Starting phenix.real_space_refine on Fri Jan 24 18:46:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n0d_24104/01_2025/7n0d_24104.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n0d_24104/01_2025/7n0d_24104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n0d_24104/01_2025/7n0d_24104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n0d_24104/01_2025/7n0d_24104.map" model { file = "/net/cci-nas-00/data/ceres_data/7n0d_24104/01_2025/7n0d_24104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n0d_24104/01_2025/7n0d_24104.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.003 sd= 0.087 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: 7 Type Number sf(0) Gaussians Zn 20 6.06 5 P 76 5.49 5 Mg 6 5.21 5 S 208 5.16 5 C 13632 2.51 5 N 3694 2.21 5 O 4210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 21846 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 955 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "B" Number of atoms: 4085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4085 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 26, 'TRANS': 485} Chain breaks: 1 Chain: "C" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 955 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "D" Number of atoms: 4085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4085 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 26, 'TRANS': 485} Chain breaks: 1 Chain: "T" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 411 Classifications: {'RNA': 19} Modifications used: {'rna3p_pur': 12, 'rna3p_pyr': 7} Link IDs: {'rna3p': 18} Chain: "K" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 292 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 8} Link IDs: {'rna3p': 13} Chain: "P" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna3p_pyr': 5} Link IDs: {'rna3p': 4} Chain: "E" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 955 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "F" Number of atoms: 4085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4085 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 26, 'TRANS': 485} Chain breaks: 1 Chain: "G" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 955 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "H" Number of atoms: 4085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4085 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 26, 'TRANS': 485} Chain breaks: 1 Chain: "I" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 411 Classifications: {'RNA': 19} Modifications used: {'rna3p_pur': 12, 'rna3p_pyr': 7} Link IDs: {'rna3p': 18} Chain: "L" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 292 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 8} Link IDs: {'rna3p': 13} Chain: "J" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna3p_pyr': 5} Link IDs: {'rna3p': 4} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 2, ' ZN': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' MG': 1, ' ZN': 3, '1N7': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 2, ' ZN': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' MG': 1, ' ZN': 3, '1N7': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 520 SG CYS A 74 26.954 99.310 63.210 1.00 86.30 S ATOM 546 SG CYS A 77 29.608 99.210 65.378 1.00 87.72 S ATOM 651 SG CYS A 90 29.200 102.111 63.684 1.00 94.03 S ATOM 854 SG CYS A 117 16.790 115.384 55.659 1.00121.51 S ATOM 874 SG CYS A 120 15.849 116.971 58.584 1.00124.45 S ATOM 935 SG CYS A 128 13.566 114.967 56.410 1.00126.88 S ATOM 947 SG CYS A 130 14.239 118.356 55.986 1.00140.78 S ATOM 2577 SG CYS B 207 30.683 78.239 38.778 1.00 98.07 S ATOM 2597 SG CYS B 210 29.444 75.322 36.209 1.00103.73 S ATOM 2718 SG CYS B 226 31.906 75.163 39.227 1.00 92.39 S ATOM 3018 SG CYS B 261 42.829 52.617 61.129 1.00 95.03 S ATOM 3148 SG CYS B 279 39.645 54.960 60.208 1.00 86.15 S ATOM 4538 SG CYS B 452 33.931 34.866 11.029 1.00155.48 S ATOM 4652 SG CYS B 477 36.694 33.845 12.468 1.00150.54 S ATOM 4694 SG CYS B 484 35.899 37.192 12.030 1.00150.30 S ATOM 5560 SG CYS C 74 52.083 115.398 100.935 1.00113.23 S ATOM 5586 SG CYS C 77 54.487 112.847 101.790 1.00108.33 S ATOM 5691 SG CYS C 90 54.111 115.714 103.548 1.00120.57 S ATOM 5894 SG CYS C 117 42.870 130.364 111.870 1.00155.02 S ATOM 5914 SG CYS C 120 41.545 129.429 115.037 1.00157.42 S ATOM 5975 SG CYS C 128 39.240 128.954 111.992 1.00155.24 S ATOM 5987 SG CYS C 130 40.122 131.911 113.282 1.00163.66 S ATOM 7617 SG CYS D 207 57.766 127.867 71.543 1.00100.47 S ATOM 7637 SG CYS D 210 57.169 128.825 68.599 1.00105.83 S ATOM 7758 SG CYS D 226 58.952 126.026 69.043 1.00 92.53 S ATOM 8058 SG CYS D 261 67.658 95.830 58.679 1.00 91.59 S ATOM 8188 SG CYS D 279 64.766 97.962 60.054 1.00 80.31 S ATOM 9578 SG CYS D 452 62.308 131.679 22.751 1.00157.38 S ATOM 9692 SG CYS D 477 65.167 131.257 20.485 1.00155.08 S ATOM 9734 SG CYS D 484 65.387 133.190 23.404 1.00154.33 S ATOM 11403 SG CYS E 74 99.084 52.344 63.212 1.00 85.83 S ATOM 11429 SG CYS E 77 96.435 52.453 65.385 1.00 87.47 S ATOM 11534 SG CYS E 90 96.851 49.546 63.689 1.00 93.75 S ATOM 11737 SG CYS E 117 109.251 36.282 55.684 1.00120.89 S ATOM 11757 SG CYS E 120 110.189 34.697 58.611 1.00124.12 S ATOM 11818 SG CYS E 128 112.477 36.698 56.440 1.00126.35 S ATOM 11830 SG CYS E 130 111.799 33.305 56.018 1.00139.91 S ATOM 13460 SG CYS F 207 95.336 73.420 38.773 1.00 98.71 S ATOM 13480 SG CYS F 210 96.581 76.342 36.204 1.00104.36 S ATOM 13601 SG CYS F 226 94.109 76.495 39.230 1.00 92.81 S ATOM 13901 SG CYS F 261 83.181 99.037 61.131 1.00 95.55 S ATOM 14031 SG CYS F 279 86.365 96.695 60.210 1.00 85.93 S ATOM 15421 SG CYS F 452 92.076 116.787 11.064 1.00155.46 S ATOM 15535 SG CYS F 477 89.300 117.799 12.477 1.00150.32 S ATOM 15577 SG CYS F 484 90.099 114.455 12.027 1.00150.15 S ATOM 16443 SG CYS G 74 73.951 36.263 100.938 1.00112.84 S ATOM 16469 SG CYS G 77 71.543 38.810 101.797 1.00107.95 S ATOM 16574 SG CYS G 90 71.926 35.942 103.553 1.00120.45 S ATOM 16777 SG CYS G 117 83.175 21.292 111.877 1.00154.69 S ATOM 16797 SG CYS G 120 84.498 22.232 115.041 1.00156.99 S ATOM 16858 SG CYS G 128 86.803 22.708 111.994 1.00155.43 S ATOM 16870 SG CYS G 130 85.925 19.752 113.289 1.00163.82 S ATOM 18500 SG CYS H 207 68.267 23.788 71.549 1.00100.23 S ATOM 18520 SG CYS H 210 68.857 22.828 68.604 1.00105.75 S ATOM 18641 SG CYS H 226 67.076 25.628 69.050 1.00 92.66 S ATOM 18941 SG CYS H 261 58.367 55.818 58.691 1.00 92.00 S ATOM 19071 SG CYS H 279 61.259 53.687 60.065 1.00 80.33 S ATOM 20461 SG CYS H 452 63.715 19.970 22.760 1.00156.59 S ATOM 20575 SG CYS H 477 60.857 20.390 20.495 1.00155.58 S ATOM 20617 SG CYS H 484 60.637 18.459 23.415 1.00154.46 S Time building chain proxies: 13.15, per 1000 atoms: 0.60 Number of scatterers: 21846 At special positions: 0 Unit cell: (127.092, 152.724, 130.