS cc_start: 0.8535 (mtpp) cc_final: 0.8208 (mtpp) REVERT: A 529 LYS cc_start: 0.8457 (mmmt) cc_final: 0.8192 (mtpp) REVERT: A 551 GLN cc_start: 0.8410 (mp10) cc_final: 0.7894 (mp10) REVERT: A 582 MET cc_start: 0.5689 (mmp) cc_final: 0.5468 (mmp) REVERT: A 629 LYS cc_start: 0.7593 (tmtt) cc_final: 0.7324 (pttt) REVERT: A 641 GLU cc_start: 0.7511 (tp30) cc_final: 0.7213 (tp30) REVERT: A 726 ILE cc_start: 0.8707 (mm) cc_final: 0.8453 (mt) REVERT: B 21 ASP cc_start: 0.7692 (p0) cc_final: 0.7275 (p0) REVERT: B 63 ASN cc_start: 0.8764 (m-40) cc_final: 0.8558 (m-40) REVERT: B 94 LYS cc_start: 0.8238 (mmmm) cc_final: 0.7638 (mmmm) REVERT: B 123 SER cc_start: 0.8351 (m) cc_final: 0.8071 (p) REVERT: B 137 VAL cc_start: 0.8617 (p) cc_final: 0.8385 (t) REVERT: B 277 PHE cc_start: 0.8024 (p90) cc_final: 0.7697 (p90) REVERT: B 286 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7255 (mm-30) REVERT: B 398 GLU cc_start: 0.7778 (tt0) cc_final: 0.7550 (tt0) REVERT: B 402 GLU cc_start: 0.7820 (mp0) cc_final: 0.7317 (mp0) REVERT: B 413 ASN cc_start: 0.8492 (t0) cc_final: 0.8189 (t0) REVERT: B 452 ASP cc_start: 0.7838 (t0) cc_final: 0.7415 (t0) REVERT: B 472 LYS cc_start: 0.7863 (tppt) cc_final: 0.7439 (tppt) REVERT: B 532 ARG cc_start: 0.8319 (tpp80) cc_final: 0.8049 (ttp80) REVERT: B 673 ARG cc_start: 0.7520 (mtm-85) cc_final: 0.6765 (mtm-85) REVERT: B 707 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7552 (mm-30) REVERT: B 708 LYS cc_start: 0.8540 (ttmm) cc_final: 0.8207 (ttmm) REVERT: B 713 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7530 (mm-30) REVERT: B 718 ARG cc_start: 0.8329 (mmt90) cc_final: 0.7958 (mmt90) REVERT: C 142 ASP cc_start: 0.7418 (p0) cc_final: 0.7106 (p0) REVERT: C 148 SER cc_start: 0.8443 (t) cc_final: 0.8095 (m) REVERT: C 331 TYR cc_start: 0.8257 (m-10) cc_final: 0.7902 (m-80) REVERT: C 413 ASN cc_start: 0.8595 (t0) cc_final: 0.8334 (t0) REVERT: C 425 ASP cc_start: 0.7738 (t0) cc_final: 0.7488 (t0) REVERT: D 94 LYS cc_start: 0.8215 (mmmm) cc_final: 0.7900 (mtmt) REVERT: D 99 THR cc_start: 0.8529 (p) cc_final: 0.8279 (t) REVERT: D 152 THR cc_start: 0.8755 (t) cc_final: 0.8328 (p) REVERT: D 286 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7316 (mp0) REVERT: D 331 TYR cc_start: 0.8417 (m-10) cc_final: 0.8046 (m-80) REVERT: D 469 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7626 (tp) REVERT: D 502 GLN cc_start: 0.6815 (mm-40) cc_final: 0.6300 (tm-30) REVERT: D 551 GLN cc_start: 0.8358 (mp10) cc_final: 0.7996 (mp10) REVERT: D 641 GLU cc_start: 0.6983 (tp30) cc_final: 0.6604 (tp30) REVERT: D 686 PHE cc_start: 0.7782 (p90) cc_final: 0.7473 (p90) REVERT: D 694 THR cc_start: 0.8290 (m) cc_final: 0.8055 (p) REVERT: D 707 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7598 (mm-30) REVERT: D 708 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8212 (ttmm) REVERT: D 713 GLU cc_start: 0.8061 (mp0) cc_final: 0.7421 (mp0) REVERT: D 735 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7710 (mm-30) REVERT: E 24 LYS cc_start: 0.8492 (ttpp) cc_final: 0.8076 (ttmm) REVERT: E 86 ARG cc_start: 0.8128 (ttt90) cc_final: 0.7907 (ttt90) REVERT: E 205 SER cc_start: 0.8690 (t) cc_final: 0.8440 (t) REVERT: E 253 GLU cc_start: 0.8275 (tt0) cc_final: 0.7827 (tt0) REVERT: E 255 LYS cc_start: 0.8507 (mttm) cc_final: 0.8136 (mttm) REVERT: E 367 LYS cc_start: 0.7721 (mtpp) cc_final: 0.7372 (mttm) REVERT: F 56 ASN cc_start: 0.7891 (OUTLIER) cc_final: 0.7615 (m-40) REVERT: F 86 ARG cc_start: 0.8064 (ttm110) cc_final: 0.7782 (ttm110) REVERT: F 107 ASP cc_start: 0.7491 (t0) cc_final: 0.7185 (t0) REVERT: F 130 ASP cc_start: 0.7859 (t0) cc_final: 0.7535 (t0) REVERT: F 201 ASP cc_start: 0.7923 (m-30) cc_final: 0.7622 (m-30) REVERT: F 216 ASP cc_start: 0.8023 (m-30) cc_final: 0.7785 (m-30) REVERT: F 237 LYS cc_start: 0.8495 (ptpt) cc_final: 0.8089 (ptmt) REVERT: F 242 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7925 (mt-10) REVERT: F 255 LYS cc_start: 0.8329 (mtpp) cc_final: 0.8102 (mtpp) REVERT: G 15 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6931 (mm-30) REVERT: G 21 GLU cc_start: 0.7642 (pm20) cc_final: 0.7365 (pm20) REVERT: G 24 LYS cc_start: 0.8347 (ttpp) cc_final: 0.7972 (ttmm) REVERT: G 41 VAL cc_start: 0.8544 (t) cc_final: 0.8312 (p) REVERT: G 95 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7943 (tm-30) REVERT: G 200 ASP cc_start: 0.7791 (p0) cc_final: 0.7564 (p0) REVERT: G 201 ASP cc_start: 0.7902 (m-30) cc_final: 0.7638 (m-30) REVERT: G 213 LEU cc_start: 0.8415 (mt) cc_final: 0.8146 (mt) REVERT: G 216 ASP cc_start: 0.8143 (m-30) cc_final: 0.7875 (m-30) REVERT: G 220 ASP cc_start: 0.8003 (m-30) cc_final: 0.7685 (m-30) REVERT: G 224 SER cc_start: 0.8753 (t) cc_final: 0.8265 (p) REVERT: G 255 LYS cc_start: 0.8509 (pttt) cc_final: 0.8185 (pttt) REVERT: G 323 ILE cc_start: 0.8405 (mm) cc_final: 0.8144 (mm) REVERT: H 95 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7814 (tm-30) REVERT: H 130 ASP cc_start: 0.7729 (t0) cc_final: 0.7446 (t0) REVERT: H 213 LEU cc_start: 0.8380 (mt) cc_final: 0.8130 (mt) REVERT: H 224 SER cc_start: 0.8673 (t) cc_final: 0.8419 (p) REVERT: H 243 LYS cc_start: 0.8444 (mtmm) cc_final: 0.8209 (mttm) REVERT: H 244 GLU cc_start: 0.7575 (tp30) cc_final: 0.7223 (tt0) outliers start: 77 outliers final: 51 residues processed: 847 average time/residue: 0.2857 time to fit residues: 385.1906 Evaluate side-chains 860 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 807 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 747 SER 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 471 GLU 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 464 PHE Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 282 VAL 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 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 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 43 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 