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 20 29.99 S 208 16.00 P 76 15.00 Mg 6 11.99 O 4210 8.00 N 3694 7.00 C 13632 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: 5.48 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS A 83 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 74 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 90 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 77 " pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 130 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 120 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 117 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 128 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" ND1 HIS B 229 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 226 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 207 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 210 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" NE2 HIS B 257 " pdb="ZN ZN B 604 " - pdb=" ND1 HIS B 264 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 261 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 279 " pdb=" ZN B 605 " pdb="ZN ZN B 605 " - pdb=" ND1 HIS B 487 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 477 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 484 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 452 " pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" NE2 HIS C 83 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 77 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 74 " pdb=" ZN C 202 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 130 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 120 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 117 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 128 " pdb=" ZN D 602 " pdb="ZN ZN D 602 " - pdb=" ND1 HIS D 229 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 210 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 207 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 226 " pdb=" ZN D 603 " pdb="ZN ZN D 603 " - pdb=" NE2 HIS D 257 " pdb="ZN ZN D 603 " - pdb=" ND1 HIS D 264 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 261 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 279 " pdb=" ZN D 604 " pdb="ZN ZN D 604 " - pdb=" ND1 HIS D 487 " pdb="ZN ZN D 604 " - pdb=" SG CYS D 477 " pdb="ZN ZN D 604 " - pdb=" SG CYS D 452 " pdb="ZN ZN D 604 " - pdb=" SG CYS D 484 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" NE2 HIS E 83 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 74 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 90 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 77 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 130 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 120 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 117 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 128 " pdb=" ZN F 603 " pdb="ZN ZN F 603 " - pdb=" ND1 HIS F 229 " pdb="ZN ZN F 603 " - pdb=" SG CYS F 226 " pdb="ZN ZN F 603 " - pdb=" SG CYS F 207 " pdb="ZN ZN F 603 " - pdb=" SG CYS F 210 " pdb=" ZN F 604 " pdb="ZN ZN F 604 " - pdb=" NE2 HIS F 257 " pdb="ZN ZN F 604 " - pdb=" ND1 HIS F 264 " pdb="ZN ZN F 604 " - pdb=" SG CYS F 261 " pdb="ZN ZN F 604 " - pdb=" SG CYS F 279 " pdb=" ZN F 605 " pdb="ZN ZN F 605 " - pdb=" ND1 HIS F 487 " pdb="ZN ZN F 605 " - pdb=" SG CYS F 477 " pdb="ZN ZN F 605 " - pdb=" SG CYS F 484 " pdb="ZN ZN F 605 " - pdb=" SG CYS F 452 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" NE2 HIS G 83 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 77 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 90 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 74 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 130 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 120 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 117 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 128 " pdb=" ZN H 703 " pdb="ZN ZN H 703 " - pdb=" ND1 HIS H 229 " pdb="ZN ZN H 703 " - pdb=" SG CYS H 210 " pdb="ZN ZN H 703 " - pdb=" SG CYS H 207 " pdb="ZN ZN H 703 " - pdb=" SG CYS H 226 " pdb=" ZN H 704 " pdb="ZN ZN H 704 " - pdb=" NE2 HIS H 257 " pdb="ZN ZN H 704 " - pdb=" ND1 HIS H 264 " pdb="ZN ZN H 704 " - pdb=" SG CYS H 261 " pdb="ZN ZN H 704 " - pdb=" SG CYS H 279 " pdb=" ZN H 705 " pdb="ZN ZN H 705 " - pdb=" ND1 HIS H 487 " pdb="ZN ZN H 705 " - pdb=" SG CYS H 477 " pdb="ZN ZN H 705 " - pdb=" SG CYS H 452 " pdb="ZN ZN H 705 " - pdb=" SG CYS H 484 " Number of angles added : 64 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4808 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 38 sheets defined 29.2% alpha, 15.8% beta 32 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 7.99 Creating SS restraints... Processing helix chain 'A' and resid 7 through 11 removed outlier: 3.510A pdb=" N ASN A 10 " --> pdb=" O VAL A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 20 Processing helix chain 'A' and resid 22 through 33 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.834A pdb=" N PHE A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.680A pdb=" N VAL B 29 " --> pdb=" O HIS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 82 Processing helix chain 'B' and resid 146 through 153 removed outlier: 3.649A pdb=" N ILE B 150 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 158 through 175 Processing helix chain 'B' and resid 187 through 199 removed outlier: 4.108A pdb=" N ALA B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 252 through 258 Processing helix chain 'B' and resid 269 through 287 Processing helix chain 'B' and resid 301 through 323 removed outlier: 3.874A pdb=" N ARG B 310 " --> pdb=" O ASN B 306 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN B 313 " --> pdb=" O CYS B 309 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 317 " --> pdb=" O GLN B 313 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 321 " --> pdb=" O VAL B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 437 removed outlier: 3.531A pdb=" N ALA B 435 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 437 " --> pdb=" O SER B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.587A pdb=" N LEU B 479 " --> pdb=" O THR B 475 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 475 through 480' Processing helix chain 'B' and resid 484 through 505 removed outlier: 3.602A pdb=" N GLY B 505 " --> pdb=" O MET B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 522 removed outlier: 3.754A pdb=" N THR B 522 " --> pdb=" O ASN B 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 9 No H-bonds generated for 'chain 'C' and resid 7 through 9' Processing helix chain 'C' and resid 10 through 17 Processing helix chain 'C' and resid 22 through 33 Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 74 through 80 Processing helix chain 'C' and resid 85 through 89 removed outlier: 4.266A pdb=" N PHE C 89 " --> pdb=" O PRO C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.683A pdb=" N LEU C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 82 Processing helix chain 'D' and resid 146 through 154 removed outlier: 3.648A pdb=" N ILE D 150 " --> pdb=" O LYS D 147 " (cutoff:3.500A) Proline residue: D 151 - end of helix removed outlier: 3.746A pdb=" N TYR D 154 " --> pdb=" O PRO D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 175 Processing helix chain 'D' and resid 187 through 199 removed outlier: 3.938A pdb=" N ALA D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 248 removed outlier: 3.594A pdb=" N GLY D 248 " --> pdb=" O GLN D 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 245 through 248' Processing helix chain 'D' and resid 252 through 258 Processing helix chain 'D' and resid 269 through 287 Processing helix chain 'D' and resid 301 through 325 removed outlier: 3.564A pdb=" N ILE D 305 " --> pdb=" O ASP D 301 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG D 310 " --> pdb=" O ASN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 437 removed outlier: 3.909A pdb=" N VAL D 437 " --> pdb=" O SER D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 504 Processing helix chain 'E' and resid 7 through 11 removed outlier: 3.510A pdb=" N ASN E 10 " --> pdb=" O VAL E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 20 Processing helix chain 'E' and resid 22 through 33 Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 74 through 80 Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.834A pdb=" N PHE E 89 " --> pdb=" O PRO E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 114 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.679A pdb=" N VAL F 29 " --> pdb=" O HIS F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 82 Processing helix chain 'F' and resid 146 through 153 removed outlier: 3.649A pdb=" N ILE F 150 " --> pdb=" O LYS F 147 " (cutoff:3.500A) Proline residue: F 151 - end of helix Processing helix chain 'F' and resid 158 through 175 Processing helix chain 'F' and resid 187 through 199 removed outlier: 4.107A pdb=" N ALA F 191 " --> pdb=" O ALA F 187 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR F 193 " --> pdb=" O GLY F 189 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR F 197 " --> pdb=" O THR F 193 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 247 No H-bonds generated for 'chain 'F' and resid 245 through 247' Processing helix chain 'F' and resid 252 through 258 Processing helix chain 'F' and resid 269 through 287 Processing helix chain 'F' and resid 301 through 323 removed outlier: 3.874A pdb=" N ARG F 310 " --> pdb=" O ASN F 306 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN F 313 " --> pdb=" O CYS F 309 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL F 317 " --> pdb=" O GLN F 313 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU F 321 " --> pdb=" O VAL F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 437 removed outlier: 3.530A pdb=" N ALA F 435 " --> pdb=" O ASP F 432 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL F 437 " --> pdb=" O SER F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 480 removed outlier: 3.586A pdb=" N LEU F 479 " --> pdb=" O THR F 475 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY F 480 " --> pdb=" O ARG F 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 475 through 480' Processing helix chain 'F' and resid 484 through 505 removed outlier: 3.602A pdb=" N GLY F 505 " --> pdb=" O MET F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 522 removed outlier: 3.753A pdb=" N THR F 522 " --> pdb=" O ASN F 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 9 No H-bonds generated for 'chain 'G' and resid 7 through 9' Processing helix chain 'G' and resid 10 through 17 Processing helix chain 'G' and resid 22 through 33 Processing helix chain 'G' and resid 71 through 73 No H-bonds generated for 'chain 'G' and resid 71 through 73' Processing helix chain 'G' and resid 74 through 80 Processing helix chain 'G' and resid 85 through 89 removed outlier: 4.267A pdb=" N PHE G 89 " --> pdb=" O PRO G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 104 No H-bonds generated for 'chain 'G' and resid 102 through 104' Processing helix chain 'G' and resid 106 through 114 removed outlier: 3.684A pdb=" N LEU G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 82 Processing helix chain 'H' and resid 146 through 154 removed outlier: 3.648A pdb=" N ILE H 150 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Proline residue: H 151 - end of helix removed outlier: 3.745A pdb=" N TYR H 154 " --> pdb=" O PRO H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 175 Processing helix chain 'H' and resid 187 through 199 removed outlier: 3.938A pdb=" N ALA H 191 " --> pdb=" O ALA H 187 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR H 197 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 248 removed outlier: 3.594A pdb=" N GLY H 248 " --> pdb=" O GLN H 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 245 through 248' Processing helix chain 'H' and resid 252 through 258 Processing helix chain 'H' and resid 269 through 287 Processing helix chain 'H' and resid 301 through 325 removed outlier: 3.565A pdb=" N ILE H 305 " --> pdb=" O ASP H 301 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG H 310 " --> pdb=" O ASN H 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 437 removed outlier: 3.909A pdb=" N VAL H 437 " --> pdb=" O SER H 434 " (cutoff:3.500A) Processing helix chain 'H' and resid 484 through 504 Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 55 removed outlier: 4.608A pdb=" N TYR B 124 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 116 through 118 removed outlier: 7.141A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N CYS B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 118 removed outlier: 7.141A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N CYS B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AA7, first strand: chain 'B' and resid 329 through 332 removed outlier: 4.641A pdb=" N TRP B 385 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N CYS B 382 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N CYS B 399 " --> pdb=" O CYS B 382 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N PHE B 384 " --> pdb=" O CYS B 399 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N PHE B 401 " --> pdb=" O PHE B 384 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N SER B 396 " --> pdb=" O TYR B 511 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 350 through 352 Processing sheet with id=AA9, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB1, first strand: chain 'B' and resid 446 through 447 removed outlier: 6.235A pdb=" N TYR B 446 " --> pdb=" O ILE B 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AB3, first