56 ASN Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 36 ILE 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 285 ILE Chi-restraints excluded: chain H residue 315 LYS 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: 7.9990 chunk 348 optimal weight: 1.9990 chunk 319 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 410 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 234 optimal weight: 0.5980 chunk 184 optimal weight: 0.0980 chunk 352 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 38 ASN B 65 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.174741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.132131 restraints weight = 58884.201| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.94 r_work: 0.3352 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 46352 Z= 0.145 Angle : 0.495 7.569 64585 Z= 0.265 Chirality : 0.039 0.226 7494 Planarity : 0.003 0.032 6606 Dihedral : 21.041 175.713 10622 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.88 % Favored : 95.01 % Rotamer: Outliers : 2.06 % Allowed : 11.39 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.13), residues: 4368 helix: 1.67 (0.11), residues: 2248 sheet: 0.74 (0.23), residues: 562 loop : -1.18 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 673 TYR 0.022 0.001 TYR E 332 PHE 0.022 0.001 PHE B 355 TRP 0.007 0.001 TRP C 697 HIS 0.006 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00332 (46352) covalent geometry : angle 0.49506 (64585) hydrogen bonds : bond 0.03500 ( 2003) hydrogen bonds : angle 3.90355 ( 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 903 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 821 time to evaluate : 1.475 Fit side-chains REVERT: A 37 SER cc_start: 0.8380 (m) cc_final: 0.7974 (p) REVERT: A 81 LYS cc_start: 0.8517 (ttpt) cc_final: 0.8175 (ttmm) REVERT: A 124 PHE cc_start: 0.8577 (m-80) cc_final: 0.8286 (m-80) REVERT: A 286 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7528 (mm-30) REVERT: A 302 ASN cc_start: 0.8487 (m-40) cc_final: 0.8262 (m-40) REVERT: A 305 LYS cc_start: 0.8539 (mtpp) cc_final: 0.8210 (mtpp) REVERT: A 452 ASP cc_start: 0.8110 (t70) cc_final: 0.7704 (t0) REVERT: A 529 LYS cc_start: 0.8447 (mmmt) cc_final: 0.8138 (mtpp) REVERT: A 542 THR cc_start: 0.8435 (m) cc_final: 0.8213 (m) REVERT: A 551 GLN cc_start: 0.8411 (mp10) cc_final: 0.7844 (mp10) REVERT: A 582 MET cc_start: 0.5714 (mmp) cc_final: 0.5509 (mmp) REVERT: A 629 LYS cc_start: 0.7594 (tmtt) cc_final: 0.7317 (pttt) REVERT: A 726 ILE cc_start: 0.8681 (mm) cc_final: 0.8419 (mt) REVERT: B 21 ASP cc_start: 0.7731 (p0) cc_final: 0.7328 (p0) REVERT: B 63 ASN cc_start: 0.8778 (m-40) cc_final: 0.8566 (m-40) REVERT: B 94 LYS cc_start: 0.8213 (mmmm) cc_final: 0.7612 (mmmm) REVERT: B 123 SER cc_start: 0.8343 (m) cc_final: 0.8013 (p) REVERT: B 137 VAL cc_start: 0.8605 (p) cc_final: 0.8365 (t) REVERT: B 277 PHE cc_start: 0.8045 (p90) cc_final: 0.7719 (p90) REVERT: B 286 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7302 (mm-30) REVERT: B 398 GLU cc_start: 0.7796 (tt0) cc_final: 0.7546 (tt0) REVERT: B 402 GLU cc_start: 0.7850 (mp0) cc_final: 0.7327 (mp0) REVERT: B 413 ASN cc_start: 0.8508 (t0) cc_final: 0.8215 (t0) REVERT: B 452 ASP cc_start: 0.7880 (t0) cc_final: 0.7427 (t0) REVERT: B 472 LYS cc_start: 0.7873 (tppt) cc_final: 0.7444 (tppt) REVERT: B 532 ARG cc_start: 0.8327 (tpp80) cc_final: 0.8039 (ttp80) REVERT: B 673 ARG cc_start: 0.7539 (mtm-85) cc_final: 0.6765 (mtm-85) REVERT: B 707 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7591 (mm-30) REVERT: B 708 LYS cc_start: 0.8523 (ttmm) cc_final: 0.8174 (ttmm) REVERT: B 713 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7577 (mm-30) REVERT: B 718 ARG cc_start: 0.8335 (mmt90) cc_final: 0.7948 (mmt90) REVERT: C 20 ARG cc_start: 0.8337 (ttm110) cc_final: 0.8046 (ptp-110) REVERT: C 142 ASP cc_start: 0.7514 (p0) cc_final: 0.7281 (p0) REVERT: C 148 SER cc_start: 0.8421 (t) cc_final: 0.8081 (m) REVERT: C 331 TYR cc_start: 0.8291 (m-10) cc_final: 0.7964 (m-10) REVERT: C 413 ASN cc_start: 0.8604 (t0) cc_final: 0.8346 (t0) REVERT: C 425 ASP cc_start: 0.7763 (t0) cc_final: 0.7526 (t0) REVERT: D 94 LYS cc_start: 0.8202 (mmmm) cc_final: 0.7854 (mtmt) REVERT: D 152 THR cc_start: 0.8739 (t) cc_final: 0.8297 (p) REVERT: D 331 TYR cc_start: 0.8434 (m-10) cc_final: 0.8123 (m-80) REVERT: D 502 GLN cc_start: 0.6884 (mm-40) cc_final: 0.6368 (tm-30) REVERT: D 551 GLN cc_start: 0.8417 (mp10) cc_final: 0.8030 (mp10) REVERT: D 694 THR cc_start: 0.8331 (m) cc_final: 0.8120 (p) REVERT: D 707 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7599 (mm-30) REVERT: D 708 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8236 (ttmm) REVERT: D 713 GLU cc_start: 0.8098 (mp0) cc_final: 0.7479 (mp0) REVERT: D 735 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7672 (mm-30) REVERT: E 24 LYS cc_start: 0.8485 (ttpp) cc_final: 0.8061 (ttmm) REVERT: E 66 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7083 (mtt180) REVERT: E 86 ARG cc_start: 0.8160 (ttt90) cc_final: 0.7934 (ttt90) REVERT: E 205 SER cc_start: 0.8716 (t) cc_final: 0.8460 (t) REVERT: E 253 GLU cc_start: 0.8312 (tt0) cc_final: 0.7859 (tt0) REVERT: E 255 LYS cc_start: 0.8543 (mttm) cc_final: 0.8161 (mttm) REVERT: F 56 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7628 (m-40) REVERT: F 86 ARG cc_start: 0.8148 (ttm110) cc_final: 0.7862 (ttm110) REVERT: F 130 ASP cc_start: 0.7901 (t0) cc_final: 0.7567 (t0) REVERT: F 181 ASP cc_start: 0.8539 (m-30) cc_final: 0.8263 (m-30) REVERT: F 201 ASP cc_start: 0.7983 (m-30) cc_final: 0.7674 (m-30) REVERT: F 216 ASP cc_start: 0.8059 (m-30) cc_final: 0.7847 (m-30) REVERT: F 237 LYS cc_start: 0.8532 (ptpt) cc_final: 0.8191 (ptmt) REVERT: F 255 LYS cc_start: 0.8361 (mtpp) cc_final: 0.8119 (mtpp) REVERT: G 15 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6932 (mm-30) REVERT: G 21 GLU cc_start: 0.7734 (pm20) cc_final: 0.7476 (pm20) REVERT: G 24 LYS cc_start: 0.8320 (ttpp) cc_final: 0.7991 (ttmm) REVERT: G 95 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7938 (tm-30) REVERT: G 213 LEU cc_start: 0.8410 (mt) cc_final: 0.8149 (mt) REVERT: G 216 ASP cc_start: 0.8179 (m-30) cc_final: 0.7920 (m-30) REVERT: G 220 ASP cc_start: 0.8035 (m-30) cc_final: 0.7707 (m-30) REVERT: G 224 SER cc_start: 0.8767 (t) cc_final: 0.8273 (p) REVERT: G 255 LYS cc_start: 0.8546 (pttt) cc_final: 0.8148 (pttt) REVERT: G 323 ILE cc_start: 0.8399 (mm) cc_final: 0.8134 (mm) REVERT: H 45 SER cc_start: 0.8684 (m) cc_final: 0.8347 (t) REVERT: H 95 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7836 (tm-30) REVERT: H 130 ASP cc_start: 0.7772 (t0) cc_final: 0.7481 (t0) REVERT: H 213 LEU cc_start: 0.8382 (mt) cc_final: 0.8138 (mt) REVERT: H 224 SER cc_start: 0.8681 (t) cc_final: 0.8428 (p) REVERT: H 243 LYS cc_start: 0.8453 (mtmm) cc_final: 0.8206 (mttm) REVERT: H 244 GLU cc_start: 0.7638 (tp30) cc_final: 0.7270 (tt0) outliers start: 82 outliers final: 65 residues processed: 851 average time/residue: 0.2666 time to fit residues: 363.5230 Evaluate side-chains 864 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 797 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 65 ASN 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 473 MET Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 471 GLU 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 474 ILE Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 282 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 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 43 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 56 ASN Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain G residue 39 LYS 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 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 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 285 ILE Chi-restraints excluded: chain H residue 315 LYS 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: 0.4980 chunk 208 optimal weight: 0.6980 chunk 303 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 430 optimal weight: 2.9990 chunk 356 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 375 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 474 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 350 GLN B 65 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN H 206 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.174279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.131448 restraints weight = 59086.011| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.82 r_work: 0.3383 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 46352 Z= 0.165 Angle : 0.508 7.795 64585 Z= 0.272 Chirality : 0.039 0.206 7494 Planarity : 0.003 0.042 6606 Dihedral : 20.999 176.255 10622 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.88 % Favored : 95.01 % Rotamer: Outliers : 2.34 % Allowed : 11.76 % Favored : 85.90 % 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: 1.57 (0.11), residues: 2272 sheet: 0.71 (0.23), residues: 550 loop : -1.17 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 86 TYR 0.022 0.001 TYR E 332 PHE 0.023 0.001 PHE B 355 TRP 0.008 0.001 TRP D 173 HIS 0.006 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00382 (46352) covalent geometry : angle 0.50831 (64585) hydrogen bonds : bond 0.03617 ( 2003) hydrogen bonds : angle 3.92438 ( 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 899 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 806 time to evaluate : 1.193 Fit side-chains REVERT: A 37 SER cc_start: 0.8388 (m) cc_final: 0.8001 (p) REVERT: A 81 LYS cc_start: 0.8550 (ttpt) cc_final: 0.8192 (ttmm) REVERT: A 87 LYS cc_start: 0.7997 (mmtp) cc_final: 0.7773 (mmtp) REVERT: A 124 PHE cc_start: 0.8610 (m-80) cc_final: 0.8274 (m-80) REVERT: A 141 VAL cc_start: 0.8367 (m) cc_final: 0.8109 (t) REVERT: A 286 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7707 (mm-30) REVERT: A 302 ASN cc_start: 0.8508 (m-40) cc_final: 0.8285 (m-40) REVERT: A 305 LYS cc_start: 0.8565 (mtpp) cc_final: 0.8230 (mtpp) REVERT: A 452 ASP cc_start: 0.8114 (t70) cc_final: 0.7711 (t0) REVERT: A 529 LYS cc_start: 0.8456 (mmmt) cc_final: 0.8176 (mtpp) REVERT: A 542 THR cc_start: 0.8401 (m) cc_final: 0.8183 (m) REVERT: A 551 GLN cc_start: 0.8400 (mp10) cc_final: 0.7859 (mp10) REVERT: A 629 LYS cc_start: 0.7605 (tmtt) cc_final: 0.7345 (pttt) REVERT: A 726 ILE cc_start: 0.8701 (mm) cc_final: 0.8442 (mt) REVERT: B 21 ASP cc_start: 0.7697 (p0) cc_final: 0.7281 (p0) REVERT: B 63 ASN cc_start: 0.8779 (m-40) cc_final: 0.8548 (m-40) REVERT: B 94 LYS cc_start: 0.8236 (mmmm) cc_final: 0.7652 (mmmm) REVERT: B 123 SER cc_start: 0.8346 (m) cc_final: 0.8049 (p) REVERT: B 137 VAL cc_start: 0.8623 (p) cc_final: 0.8369 (t) REVERT: B 277 PHE cc_start: 0.8095 (p90) cc_final: 0.7767 (p90) REVERT: B 286 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7270 (mm-30) REVERT: B 398 GLU cc_start: 0.7773 (tt0) cc_final: 0.7510 (tt0) REVERT: B 402 GLU cc_start: 0.7834 (mp0) cc_final: 0.7328 (mp0) REVERT: B 413 ASN cc_start: 0.8496 (t0) cc_final: 0.8201 (t0) REVERT: B 452 ASP cc_start: 0.7828 (t0) cc_final: 0.7390 (t0) REVERT: B 472 LYS cc_start: 0.7844 (tppt) cc_final: 0.7417 (tppt) REVERT: B 532 ARG cc_start: 0.8370 (tpp80) cc_final: 0.8081 (ttp80) REVERT: B 673 ARG cc_start: 0.7580 (mtm-85) cc_final: 0.6790 (mtm-85) REVERT: B 707 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7599 (mm-30) REVERT: B 708 LYS cc_start: 0.8539 (ttmm) cc_final: 0.8189 (ttmm) REVERT: B 713 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7647 (mm-30) REVERT: B 718 ARG cc_start: 0.8334 (mmt90) cc_final: 0.7909 (mmt90) REVERT: C 20 ARG cc_start: 0.8323 (ttm110) cc_final: 0.8059 (ptp-110) REVERT: C 148 SER cc_start: 0.8425 (t) cc_final: 0.8088 (m) REVERT: C 331 TYR cc_start: 