strand: chain 'D' and resid 34 through 35 Processing sheet with id=AB4, first strand: chain 'D' and resid 53 through 55 removed outlier: 4.663A pdb=" N TYR D 124 " --> pdb=" O ILE D 55 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 116 through 118 removed outlier: 7.074A pdb=" N ASN D 104 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA D 96 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS D 94 " --> pdb=" O PRO D 106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 116 through 118 removed outlier: 7.074A pdb=" N ASN D 104 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA D 96 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS D 94 " --> pdb=" O PRO D 106 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 223 through 225 removed outlier: 3.697A pdb=" N THR D 223 " --> pdb=" O SER D 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 347 through 351 removed outlier: 6.863A pdb=" N LEU D 329 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N TYR D 351 " --> pdb=" O LEU D 329 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP D 331 " --> pdb=" O TYR D 351 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N CYS D 382 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N CYS D 399 " --> pdb=" O CYS D 382 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AC1, first strand: chain 'D' and resid 446 through 447 removed outlier: 6.315A pdb=" N TYR D 446 " --> pdb=" O ILE D 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 55 through 56 Processing sheet with id=AC3, first strand: chain 'F' and resid 34 through 35 Processing sheet with id=AC4, first strand: chain 'F' and resid 53 through 55 removed outlier: 4.609A pdb=" N TYR F 124 " --> pdb=" O ILE F 55 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 116 through 118 removed outlier: 7.142A pdb=" N ASN F 104 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA F 96 " --> pdb=" O ASN F 104 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N CYS F 94 " --> pdb=" O PRO F 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 116 through 118 removed outlier: 7.142A pdb=" N ASN F 104 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA F 96 " --> pdb=" O ASN F 104 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N CYS F 94 " --> pdb=" O PRO F 106 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 224 through 225 Processing sheet with id=AC8, first strand: chain 'F' and resid 329 through 332 removed outlier: 4.641A pdb=" N TRP F 385 " --> pdb=" O ILE F 332 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N CYS F 382 " --> pdb=" O ILE F 397 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N CYS F 399 " --> pdb=" O CYS F 382 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N PHE F 384 " --> pdb=" O CYS F 399 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N PHE F 401 " --> pdb=" O PHE F 384 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER F 396 " --> pdb=" O TYR F 511 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 350 through 352 Processing sheet with id=AD1, first strand: chain 'F' and resid 410 through 412 Processing sheet with id=AD2, first strand: chain 'F' and resid 446 through 447 removed outlier: 6.236A pdb=" N TYR F 446 " --> pdb=" O ILE F 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'G' and resid 55 through 56 Processing sheet with id=AD4, first strand: chain 'H' and resid 34 through 35 Processing sheet with id=AD5, first strand: chain 'H' and resid 53 through 55 removed outlier: 4.662A pdb=" N TYR H 124 " --> pdb=" O ILE H 55 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 116 through 118 removed outlier: 7.074A pdb=" N ASN H 104 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA H 96 " --> pdb=" O ASN H 104 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N CYS H 94 " --> pdb=" O PRO H 106 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 116 through 118 removed outlier: 7.074A pdb=" N ASN H 104 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA H 96 " --> pdb=" O ASN H 104 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N CYS H 94 " --> pdb=" O PRO H 106 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 223 through 225 removed outlier: 3.698A pdb=" N THR H 223 " --> pdb=" O SER H 218 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 347 through 351 removed outlier: 6.863A pdb=" N LEU H 329 " --> pdb=" O LYS H 349 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N TYR H 351 " --> pdb=" O LEU H 329 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP H 331 " --> pdb=" O TYR H 351 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N CYS H 382 " --> pdb=" O ILE H 397 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N CYS H 399 " --> pdb=" O CYS H 382 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 410 through 412 Processing sheet with id=AE2, first strand: chain 'H' and resid 446 through 447 removed outlier: 6.315A pdb=" N TYR H 446 " --> pdb=" O ILE H 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 630 hydrogen bonds defined for protein. 1752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 8.90 Time building geometry restraints manager: 6.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3399 1.32 - 1.45: 6827 1.45 - 1.57: 11916 1.57 - 1.70: 146 1.70 - 1.82: 272 Bond restraints: 22560 Sorted by residual: bond pdb=" CA CYS H 452 " pdb=" C CYS H 452 " ideal model delta sigma weight residual 1.521 1.473 0.048 1.20e-02 6.94e+03 1.59e+01 bond pdb=" CA CYS D 452 " pdb=" C CYS D 452 " ideal model delta sigma weight residual 1.521 1.473 0.048 1.20e-02 6.94e+03 1.58e+01 bond pdb=" CA ALA B 85 " pdb=" CB ALA B 85 " ideal model delta sigma weight residual 1.534 1.470 0.063 1.71e-02 3.42e+03 1.37e+01 bond pdb=" CA ALA F 85 " pdb=" CB ALA F 85 " ideal model delta sigma weight residual 1.534 1.470 0.063 1.71e-02 3.42e+03 1.37e+01 bond pdb=" CA ALA F 425 " pdb=" CB ALA F 425 " ideal model delta sigma weight residual 1.527 1.479 0.048 1.30e-02 5.92e+03 1.36e+01 ... (remaining 22555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 30049 2.25 - 4.50: 851 4.50 - 6.75: 104 6.75 - 8.99: 22 8.99 - 11.24: 2 Bond angle restraints: 31028 Sorted by residual: angle pdb=" N CYS H 208 " pdb=" CA CYS H 208 " pdb=" C CYS H 208 " ideal model delta sigma weight residual 110.32 99.08 11.24 1.59e+00 3.96e-01 5.00e+01 angle pdb=" N CYS D 208 " pdb=" CA CYS D 208 " pdb=" C CYS D 208 " ideal model delta sigma weight residual 110.32 99.14 11.18 1.59e+00 3.96e-01 4.95e+01 angle pdb=" C ALA F 425 " pdb=" N PHE F 426 " pdb=" CA PHE F 426 " ideal model delta sigma weight residual 123.00 115.11 7.89 1.38e+00 5.25e-01 3.27e+01 angle pdb=" C ALA B 425 " pdb=" N PHE B 426 " pdb=" CA PHE B 426 " ideal model delta sigma weight residual 122.72 115.19 7.53 1.38e+00 5.25e-01 2.98e+01 angle pdb=" CB HIS D 229 " pdb=" CG