0.8301 (m-10) cc_final: 0.7945 (m-80) REVERT: C 413 ASN cc_start: 0.8592 (t0) cc_final: 0.8343 (t0) REVERT: C 425 ASP cc_start: 0.7742 (t0) cc_final: 0.7525 (t0) REVERT: D 87 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7822 (mtpt) REVERT: D 94 LYS cc_start: 0.8202 (mmmm) cc_final: 0.7880 (mtmt) REVERT: D 152 THR cc_start: 0.8750 (t) cc_final: 0.8305 (p) REVERT: D 286 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7333 (mp0) REVERT: D 331 TYR cc_start: 0.8401 (m-10) cc_final: 0.8079 (m-80) REVERT: D 502 GLN cc_start: 0.6940 (mm-40) cc_final: 0.6463 (tm-30) REVERT: D 551 GLN cc_start: 0.8424 (mp10) cc_final: 0.8054 (mp10) REVERT: D 694 THR cc_start: 0.8343 (m) cc_final: 0.8126 (p) REVERT: D 707 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7628 (mm-30) REVERT: D 708 LYS cc_start: 0.8466 (ttmm) cc_final: 0.8233 (ttmm) REVERT: D 713 GLU cc_start: 0.8086 (mp0) cc_final: 0.7429 (mp0) REVERT: D 735 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7720 (mm-30) REVERT: E 24 LYS cc_start: 0.8485 (ttpp) cc_final: 0.8076 (ttmm) REVERT: E 66 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7118 (mtt180) REVERT: E 86 ARG cc_start: 0.8102 (ttt90) cc_final: 0.7885 (ttt90) REVERT: E 205 SER cc_start: 0.8690 (t) cc_final: 0.8428 (t) REVERT: E 253 GLU cc_start: 0.8245 (tt0) cc_final: 0.7769 (tt0) REVERT: E 255 LYS cc_start: 0.8505 (mttm) cc_final: 0.8111 (mttm) REVERT: F 56 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7599 (m-40) REVERT: F 86 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7843 (ttm110) REVERT: F 130 ASP cc_start: 0.7866 (t0) cc_final: 0.7531 (t0) REVERT: F 181 ASP cc_start: 0.8521 (m-30) cc_final: 0.8241 (m-30) REVERT: F 216 ASP cc_start: 0.8054 (m-30) cc_final: 0.7853 (m-30) REVERT: F 237 LYS cc_start: 0.8520 (ptpt) cc_final: 0.8168 (ptmt) REVERT: F 255 LYS cc_start: 0.8351 (mtpp) cc_final: 0.8112 (mtpp) REVERT: G 15 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6941 (mm-30) REVERT: G 24 LYS cc_start: 0.8312 (ttpp) cc_final: 0.7915 (ttmm) REVERT: G 95 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7931 (tm-30) REVERT: G 213 LEU cc_start: 0.8420 (mt) cc_final: 0.8150 (mt) REVERT: G 216 ASP cc_start: 0.8172 (m-30) cc_final: 0.7899 (m-30) REVERT: G 220 ASP cc_start: 0.8012 (m-30) cc_final: 0.7701 (m-30) REVERT: G 224 SER cc_start: 0.8782 (t) cc_final: 0.8275 (p) REVERT: G 323 ILE cc_start: 0.8427 (mm) cc_final: 0.8166 (mm) REVERT: H 49 LYS cc_start: 0.8267 (ptpt) cc_final: 0.8034 (pttt) REVERT: H 95 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7828 (tm-30) REVERT: H 130 ASP cc_start: 0.7730 (t0) cc_final: 0.7441 (t0) REVERT: H 213 LEU cc_start: 0.8395 (mt) cc_final: 0.8154 (mt) REVERT: H 224 SER cc_start: 0.8702 (t) cc_final: 0.8433 (p) REVERT: H 243 LYS cc_start: 0.8458 (mtmm) cc_final: 0.8227 (mttm) REVERT: H 244 GLU cc_start: 0.7594 (tp30) cc_final: 0.7240 (tt0) REVERT: H 266 LEU cc_start: 0.8250 (mp) cc_final: 0.7982 (mt) outliers start: 93 outliers final: 71 residues processed: 840 average time/residue: 0.2461 time to fit residues: 331.1213 Evaluate side-chains 867 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 793 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER 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 350 GLN 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 540 THR Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 15 ASP 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 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 453 THR Chi-restraints excluded: chain C residue 474 ILE 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 87 LYS Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 282 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 D residue 732 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 151 GLU Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 21 GLU 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 65 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 351 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 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 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: 0.9990 chunk 91 optimal weight: 0.7980 chunk 337 optimal weight: 0.9990 chunk 255 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 308 optimal weight: 0.9980 chunk 460 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 280 optimal weight: 4.9990 chunk 367 optimal weight: 0.0270 chunk 361 optimal weight: 0.6980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 350 GLN B 65 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN G 26 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.174626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.132191 restraints weight = 58696.577| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.89 r_work: 0.3388 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2286 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= 0.146 Angle : 0.501 10.223 64585 Z= 0.268 Chirality : 0.039 0.267 7494 Planarity : 0.003 0.040 6606 Dihedral : 20.963 176.077 10622 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.92 % Rotamer: Outliers : 2.26 % Allowed : 12.27 % Favored : 85.47 % 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: 1.67 (0.11), residues: 2248 sheet: 0.70 (0.23), residues: 562 loop : -1.17 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 86 TYR 0.022 0.001 TYR E 332 PHE 0.018 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 covalent geometry : bond 0.00336 (46352) covalent geometry : angle 0.50095 (64585) hydrogen bonds : bond 0.03485 ( 2003) hydrogen bonds : angle 3.88487 ( 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 895 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 805 time to evaluate : 1.525 Fit side-chains REVERT: A 37 SER cc_start: 0.8386 (m) cc_final: 0.7988 (p) REVERT: A 81 LYS cc_start: 0.8541 (ttpt) cc_final: 0.8197 (ttmm) REVERT: A 87 LYS cc_start: 0.8003 (mmtp) cc_final: 0.7782 (mmtp) REVERT: A 124 PHE cc_start: 0.8604 (m-80) cc_final: 0.8267 (m-80) REVERT: A 286 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7712 (mm-30) REVERT: A 302 ASN cc_start: 0.8512 (m-40) cc_final: 0.8288 (m-40) REVERT: A 305 LYS cc_start: 0.8556 (mtpp) cc_final: 0.8224 (mtpp) REVERT: A 452 ASP cc_start: 0.8141 (t70) cc_final: 0.7733 (t0) REVERT: A 529 LYS cc_start: 0.8453 (mmmt) cc_final: 0.8150 (mtpp) REVERT: A 551 GLN cc_start: 0.8382 (mp10) cc_final: 0.7843 (mp10) REVERT: A 629 LYS cc_start: 0.7615 (tmtt) cc_final: 0.7349 (pttt) REVERT: A 726 ILE cc_start: 0.8692 (mm) cc_final: 0.8430 (mt) REVERT: B 21 ASP cc_start: 0.7711 (p0) cc_final: 0.7302 (p0) REVERT: B 63 ASN cc_start: 0.8775 (m-40) cc_final: 0.8535 (m-40) REVERT: B 94 LYS cc_start: 0.8245 (mmmm) cc_final: 0.7661 (mmmm) REVERT: B 123 SER cc_start: 0.8346 (m) cc_final: 0.8036 (p) REVERT: B 137 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8362 (t) REVERT: B 277 PHE cc_start: 0.8090 (p90) cc_final: 0.7789 (p90) REVERT: B 286 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7272 (mm-30) REVERT: B 398 GLU cc_start: 0.7761 (tt0) cc_final: 0.7479 (tt0) REVERT: B 402 GLU cc_start: 0.7836 (mp0) cc_final: 0.7316 (mp0) REVERT: B 413 ASN cc_start: 0.8499 (t0) cc_final: 0.8201 (t0) REVERT: B 452 ASP cc_start: 0.7832 (t0) cc_final: 0.7374 (t0) REVERT: B 472 LYS cc_start: 0.7865 (tppt) cc_final: 0.7427 (tppt) REVERT: B 532 ARG cc_start: 0.8358 (tpp80) cc_final: 0.8064 (ttp80) REVERT: B 707 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7592 (mm-30) REVERT: B 708 LYS cc_start: 0.8540 (ttmm) cc_final: 0.8185 (ttmm) REVERT: B 713 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7650 (mm-30) REVERT: B 718 ARG cc_start: 0.8345 (mmt90) cc_final: 0.7915 (mmt90) REVERT: C 148 SER cc_start: 0.8405 (t) cc_final: 0.8082 (m) REVERT: C 331 TYR cc_start: 0.8301 (m-10) cc_final: 0.7964 (m-10) REVERT: C 413 ASN cc_start: 0.8592 (t0) cc_final: 0.8339 (t0) REVERT: C 456 ASP cc_start: 0.7476 (p0) cc_final: 0.7155 (p0) REVERT: D 87 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7806 (mtpt) REVERT: D 94 LYS cc_start: 0.8213 (mmmm) cc_final: 0.7875 (mtmt) REVERT: D 152 THR cc_start: 0.8748 (t) cc_final: 0.8299 (p) REVERT: D 286 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7325 (mp0) REVERT: D 331 TYR cc_start: 0.8390 (m-10) cc_final: 0.8080 (m-80) REVERT: D 502 GLN cc_start: 0.6969 (mm-40) cc_final: 0.6510 (tm-30) REVERT: D 551 GLN cc_start: 0.8419 (mp10) cc_final: 0.8044 (mp10) REVERT: D 629 LYS cc_start: 0.6673 (mtmt) cc_final: 0.6132 (mtmt) REVERT: D 694 THR cc_start: 0.8362 (m) cc_final: 0.8125 (p) REVERT: D 707 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7641 (mm-30) REVERT: D 708 LYS cc_start: 0.8457 (ttmm) cc_final: 0.8218 (ttmm) REVERT: D 713 GLU cc_start: 0.8087 (mp0) cc_final: 0.7420 (mp0) REVERT: D 735 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7728 (mm-30) REVERT: E 24 LYS cc_start: 0.8470 (ttpp) cc_final: 0.8073 (ttmm) REVERT: E 66 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7133 (mtt180) REVERT: E 86 ARG cc_start: 0.8163 (ttt90) cc_final: 0.7938 (ttt90) REVERT: E 205 SER cc_start: 0.8700 (t) cc_final: 0.8450 (t) REVERT: E 253 GLU cc_start: 0.8283 (tt0) cc_final: 0.7816 (tt0) REVERT: E 255 LYS cc_start: 0.8520 (mttm) cc_final: 0.8122 (mttm) REVERT: E 367 LYS cc_start: 0.7714 (mtpp) cc_final: 0.7348 (mttm) REVERT: F 18 LEU cc_start: 0.8431 (mt) cc_final: 0.8196 (mp) REVERT: F 56 ASN cc_start: 0.7901 (OUTLIER) cc_final: 0.7632 (m-40) REVERT: F 86 ARG cc_start: 0.8132 (ttm110) cc_final: 0.7854 (ttm110) REVERT: F 130 ASP cc_start: 0.7880 (t0) cc_final: 0.7541 (t0) REVERT: F 181 ASP cc_start: 0.8518 (m-30) cc_final: 0.8236 (m-30) REVERT: F 237 LYS cc_start: 0.8549 (ptpt) cc_final: 0.8195 (ptmt) REVERT: F 255 LYS cc_start: 0.8362 (mtpp) cc_final: 0.8125 (mtpp) REVERT: G 15 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6948 (mm-30) REVERT: G 24 LYS cc_start: 0.8315 (ttpp) cc_final: 0.7970 (ttmm) REVERT: G 95 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7931 (tm-30) REVERT: G 105 ARG cc_start: 0.8689 (ttp-170) cc_final: 0.8459 (ttt180) REVERT: G 213 LEU cc_start: 0.8424 (mt) cc_final: 0.8162 (mt) REVERT: G 216 ASP cc_start: 0.8165 (m-30) cc_final: 0.7886 (m-30) REVERT: G 220 ASP cc_start: 0.8046 (m-30) cc_final: 0.7738 (m-30) REVERT: G 224 SER cc_start: 0.8766 (t) cc_final: 0.8281 (p) REVERT: G 323 ILE cc_start: 0.8420 (mm) cc_final: 0.8162 (mm) REVERT: H 49 LYS cc_start: 0.8244 (ptpt) cc_final: 0.8029 (pttt) REVERT: H 95 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7816 (tm-30) REVERT: H 130 ASP cc_start: 0.7737 (t0) cc_final: 0.7460 (t0) REVERT: H 213 LEU cc_start: 0.8391 (mt) cc_final: 0.8143 (mt) REVERT: H 224 SER cc_start: 0.8693 (t) cc_final: 0.8430 (p) REVERT: H 243 LYS cc_start: 0.8465 (mtmm) cc_final: 0.8228 (mttm) REVERT: H 244 GLU cc_start: 0.7608 (tp30) cc_final: 0.7258 (tt0) outliers start: 90 outliers final: 72 residues processed: 842 average time/residue: 0.2875 time to fit residues: 386.2000 Evaluate side-chains 868 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 792 time to evaluate : 1.422 ------------------------------------------------------------------------------- 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 350 GLN 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 540 THR Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 471 GLU 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 453 THR Chi-restraints excluded: chain C residue 542 THR 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 102 LYS Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 282 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 D residue 732 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 65 LEU Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain G residue 39 LYS 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 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 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: 1.9990 chunk 99 optimal weight: 2.9990 chunk 451 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 chunk 325 optimal weight: 1.9990 chunk 432 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 208 optimal weight: 0.2980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 350 GLN B 65 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.174018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.131685 restraints weight = 58962.899| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.88 r_work: 0.3384 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 46352 Z= 0.153 Angle : 0.508 11.036 64585 Z= 0.270 Chirality : 0.039 0.286 7494 Planarity : 0.003 0.040 6606 Dihedral : 20.940 176.276 10622 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.97 % Favored : 94.94 % Rotamer: Outliers : 2.26 % Allowed : 12.62 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.13), residues: 4368 helix: 1.67 (0.11), residues: 2248 sheet: 0.68 (0.23), residues: 562 loop : -1.16 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 86 TYR 0.023 0.001 TYR E 332 PHE 0.019 0.001 PHE B 355 TRP 0.008 0.001 TRP C 697 HIS 0.006 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00353 (46352) covalent geometry : angle 0.50806 (64585) hydrogen bonds : bond 0.03507 ( 2003) hydrogen bonds : angle 3.88990 ( 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 886 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 796 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 37 SER cc_start: 0.8385 (m) cc_final: 0.8000 (p) REVERT: A 81 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8202 (ttmm) REVERT: A 87 LYS cc_start: 0.7999 (mmtp) cc_final: 0.7769 (mmtp) REVERT: A 124 PHE cc_start: 0.8608 (m-80) cc_final: 0.8263 (m-80) REVERT: A 141 VAL cc_start: 0.8393 (m) cc_final: 0.8150 (t) REVERT: A 286 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7718 (mm-30) REVERT: A 302 ASN cc_start: 0.8526 (m-40) cc_final: 0.8295 (m-40) REVERT: A 305 LYS cc_start: 0.8554 (mtpp) cc_final: 0.8213 (mtpp) REVERT: A 452 ASP cc_start: 0.8143 (t70) cc_final: 0.7754 (t0) REVERT: A 529 LYS cc_start: 0.8453 (mmmt) cc_final: 0.8177 (mtpp) REVERT: A 551 GLN cc_start: 0.8387 (mp10) cc_final: 0.7854 (mp10) REVERT: A 629 LYS cc_start: 0.7616 (tmtt) cc_final: 0.7346 (pttt) REVERT: A 726 ILE cc_start: 0.8695 (mm) cc_final: 0.8437 (mt) REVERT: B 21 ASP cc_start: 0.7708 (p0) cc_final: 0.7301 (p0) REVERT: B 63 ASN cc_start: 0.8782 (m-40) cc_final: 0.8539 (m-40) REVERT: B 94 LYS cc_start: 0.8254 (mmmm) cc_final: 0.8044 (mmmm) REVERT: B 123 SER cc_start: 0.8343 (m) cc_final: 0.8049 (p) REVERT: B 137 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8352 (t) REVERT: B 277 PHE cc_start: 0.8112 (p90) cc_final: 0.7809 (p90) REVERT: B 286 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7293 (mm-30) REVERT: B 398 GLU cc_start: 0.7770 (tt0) cc_final: 0.7470 (tt0) REVERT: B 402 GLU cc_start: 0.7815 (mp0) cc_final: 0.7304 (mp0) REVERT: B 413 ASN cc_start: 0.8510 (t0) cc_final: 0.8212 (t0) REVERT: B 452 ASP cc_start: 0.7823 (t0) cc_final: 0.7375 (t0) REVERT: B 472 LYS cc_start: 0.7867 (tppt) cc_final: 0.7421 (tppt) REVERT: B 532 ARG cc_start: 0.8373 (tpp80) cc_final: 0.8075 (ttp80) REVERT: B 707 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7600 (mm-30) REVERT: B 708 LYS cc_start: 0.8548 (ttmm) cc_final: 0.8206 (ttmm) REVERT: B 713 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7665 (mm-30) REVERT: B 718 ARG cc_start: 0.8351 (mmt90) cc_final: 0.7925 (mmt90) REVERT: C 148 SER cc_start: 0.8413 (t) cc_final: 0.8098 (m) REVERT: C 331 TYR cc_start: 0.8313 (m-10) cc_final: 0.7977 (m-80) REVERT: C 413 ASN cc_start: 0.8594 (t0) cc_final: 0.8341 (t0) REVERT: C 456 ASP cc_start: 0.7498 (p0) cc_final: 0.7173 (p0) REVERT: D 94 LYS cc_start: 0.8202 (mmmm) cc_final: 0.7878 (mtmt) REVERT: D 152 THR cc_start: 0.8749 (t) cc_final: 0.8315 (p) REVERT: D 286 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7324 (mp0) REVERT: D 331 TYR cc_start: 0.8395 (m-10) cc_final: 0.8084 (m-80) REVERT: D 502 GLN cc_start: 0.6963 (mm-40) cc_final: 0.6530 (tm-30) REVERT: D 551 GLN cc_start: 0.8418 (mp10) cc_final: 0.8051 (mp10) REVERT: D 641 GLU cc_start: 0.6962 (tp30) cc_final: 0.6752 (tp30) REVERT: D 694 THR cc_start: 0.8367 (m) cc_final: 0.8117 (p) REVERT: D 707 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7645 (mm-30) REVERT: D 708 LYS cc_start: 0.8476 (ttmm) cc_final: 0.8237 (ttmm) REVERT: D 713 GLU cc_start: 0.8099 (mp0) cc_final: 0.7432 (mp0) REVERT: D 735 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7735 (mm-30) REVERT: E 24 LYS cc_start: 0.8475 (ttpp) cc_final: 0.8085 (ttmm) REVERT: E 40 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7653 (mt-10) REVERT: E 66 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7194 (mtt180) REVERT: E 86 ARG cc_start: 0.8171 (ttt90) cc_final: 0.7953 (ttt90) REVERT: E 205 SER cc_start: 0.8685 (t) cc_final: 0.8433 (t) REVERT: E 253 GLU cc_start: 0.8281 (tt0) cc_final: 0.7814 (tt0) REVERT: E 255 LYS cc_start: 0.8530 (mttm) cc_final: 0.8136 (mttm) REVERT: F 18 LEU cc_start: 0.8445 (mt) cc_final: 0.8219 (mp) REVERT: F 56 ASN cc_start: 0.7878 (OUTLIER) cc_final: 0.7608 (m-40) REVERT: F 86 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7858 (ttm110) REVERT: F 130 ASP cc_start: 0.7884 (t0) cc_final: 0.7548 (t0) REVERT: F 181 ASP cc_start: 0.8512 (m-30) cc_final: 0.8234 (m-30) REVERT: F 237 LYS cc_start: 0.8546 (ptpt) cc_final: 0.8273 (ptmt) REVERT: F 255 LYS cc_start: 0.8363 (mtpp) cc_final: 0.8126 (mtpp) REVERT: G 15 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6958 (mm-30) REVERT: G 21 GLU cc_start: 0.7676 (pm20) cc_final: 0.7359 (pm20) REVERT: G 24 LYS cc_start: 0.8306 (ttpp) cc_final: 0.7915 (ttmm) REVERT: G 95 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7929 (tm-30) REVERT: G 213 LEU cc_start: 0.8420 (mt) cc_final: 0.8153 (mt) REVERT: G 216 ASP cc_start: 0.8162 (m-30) cc_final: 0.7888 (m-30) REVERT: G 220 ASP cc_start: 0.8031 (m-30) cc_final: 0.7721 (m-30) REVERT: G 224 SER cc_start: 0.8769 (t) cc_final: 0.8282 (p) REVERT: G 323 ILE cc_start: 0.8422 (mm) cc_final: 0.8171 (mm) REVERT: H 49 LYS cc_start: 0.8259 (ptpt) cc_final: 0.8051 (pttt) REVERT: H 95 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7816 (tm-30) REVERT: H 130 ASP cc_start: 0.7729 (t0) cc_final: 0.7440 (t0) REVERT: H 181 ASP cc_start: 0.8496 (m-30) cc_final: 0.8283 (m-30) REVERT: H 213 LEU cc_start: 0.8395 (mt) cc_final: 0.8148 (mt) REVERT: H 224 SER cc_start: 0.8693 (t) cc_final: 0.8427 (p) REVERT: H 243 LYS cc_start: 0.8469 (mtmm) cc_final: 0.8238 (mttm) REVERT: H 244 GLU cc_start: 0.7612 (tp30) cc_final: 0.7271 (tt0) REVERT: H 266 LEU cc_start: 0.8237 (mp) cc_final: 0.7967 (mt) outliers start: 90 outliers final: 75 residues processed: 832 average time/residue: 0.1849 time to fit residues: 248.4088 Evaluate side-chains 866 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 788 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER 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 348 LYS Chi-restraints excluded: chain A residue 350 GLN 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 540 THR Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 471 GLU 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 289 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 595 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 102 LYS 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 D residue 732 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 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 65 LEU Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain G residue 39 LYS 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 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 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: 2.9990 chunk 135 optimal weight: 0.0050 chunk 435 optimal weight: 0.9990 chunk 410 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 467 optimal weight: 8.9990 chunk 154 optimal weight: 0.0870 chunk 297 optimal weight: 2.9990 chunk 59 optimal weight: 50.0000 chunk 145 optimal weight: 5.9990 chunk 259 optimal weight: 1.9990 overall best weight: 1.0178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 65 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN E 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.173173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130633 restraints weight = 58662.256| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.77 r_work: 0.3367 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 46352 Z= 0.189 Angle : 0.530 11.023 64585 Z= 0.281 Chirality : 0.041 0.287 7494 Planarity : 0.003 0.040 6606 Dihedral : 20.935 176.785 10622 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.57 % Rotamer: Outliers : 2.14 % Allowed : 13.07 % Favored : 84.79 % 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: 0.76 (0.13), residues: 4368 helix: 1.57 (0.11), residues: 2258 sheet: 0.63 (0.23), residues: 550 loop : -1.13 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 20 TYR 0.024 0.001 TYR E 332 PHE 0.026 0.002 PHE B 355 TRP 0.008 0.001 TRP C 697 HIS 0.006 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00445 (46352) covalent geometry : angle 0.53012 (64585) hydrogen bonds : bond 0.03717 ( 2003) hydrogen bonds : angle 3.93543 ( 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 898 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 813 time to evaluate : 0.878 Fit side-chains REVERT: A 37 SER cc_start: 0.8351 (m) cc_final: 0.7962 (p) REVERT: A 81 LYS cc_start: 0.8468 (ttpt) cc_final: 0.8119 (ttmm) REVERT: A 87 LYS cc_start: 0.7971 (mmtp) cc_final: 0.7692 (mmtp) REVERT: A 124 PHE cc_start: 0.8603 (m-80) cc_final: 0.8225 (m-80) REVERT: A 286 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7511 (mm-30) REVERT: A 302 ASN cc_start: 0.8484 (m-40) cc_final: 0.8241 (m-40) REVERT: A 305 LYS cc_start: 0.8493 (mtpp) cc_final: 0.8154 (mtpp) REVERT: A 452 ASP cc_start: 0.8168 (t70) cc_final: 0.7752 (t0) REVERT: A 529 LYS cc_start: 0.8423 (mmmt) cc_final: 0.8121 (mtpp) REVERT: A 542 THR cc_start: 0.8382 (m) cc_final: 0.8111 (t) REVERT: A 551 GLN cc_start: 0.8379 (mp10) cc_final: 0.7813 (mp10) REVERT: A 629 LYS cc_start: 0.7632 (tmtt) cc_final: 0.7347 (pttt) REVERT: A 726 ILE cc_start: 0.8651 (mm) cc_final: 0.8387 (mt) REVERT: B 21 ASP cc_start: 0.7687 (p0) cc_final: 0.7273 (p0) REVERT: B 63 ASN cc_start: 0.8789 (m-40) cc_final: 0.8545 (m-40) REVERT: B 94 LYS cc_start: 0.8211 (mmmm) cc_final: 0.7889 (mmmm) REVERT: B 123 SER cc_start: 0.8335 (m) cc_final: 0.7969 (p) REVERT: B 286 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7245 (mm-30) REVERT: B 398 GLU cc_start: 0.7791 (tt0) cc_final: 0.7469 (tt0) REVERT: B 402 GLU cc_start: 0.7810 (mp0) cc_final: 0.7276 (mp0) REVERT: B 413 ASN cc_start: 0.8493 (t0) cc_final: 0.8192 (t0) REVERT: B 452 ASP cc_start: 0.7842 (t0) cc_final: 0.7444 (t0) REVERT: B 472 LYS cc_start: 0.7801 (tppt) cc_final: 0.7363 (tppt) REVERT: B 532 ARG cc_start: 0.8353 (tpp80) cc_final: 0.8046 (ttp80) REVERT: B 707 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7548 (mm-30) REVERT: B 708 LYS cc_start: 0.8514 (ttmm) cc_final: 0.8164 (ttmm) REVERT: B 713 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7646 (mm-30) REVERT: B 718 ARG cc_start: 0.8327 (mmt90) cc_final: 0.7893 (mmt90) REVERT: C 94 LYS cc_start: 0.8237 (mttt) cc_final: 0.7940 (mtmm) REVERT: C 148 SER cc_start: 0.8368 (t) cc_final: 0.8039 (m) REVERT: C 331 TYR cc_start: 0.8316 (m-10) cc_final: 0.8028 (m-10) REVERT: C 413 ASN cc_start: 0.8570 (t0) cc_final: 0.8308 (t0) REVERT: C 449 LYS cc_start: 0.8560 (mtpp) cc_final: 0.8330 (mttp) REVERT: C 456 ASP cc_start: 0.7499 (p0) cc_final: 0.7170 (p0) REVERT: D 87 LYS cc_start: 0.8172 (mtpt) cc_final: 0.7929 (mttt) REVERT: D 94 LYS cc_start: 0.8115 (mmmm) cc_final: 0.7772 (mtmt) REVERT: D 152 THR cc_start: 0.8737 (t) cc_final: 0.8291 (p) REVERT: D 286 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7331 (mp0) REVERT: D 331 TYR cc_start: 0.8391 (m-10) cc_final: 0.8076 (m-80) REVERT: D 502 GLN cc_start: 0.7042 (mm-40) cc_final: 0.6614 (tm-30) REVERT: D 551 GLN cc_start: 0.8455 (mp10) cc_final: 0.8047 (mp10) REVERT: D 641 GLU cc_start: 0.6989 (tp30) cc_final: 0.6687 (tp30) REVERT: D 694 THR cc_start: 0.8382 (m) cc_final: 0.8117 (p) REVERT: D 707 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7604 (mm-30) REVERT: D 708 LYS cc_start: 0.8455 (ttmm) cc_final: 0.8204 (ttmm) REVERT: D 713 GLU cc_start: 0.8085 (mp0) cc_final: 0.7349 (mp0) REVERT: D 735 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7686 (mm-30) REVERT: E 24 LYS cc_start: 0.8484 (ttpp) cc_final: 0.8102 (ttmm) REVERT: E 40 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7644 (mt-10) REVERT: E 66 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7125 (mtt180) REVERT: E 86 ARG cc_start: 0.8164 (ttt90) cc_final: 0.7928 (ttt90) REVERT: E 205 SER cc_start: 0.8718 (t) cc_final: 0.8455 (t) REVERT: E 253 GLU cc_start: 0.8278 (tt0) cc_final: 0.7805 (tt0) REVERT: E 255 LYS cc_start: 0.8522 (mttm) cc_final: 0.8119 (mttm) REVERT: E 367 LYS cc_start: 0.7698 (mtpp) cc_final: 0.7307 (mttm) REVERT: F 56 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7629 (m-40) REVERT: F 86 ARG cc_start: 0.8159 (ttm110) cc_final: 0.7865 (ttm110) REVERT: F 130 ASP cc_start: 0.7889 (t0) cc_final: 0.7541 (t0) REVERT: F 181 ASP cc_start: 0.8521 (m-30) cc_final: 0.8228 (m-30) REVERT: F 211 LYS cc_start: 0.8755 (mttp) cc_final: 0.8427 (mttp) REVERT: F 237 LYS cc_start: 0.8573 (ptpt) cc_final: 0.8287 (ptmt) REVERT: F 255 LYS cc_start: 0.8369 (mtpp) cc_final: 0.8114 (mtpp) REVERT: G 15 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6924 (mm-30) REVERT: G 24 LYS cc_start: 0.8295 (ttpp) cc_final: 0.7886 (ttmm) REVERT: G 95 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7897 (tm-30) REVERT: G 181 ASP cc_start: 0.8474 (m-30) cc_final: 0.8141 (m-30) REVERT: G 213 LEU cc_start: 0.8397 (mt) cc_final: 0.8159 (mt) REVERT: G 216 ASP cc_start: 0.8133 (m-30) cc_final: 0.7870 (m-30) REVERT: G 220 ASP cc_start: 0.8023 (m-30) cc_final: 0.7690 (m-30) REVERT: G 224 SER cc_start: 0.8784 (t) cc_final: 0.8264 (p) REVERT: G 323 ILE cc_start: 0.8393 (mm) cc_final: 0.8133 (mm) REVERT: H 35 LYS cc_start: 0.8219 (mtpt) cc_final: 0.7957 (mtmt) REVERT: H 49 LYS cc_start: 0.8264 (ptpt) cc_final: 0.8032 (pttt) REVERT: H 95 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7778 (tm-30) REVERT: H 130 ASP cc_start: 0.7734 (t0) cc_final: 0.7464 (t0) REVERT: H 180 MET cc_start: 0.8405 (tpp) cc_final: 0.7647 (tpp) REVERT: H 213 LEU cc_start: 0.8361 (mt) cc_final: 0.8120 (mt) REVERT: H 224 SER cc_start: 0.8676 (t) cc_final: 0.8380 (p) REVERT: H 243 LYS cc_start: 0.8452 (mtmm) cc_final: 0.8201 (mttm) REVERT: H 244 GLU cc_start: 0.7657 (tp30) cc_final: 0.7303 (tt0) outliers start: 85 outliers final: 74 residues processed: 846 average time/residue: 0.1808 time to fit residues: 246.3854 Evaluate side-chains 882 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 806 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 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 540 THR Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 471 GLU 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 289 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 595 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 102 LYS 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 D residue 732 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 151 GLU 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 65 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain G residue 39 LYS 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 201 ASP 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 336 LEU 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.4784 > 50: distance: 84 - 88: 33.964 distance: 88 - 89: 39.281 distance: 89 - 90: 40.621 distance: 90 - 91: 56.728 distance: 92 - 93: 39.624 distance: 93 - 94: 40.402 distance: 93 - 96: 56.981 distance: 94 - 99: 57.485 distance: 96 - 97: 39.629 distance: 100 - 101: 22.361 distance: 101 - 102: 46.998 distance: 101 - 103: 15.405 distance: 104 - 105: 40.317 distance: 104 - 107: 56.703 distance: 108 - 109: 55.606 distance: 109 - 110: 40.571 distance: 110 - 111: 36.162 distance: 111 - 112: 4.368 distance: 111 - 113: 57.829 distance: 114 - 115: 6.365 distance: 115 - 116: 8.126 distance: 115 - 118: 50.362 distance: 116 - 126: 15.825 distance: 119 - 121: 56.492 distance: 122 - 124: 56.603 distance: 124 - 125: 56.873 distance: 126 - 127: 16.367 distance: 127 - 128: 55.438 distance: 127 - 130: 40.755 distance: 128 - 129: 40.827 distance: 130 - 131: 40.512 distance: 131 - 132: 9.271 distance: 132 - 133: 11.144 distance: 133 - 134: 39.827 distance: 136 - 137: 48.947 distance: 136 - 139: 41.238 distance: 137 - 138: 31.753 distance: 137 - 142: 46.925 distance: 139 - 140: 56.369 distance: 142 - 143: 40.543 distance: 142 - 148: 39.809 distance: 143 - 144: 41.134 distance: 144 - 145: 39.081 distance: 144 - 149: 56.944 distance: 146 - 147: 39.718 distance: 147 - 148: 39.350 distance: 149 - 150: 56.154 distance: 150 - 151: 56.048 distance: 150 - 153: 57.482 distance: 151 - 161: 39.509 distance: 153 - 154: 39.239 distance: 154 - 155: 69.583 distance: 154 - 156: 56.892 distance: 155 - 157: 40.932 distance: 159 - 160: 39.382 distance: 161 - 162: 57.278 distance: 162 - 165: 39.006 distance: 163 - 164: 40.411 distance: 163 - 168: 34.996 distance: 165 - 166: 57.373 distance: 166 - 167: 40.157