HIS D 229 " pdb=" CD2 HIS D 229 " ideal model delta sigma weight residual 131.20 124.19 7.01 1.30e+00 5.92e-01 2.91e+01 ... (remaining 31023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 12126 17.65 - 35.30: 942 35.30 - 52.94: 224 52.94 - 70.59: 106 70.59 - 88.24: 34 Dihedral angle restraints: 13432 sinusoidal: 5944 harmonic: 7488 Sorted by residual: dihedral pdb=" CA VAL D 83 " pdb=" C VAL D 83 " pdb=" N ARG D 84 " pdb=" CA ARG D 84 " ideal model delta harmonic sigma weight residual -180.00 -153.90 -26.10 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA VAL H 83 " pdb=" C VAL H 83 " pdb=" N ARG H 84 " pdb=" CA ARG H 84 " ideal model delta harmonic sigma weight residual 180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA HIS B 268 " pdb=" C HIS B 268 " pdb=" N VAL B 269 " pdb=" CA VAL B 269 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 13429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3077 0.083 - 0.166: 377 0.166 - 0.250: 21 0.250 - 0.333: 1 0.333 - 0.416: 2 Chirality restraints: 3478 Sorted by residual: chirality pdb=" CA CYS H 208 " pdb=" N CYS H 208 " pdb=" C CYS H 208 " pdb=" CB CYS H 208 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CA CYS D 208 " pdb=" N CYS D 208 " pdb=" C CYS D 208 " pdb=" CB CYS D 208 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA LYS D 423 " pdb=" N LYS D 423 " pdb=" C LYS D 423 " pdb=" CB LYS D 423 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 3475 not shown) Planarity restraints: 3688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 229 " 0.059 2.00e-02 2.50e+03 4.40e-02 2.90e+01 pdb=" CG HIS D 229 " -0.063 2.00e-02 2.50e+03 pdb=" ND1 HIS D 229 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 HIS D 229 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS D 229 " 0.039 2.00e-02 2.50e+03 pdb=" NE2 HIS D 229 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 229 " -0.059 2.00e-02 2.50e+03 4.39e-02 2.89e+01 pdb=" CG HIS H 229 " 0.063 2.00e-02 2.50e+03 pdb=" ND1 HIS H 229 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS H 229 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 HIS H 229 " -0.039 2.00e-02 2.50e+03 pdb=" NE2 HIS H 229 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 211 " 0.017 2.00e-02 2.50e+03 3.37e-02 1.13e+01 pdb=" C ASP B 211 " -0.058 2.00e-02 2.50e+03 pdb=" O ASP B 211 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG B 212 " 0.020 2.00e-02 2.50e+03 ... (remaining 3685 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 190 2.61 - 3.18: 17827 3.18 - 3.75: 34575 3.75 - 4.33: 50690 4.33 - 4.90: 80351 Nonbonded interactions: 183633 Sorted by model distance: nonbonded pdb=" OP1 C L 71 " pdb="MG MG F 601 " model vdw 2.032 2.170 nonbonded pdb=" OP1 C P 71 " pdb="MG MG D 601 " model vdw 2.180 2.170 nonbonded pdb=" OP1 C K 71 " pdb="MG MG B 601 " model vdw 2.207 2.170 nonbonded pdb=" OP1 C J 71 " pdb="MG MG H 702 " model vdw 2.249 2.170 nonbonded pdb=" OG SER D 218 " pdb=" O SER D 221 " model vdw 2.257 3.040 ... (remaining 183628 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = (chain 'B' and (resid 2 through 523 or resid 603 through 604)) selection = (chain 'D' and (resid 2 through 523 or resid 603 through 604)) selection = (chain 'F' and (resid 2 through 523 or resid 603 through 604)) selection = (chain 'H' and (resid 2 through 523 or resid 703 through 704)) } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'P' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.650 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: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 59.320 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.130 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:14.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 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 : 0.005 0.063 22560 Z= 0.358 Angle : 0.848 11.243 31028 Z= 0.523 Chirality : 0.052 0.416 3478 Planarity : 0.006 0.072 3688 Dihedral : 14.937 88.240 8624 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.14), residues: 2548 helix: -2.15 (0.15), residues: 640 sheet: -1.58 (0.30), residues: 224 loop : -1.69 (0.13), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 348 HIS 0.016 0.002 HIS H 487 PHE 0.015 0.002 PHE A 68 TYR 0.030 0.002 TYR A 76 ARG 0.006 0.000 ARG F 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 2.133 Fit side-chains revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7863 (mt-10) REVERT: B 36 GLU cc_start: 0.7323 (tm-30) cc_final: 0.6942 (tm-30) REVERT: B 77 GLU cc_start: 0.7519 (tt0) cc_final: 0.7005 (mp0) REVERT: B 147 LYS cc_start: 0.8713 (ptmt) cc_final: 0.8192 (ttmt) REVERT: B 165 LYS cc_start: 0.8436 (mtpt) cc_final: 0.8134 (mtpp) REVERT: B 168 GLN cc_start: 0.6927 (tp-100) cc_final: 0.6695 (tt0) REVERT: B 276 MET cc_start: 0.8290 (mtt) cc_final: 0.8026 (mtm) REVERT: B 302 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6926 (mt-10) REVERT: B 340 CYS cc_start: 0.7033 (m) cc_final: 0.6598 (m) REVERT: B 347 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7961 (tm-30) REVERT: B 382 CYS cc_start: 0.7694 (m) cc_final: 0.7150 (m) REVERT: B 391 ARG cc_start: 0.8464 (ttm170) cc_final: 0.8187 (ttm-80) REVERT: B 492 ARG cc_start: 0.8010 (mtt90) cc_final: 0.7692 (mtt90) REVERT: C 3 ASN cc_start: 0.8066 (t0) cc_final: 0.7855 (m110) REVERT: C 40 ASN cc_start: 0.8577 (t0) cc_final: 0.7766 (t0) REVERT: C 62 ASN cc_start: 0.6624 (m-40) cc_final: 0.6294 (m110) REVERT: C 85 ASN cc_start: 0.7162 (t0) cc_final: 0.6831 (t0) REVERT: C 114 ASN cc_start: 0.7957 (m110) cc_final: 0.7653 (m110) REVERT: D 327 PRO cc_start: 0.7298 (Cg_exo) cc_final: 0.6993 (Cg_endo) REVERT: D 331 ASP cc_start: 0.6546 (t0) cc_final: 0.5968 (t70) REVERT: D 476 ARG cc_start: 0.7524 (ptp-110) cc_final: 0.7157 (ttp-110) REVERT: E 43 LYS cc_start: 0.8200 (ttmt) cc_final: 0.7993 (ttpp) REVERT: E 66 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7849 (mt-10) REVERT: F 36 GLU cc_start: 0.7358 (tm-30) cc_final: 0.6981 (tm-30) REVERT: F 77 GLU cc_start: 0.7520 (tt0) cc_final: 0.6987 (mp0) REVERT: F 147 LYS cc_start: 0.8717 (ptmt) cc_final: 0.8173 (ttmt) REVERT: F 165 LYS cc_start: 0.8428 (mtpt) cc_final: 0.8099 (mtpp) REVERT: F 168 GLN cc_start: 0.6933 (tp-100) cc_final: 0.6679 (tt0) REVERT: F 276 MET cc_start: 0.8292 (mtt) cc_final: 0.8032 (mtm) REVERT: F 302 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6872 (mt-10) REVERT: F 340 CYS cc_start: 0.7134 (m) cc_final: 0.6730 (m) REVERT: F 347 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7923 (tm-30) REVERT: F 382 CYS cc_start: 0.7791 (m) cc_final: 0.7222 (m) REVERT: F 492 ARG cc_start: 0.8023 (mtt90) cc_final: 0.7690 (mtt90) REVERT: G 3 ASN cc_start: 0.8061 (t0) cc_final: 0.7852 (m110) REVERT: G 40 ASN cc_start: 0.8586 (t0) cc_final: 0.7783 (t0) REVERT: G 48 HIS cc_start: 0.7568 (m-70) cc_final: 0.7358 (m-70) REVERT: G 62 ASN cc_start: 0.6547 (m-40) cc_final: 0.6232 (m110) REVERT: G 85 ASN cc_start: 0.7201 (t0) cc_final: 0.6886 (t0) REVERT: G 114 ASN cc_start: 0.7972 (m110) cc_final: 0.7677 (m110) REVERT: H 195 MET cc_start: 0.8840 (mtt) cc_final: 0.8606 (mtt) REVERT: H 327 PRO cc_start: 0.7295 (Cg_exo) cc_final: 0.6989 (Cg_endo) REVERT: H 331 ASP cc_start: 0.6544 (t0) cc_final: 0.6031 (t70) REVERT: H 476 ARG cc_start: 0.7518 (ptp-110) cc_final: 0.7154 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 1.4382 time to fit residues: 501.7297 Evaluate side-chains 222 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 1.9990 chunk 197 optimal weight: 0.3980 chunk 109 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 203 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 236 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 246 GLN B 268 HIS B 388 ASN B 424 HIS D 22 GLN D 108 GLN D 246 GLN D 499 ASN E 40 ASN F 246 GLN F 268 HIS F 388 ASN H 22 GLN H 108 GLN H 246 GLN H 499 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.131191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.086404 restraints weight = 30469.644| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.49 r_work: 0.3090 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 22560 Z= 0.178 Angle : 0.527 7.382 31028 Z= 0.277 Chirality : 0.042 0.156 3478 Planarity : 0.004 0.053 3688 Dihedral : 13.481 86.696 4044 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.04 % Allowed : 9.81 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.15), residues: 2548 helix: -0.72 (0.19), residues: 664 sheet: -1.77 (0.30), residues: 268 loop : -1.09 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 348 HIS 0.006 0.001 HIS F 424 PHE 0.021 0.001 PHE F 350 TYR 0.019 0.001 TYR D 446 ARG 0.003 0.000 ARG B 476 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 244 time to evaluate : 2.595 Fit side-chains REVERT: A 43 LYS cc_start: 0.8005 (ttpt) cc_final: 0.7685 (tppp) REVERT: B 36 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7450 (tm-30) REVERT: B 77 GLU cc_start: 0.7879 (tt0) cc_final: 0.7075 (mp0) REVERT: B 147 LYS cc_start: 0.8797 (ptmt) cc_final: 0.8061 (ttmt) REVERT: B 165 LYS cc_start: 0.8377 (mtpt) cc_final: 0.8070 (mtpp) REVERT: B 168 GLN cc_start: 0.7074 (tp-100) cc_final: 0.6643 (tt0) REVERT: B 302 GLU cc_start: 0.6655 (mt-10) cc_final: 0.6121 (mt-10) REVERT: B 304 LYS cc_start: 0.7990 (mttt) cc_final: 0.7750 (mtmm) REVERT: B 347 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8005 (tm-30) REVERT: B 350 PHE cc_start: 0.7855 (m-80) cc_final: 0.7586 (m-80) REVERT: B 382 CYS cc_start: 0.7738 (m) cc_final: 0.7274 (m) REVERT: B 391 ARG cc_start: 0.8208 (ttm170) cc_final: 0.7949 (ttm-80) REVERT: B 485 ARG cc_start: 0.5701 (OUTLIER) cc_final: 0.5307 (mmp-170) REVERT: B 489 ASN cc_start: 0.7010 (p0) cc_final: 0.6804 (p0) REVERT: B 517 TYR cc_start: 0.7954 (t80) cc_final: 0.7502 (t80) REVERT: C 3 ASN cc_start: 0.8015 (t0) cc_final: 0.7665 (m110) REVERT: C 40 ASN cc_start: 0.8296 (t0) cc_final: 0.7420 (t0) REVERT: C 62 ASN cc_start: 0.5673 (m-40) cc_final: 0.5400 (m110) REVERT: C 95 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6994 (mttp) REVERT: D 331 ASP cc_start: 0.6583 (t0) cc_final: 0.6217 (t70) REVERT: D 476 ARG cc_start: 0.7438 (ptp-110) cc_final: 0.7123 (ttp-110) REVERT: F 36 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7436 (tm-30) REVERT: F 77 GLU cc_start: 0.7877 (tt0) cc_final: 0.7073 (mp0) REVERT: F 165 LYS cc_start: 0.8373 (mtpt) cc_final: 0.8073 (mtpp) REVERT: F 168 GLN cc_start: 0.7060 (tp-100) cc_final: 0.6628 (tt0) REVERT: F 302 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6210 (mt-10) REVERT: F 304 LYS cc_start: 0.7938 (mttt) cc_final: 0.7697 (mtmm) REVERT: F 347 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7918 (tm-30) REVERT: F 382 CYS cc_start: 0.7871 (m) cc_final: 0.7316 (m) REVERT: F 391 ARG cc_start: 0.8231 (ttp80) cc_final: 0.7807 (ttm-80) REVERT: F 485 ARG cc_start: 0.5586 (OUTLIER) cc_final: 0.5187 (mmp-170) REVERT: F 489 ASN cc_start: 0.7079 (p0) cc_final: 0.6841 (p0) REVERT: F 517 TYR cc_start: 0.7984 (t80) cc_final: 0.7468 (t80) REVERT: G 3 ASN cc_start: 0.8015 (t0) cc_final: 0.7667 (m110) REVERT: G 40 ASN cc_start: 0.8293 (t0) cc_final: 0.7459 (t0) REVERT: G 62 ASN cc_start: 0.5716 (m-40) cc_final: 0.5488 (m110) REVERT: G 95 LYS cc_start: 0.7168 (mptm) cc_final: 0.6873 (mttp) REVERT: H 195 MET cc_start: 0.8912 (mtt) cc_final: 0.8655 (mtt) REVERT: H 331 ASP cc_start: 0.6653 (t0) cc_final: 0.6222 (t70) REVERT: H 476 ARG cc_start: 0.7425 (ptp-110) cc_final: 0.7113 (ttp-110) outliers start: 23 outliers final: 3 residues processed: 256 average time/residue: 1.3419 time to fit residues: 393.8805 Evaluate side-chains 219 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 213 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain H residue 340 CYS Chi-restraints excluded: chain H residue 341 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 113 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 169 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 131 optimal weight: 0.5980 chunk 135 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 HIS D 95 HIS F 268 HIS F 424 HIS H 95 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.129909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.085117 restraints weight = 30682.100| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.50 r_work: 0.3071 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22560 Z= 0.234 Angle : 0.515 7.213 31028 Z= 0.272 Chirality : 0.043 0.176 3478 Planarity : 0.004 0.052 3688 Dihedral : 13.309 85.564 4044 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.54 % Allowed : 11.12 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.16), residues: 2548 helix: -0.16 (0.20), residues: 644 sheet: -1.77 (0.26), residues: 348 loop : -0.74 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 348 HIS 0.006 0.001 HIS F 424 PHE 0.021 0.002 PHE F 326 TYR 0.023 0.001 TYR D 446 ARG 0.008 0.000 ARG B 492 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 2.085 Fit side-chains REVERT: A 43 LYS cc_start: 0.8279 (ttpt) cc_final: 0.7918 (tppp) REVERT: A 63 MET cc_start: 0.8112 (mmt) cc_final: 0.7828 (mmt) REVERT: B 36 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7428 (tm-30) REVERT: B 77 GLU cc_start: 0.7852 (tt0) cc_final: 0.7063 (mp0) REVERT: B 165 LYS cc_start: 0.8324 (mtpt) cc_final: 0.8095 (mtpp) REVERT: B 168 GLN cc_start: 0.7153 (tp-100) cc_final: 0.6735 (tt0) REVERT: B 302 GLU cc_start: 0.6630 (mt-10) cc_final: 0.6133 (mt-10) REVERT: B 304 LYS cc_start: 0.7924 (mttt) cc_final: 0.7699 (mtmm) REVERT: B 313 GLN cc_start: 0.7554 (tt0) cc_final: 0.6978 (tm-30) REVERT: B 324 ASP cc_start: 0.7754 (m-30) cc_final: 0.7336 (m-30) REVERT: B 325 LYS cc_start: 0.8453 (mppt) cc_final: 0.7748 (mppt) REVERT: B 340 CYS cc_start: 0.6811 (m) cc_final: 0.5271 (m) REVERT: B 347 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7742 (tm-30) REVERT: B 382 CYS cc_start: 0.7840 (m) cc_final: 0.7308 (m) REVERT: B 391 ARG cc_start: 0.8199 (ttm170) cc_final: 0.7926 (ttm-80) REVERT: B 517 TYR cc_start: 0.7915 (t80) cc_final: 0.7421 (t80) REVERT: C 40 ASN cc_start: 0.8249 (t0) cc_final: 0.7439 (t0) REVERT: C 48 HIS cc_start: 0.7266 (m-70) cc_final: 0.7004 (m-70) REVERT: C 62 ASN cc_start: 0.5701 (m-40) cc_final: 0.5379 (m110) REVERT: C 95 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.7208 (mttp) REVERT: D 61 LYS cc_start: 0.8391 (mtpt) cc_final: 0.7972 (mttp) REVERT: D 77 GLU cc_start: 0.7486 (pt0) cc_final: 0.7225 (tt0) REVERT: D 331 ASP cc_start: 0.6697 (t0) cc_final: 0.6269 (t70) REVERT: D 476 ARG cc_start: 0.7398 (ptp-110) cc_final: 0.7108 (ttp-110) REVERT: E 43 LYS cc_start: 0.8386 (ttpt) cc_final: 0.8112 (tttt) REVERT: E 63 MET cc_start: 0.8064 (mmt) cc_final: 0.7776 (mmt) REVERT: F 36 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7364 (tm-30) REVERT: F 77 GLU cc_start: 0.7813 (tt0) cc_final: 0.7036 (mp0) REVERT: F 165 LYS cc_start: 0.8357 (mtpt) cc_final: 0.8093 (mtpp) REVERT: F 168 GLN cc_start: 0.7148 (tp-100) cc_final: 0.6729 (tt0) REVERT: F 302 GLU cc_start: 0.6612 (mt-10) cc_final: 0.6127 (mt-10) REVERT: F 304 LYS cc_start: 0.7919 (mttt) cc_final: 0.7696 (mtmm) REVERT: F 313 GLN cc_start: 0.7612 (tt0) cc_final: 0.7071 (tm-30) REVERT: F 324 ASP cc_start: 0.7758 (m-30) cc_final: 0.7341 (m-30) REVERT: F 325 LYS cc_start: 0.8474 (mppt) cc_final: 0.7788 (mppt) REVERT: F 340 CYS cc_start: 0.6735 (m) cc_final: 0.5340 (m) REVERT: F 382 CYS cc_start: 0.7891 (m) cc_final: 0.7343 (m) REVERT: F 485 ARG cc_start: 0.5838 (OUTLIER) cc_final: 0.5331 (mmp-170) REVERT: F 489 ASN cc_start: 0.7089 (p0) cc_final: 0.6806 (p0) REVERT: F 517 TYR cc_start: 0.7915 (t80) cc_final: 0.7424 (t80) REVERT: G 3 ASN cc_start: 0.8023 (t0) cc_final: 0.7668 (m110) REVERT: G 40 ASN cc_start: 0.8277 (t0) cc_final: 0.7465 (t0) REVERT: G 48 HIS cc_start: 0.7385 (m-70) cc_final: 0.7166 (m-70) REVERT: G 95 LYS cc_start: 0.7458 (mptm) cc_final: 0.7154 (mttp) REVERT: H 61 LYS cc_start: 0.8394 (mtpt) cc_final: 0.7977 (mttm) REVERT: H 331 ASP cc_start: 0.6696 (t0) cc_final: 0.6321 (t70) REVERT: H 476 ARG cc_start: 0.7371 (ptp-110) cc_final: 0.7057 (ttp-110) outliers start: 34 outliers final: 8 residues processed: 255 average time/residue: 1.3267 time to fit residues: 388.6172 Evaluate side-chains 228 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 218 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain F residue 502 ILE Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 341 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 100 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 247 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 HIS C 105 ASN F 252 ASN F 268 HIS G 105 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.128926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.084144 restraints weight = 30900.295| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.50 r_work: 0.3055 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22560 Z= 0.285 Angle : 0.530 9.469 31028 Z= 0.279 Chirality : 0.043 0.193 3478 Planarity : 0.004 0.052 3688 Dihedral : 13.271 85.870 4044 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.81 % Allowed : 12.88 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.16), residues: 2548 helix: 0.07 (0.21), residues: 640 sheet: -1.57 (0.26), residues: 356 loop : -0.67 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 292 HIS 0.005 0.001 HIS D 424 PHE 0.020 0.002 PHE H 444 TYR 0.027 0.001 TYR D 446 ARG 0.009 0.000 ARG F 492 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 227 time to evaluate : 2.371 Fit side-chains REVERT: A 43 LYS cc_start: 0.8352 (ttpt) cc_final: 0.8042 (tttt) REVERT: A 63 MET cc_start: 0.8188 (mmt) cc_final: 0.7928 (mmt) REVERT: B 36 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7532 (tm-30) REVERT: B 77 GLU cc_start: 0.7786 (tt0) cc_final: 0.7017 (mp0) REVERT: B 168 GLN cc_start: 0.7183 (tp-100) cc_final: 0.6780 (tt0) REVERT: B 304 LYS cc_start: 0.7906 (mttt) cc_final: 0.7688 (mtmm) REVERT: B 313 GLN cc_start: 0.7744 (tt0) cc_final: 0.7206 (tm-30) REVERT: B 325 LYS cc_start: 0.8506 (mppt) cc_final: 0.7802 (mppt) REVERT: B 340 CYS cc_start: 0.6780 (m) cc_final: 0.5526 (m) REVERT: B 382 CYS cc_start: 0.7832 (m) cc_final: 0.7460 (m) REVERT: B 408 ASN cc_start: 0.8171 (m-40) cc_final: 0.7609 (p0) REVERT: B 492 ARG cc_start: 0.7947 (mtt90) cc_final: 0.7614 (mtt90) REVERT: B 517 TYR cc_start: 0.7890 (t80) cc_final: 0.7395 (t80) REVERT: C 40 ASN cc_start: 0.8240 (t0) cc_final: 0.7365 (t0) REVERT: D 61 LYS cc_start: 0.8422 (mtpt) cc_final: 0.8022 (mttm) REVERT: D 77 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: D 331 ASP cc_start: 0.6603 (t0) cc_final: 0.6226 (t70) REVERT: D 476 ARG cc_start: 0.7577 (ptp-110) cc_final: 0.7222 (ttp-110) REVERT: E 43 LYS cc_start: 0.8383 (ttpt) cc_final: 0.8106 (tttt) REVERT: E 63 MET cc_start: 0.8173 (mmt) cc_final: 0.7821 (mmt) REVERT: F 36 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7482 (tm-30) REVERT: F 77 GLU cc_start: 0.7804 (tt0) cc_final: 0.7028 (mp0) REVERT: F 168 GLN cc_start: 0.7167 (tp-100) cc_final: 0.6765 (tt0) REVERT: F 304 LYS cc_start: 0.7910 (mttt) cc_final: 0.7696 (mtmm) REVERT: F 313 GLN cc_start: 0.7693 (tt0) cc_final: 0.7117 (tm-30) REVERT: F 325 LYS cc_start: 0.8493 (mppt) cc_final: 0.7843 (mppt) REVERT: F 340 CYS cc_start: 0.6744 (m) cc_final: 0.5410 (m) REVERT: F 382 CYS cc_start: 0.7794 (m) cc_final: 0.7467 (m) REVERT: F 408 ASN cc_start: 0.8163 (m-40) cc_final: 0.7605 (p0) REVERT: F 489 ASN cc_start: 0.7146 (p0) cc_final: 0.6847 (p0) REVERT: F 492 ARG cc_start: 0.7998 (mtt90) cc_final: 0.7679 (mtt90) REVERT: F 517 TYR cc_start: 0.7886 (t80) cc_final: 0.7442 (t80) REVERT: G 40 ASN cc_start: 0.8239 (t0) cc_final: 0.7386 (t0) REVERT: G 45 LEU cc_start: 0.7111 (mt) cc_final: 0.6699 (mt) REVERT: H 61 LYS cc_start: 0.8427 (mtpt) cc_final: 0.8026 (mttm) REVERT: H 331 ASP cc_start: 0.6592 (t0) cc_final: 0.6196 (t70) REVERT: H 476 ARG cc_start: 0.7555 (ptp-110) cc_final: 0.7202 (ttp-110) outliers start: 40 outliers final: 18 residues processed: 247 average time/residue: 1.2997 time to fit residues: 369.9629 Evaluate side-chains 229 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 210 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 502 ILE Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 341 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 94 optimal weight: 3.9990 chunk 78 optimal weight: 0.0370 chunk 0 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 183 optimal weight: 0.0570 chunk 74 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 196 optimal weight: 0.6980 chunk 162 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN B 268 HIS B 354 GLN C 62 ASN D 82 HIS D 518 ASN F 245 GLN F 268 HIS F 354 GLN H 518 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.132674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.088537 restraints weight = 30566.376| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.50 r_work: 0.3110 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 22560 Z= 0.130 Angle : 0.467 7.156 31028 Z= 0.244 Chirality : 0.041 0.156 3478 Planarity : 0.003 0.047 3688 Dihedral : 13.062 84.541 4044 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.81 % Allowed : 14.33 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.16), residues: 2548 helix: 0.34 (0.21), residues: 660 sheet: -1.48 (0.30), residues: 284 loop : -0.60 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 292 HIS 0.006 0.001 HIS D 424 PHE 0.022 0.001 PHE H 444 TYR 0.011 0.001 TYR D 447 ARG 0.006 0.000 ARG B 492 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 241 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8230 (ttpt) cc_final: 0.7973 (tttt) REVERT: A 53 GLN cc_start: 0.8268 (mt0) cc_final: 0.7804 (mm-40) REVERT: B 36 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7522 (tm-30) REVERT: B 77 GLU cc_start: 0.7757 (tt0) cc_final: 0.7105 (mp0) REVERT: B 168 GLN cc_start: 0.7119 (tp-100) cc_final: 0.6847 (tt0) REVERT: B 313 GLN cc_start: 0.7595 (tt0) cc_final: 0.7044 (tm-30) REVERT: B 325 LYS cc_start: 0.8493 (mppt) cc_final: 0.7840 (mppt) REVERT: B 340 CYS cc_start: 0.6664 (m) cc_final: 0.5298 (m) REVERT: B 382 CYS cc_start: 0.7770 (m) cc_final: 0.7188 (m) REVERT: B 408 ASN cc_start: 0.8155 (m-40) cc_final: 0.7629 (p0) REVERT: B 492 ARG cc_start: 0.7869 (mtt90) cc_final: 0.7541 (mtt90) REVERT: B 517 TYR cc_start: 0.7757 (t80) cc_final: 0.7306 (t80) REVERT: C 40 ASN cc_start: 0.8138 (t0) cc_final: 0.7371 (t0) REVERT: C 43 LYS cc_start: 0.7602 (tttt) cc_final: 0.7232 (tttm) REVERT: D 61 LYS cc_start: 0.8373 (mtpt) cc_final: 0.7979 (mttp) REVERT: D 76 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7508 (ttm170) REVERT: D 77 GLU cc_start: 0.7483 (pt0) cc_final: 0.7242 (tt0) REVERT: D 154 TYR cc_start: 0.8498 (m-80) cc_final: 0.8235 (m-80) REVERT: D 331 ASP cc_start: 0.6606 (t0) cc_final: 0.6309 (t70) REVERT: D 476 ARG cc_start: 0.7537 (ptp-110) cc_final: 0.7203 (ttp-110) REVERT: E 43 LYS cc_start: 0.8250 (ttpt) cc_final: 0.7987 (tttt) REVERT: F 36 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7518 (tm-30) REVERT: F 77 GLU cc_start: 0.7763 (tt0) cc_final: 0.7108 (mp0) REVERT: F 168 GLN cc_start: 0.7118 (tp-100) cc_final: 0.6845 (tt0) REVERT: F 304 LYS cc_start: 0.7933 (mttt) cc_final: 0.7731 (mtmm) REVERT: F 313 GLN cc_start: 0.7581 (tt0) cc_final: 0.7034 (tm-30) REVERT: F 325 LYS cc_start: 0.8511 (mppt) cc_final: 0.7856 (mppt) REVERT: F 340 CYS cc_start: 0.6626 (m) cc_final: 0.5277 (m) REVERT: F 382 CYS cc_start: 0.7825 (m) cc_final: 0.7351 (m) REVERT: F 408 ASN cc_start: 0.8148 (m-40) cc_final: 0.7624 (p0) REVERT: F 489 ASN cc_start: 0.7076 (p0) cc_final: 0.6819 (p0) REVERT: F 492 ARG cc_start: 0.7914 (mtt90) cc_final: 0.7600 (mtt90) REVERT: F 517 TYR cc_start: 0.7677 (t80) cc_final: 0.7164 (t80) REVERT: G 40 ASN cc_start: 0.8166 (t0) cc_final: 0.7415 (t0) REVERT: G 95 LYS cc_start: 0.7334 (mptm) cc_final: 0.7061 (mttp) REVERT: H 61 LYS cc_start: 0.8379 (mtpt) cc_final: 0.7985 (mttp) REVERT: H 154 TYR cc_start: 0.8496 (m-80) cc_final: 0.8231 (m-80) REVERT: H 331 ASP cc_start: 0.6604 (t0) cc_final: 0.6353 (t70) REVERT: H 476 ARG cc_start: 0.7535 (ptp-110) cc_final: 0.7203 (ttp-110) outliers start: 40 outliers final: 17 residues processed: 268 average time/residue: 1.2892 time to fit residues: 396.7324 Evaluate side-chains 231 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 326 PHE Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 341 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 236 optimal weight: 0.7980 chunk 205 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 239 optimal weight: 9.9990 chunk 144 optimal weight: 0.0980 chunk 210 optimal weight: 4.9990 chunk 240 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 HIS B 354 GLN C 105 ASN D 188 HIS F 245 GLN F 252 ASN F 268 HIS G 62 ASN G 105 ASN H 188 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.129939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.085300 restraints weight = 30545.674| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.50 r_work: 0.3058 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22560 Z= 0.241 Angle : 0.503 9.139 31028 Z= 0.264 Chirality : 0.042 0.151 3478 Planarity : 0.004 0.050 3688 Dihedral : 13.050 85.041 4044 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.36 % Allowed : 14.78 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.16), residues: 2548 helix: 0.42 (0.21), residues: 640 sheet: -1.29 (0.26), residues: 356 loop : -0.51 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 292 HIS 0.009 0.001 HIS F 330 PHE 0.017 0.001 PHE H 350 TYR 0.015 0.001 TYR D 446 ARG 0.005 0.000 ARG B 492 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8295 (ttpt) cc_final: 0.7989 (tttt) REVERT: B 36 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7586 (tm-30) REVERT: B 77 GLU cc_start: 0.7787 (tt0) cc_final: 0.7120 (mp0) REVERT: B 168 GLN cc_start: 0.7118 (tp-100) cc_final: 0.6743 (tt0) REVERT: B 313 GLN cc_start: 0.7719 (tt0) cc_final: 0.7129 (tm-30) REVERT: B 325 LYS cc_start: 0.8521 (mppt) cc_final: 0.7813 (mppt) REVERT: B 340 CYS cc_start: 0.6786 (m) cc_final: 0.5424 (m) REVERT: B 382 CYS cc_start: 0.7888 (m) cc_final: 0.7495 (m) REVERT: B 408 ASN cc_start: 0.8150 (m-40) cc_final: 0.7634 (p0) REVERT: B 492 ARG cc_start: 0.7934 (mtt90) cc_final: 0.7630 (mtt90) REVERT: B 517 TYR cc_start: 0.7666 (t80) cc_final: 0.7199 (t80) REVERT: C 40 ASN cc_start: 0.8299 (t0) cc_final: 0.7554 (t0) REVERT: C 43 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7293 (tttm) REVERT: D 61 LYS cc_start: 0.8395 (mtpt) cc_final: 0.8011 (mttm) REVERT: D 77 GLU cc_start: 0.7548 (pt0) cc_final: 0.7325 (tt0) REVERT: D 331 ASP cc_start: 0.6359 (t0) cc_final: 0.6060 (t70) REVERT: D 476 ARG cc_start: 0.7514 (ptp-110) cc_final: 0.7172 (ttp-110) REVERT: E 43 LYS cc_start: 0.8334 (ttpt) cc_final: 0.8049 (tttt) REVERT: F 36 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7574 (tm-30) REVERT: F 77 GLU cc_start: 0.7797 (tt0) cc_final: 0.7131 (mp0) REVERT: F 168 GLN cc_start: 0.7109 (tp-100) cc_final: 0.6735 (tt0) REVERT: F 304 LYS cc_start: 0.7873 (mttt) cc_final: 0.7591 (mtpt) REVERT: F 313 GLN cc_start: 0.7709 (tt0) cc_final: 0.7128 (tm-30) REVERT: F 325 LYS cc_start: 0.8568 (mppt) cc_final: 0.7869 (mppt) REVERT: F 340 CYS cc_start: 0.6788 (m) cc_final: 0.5439 (m) REVERT: F 382 CYS cc_start: 0.7795 (m) cc_final: 0.7376 (m) REVERT: F 408 ASN cc_start: 0.8164 (m-40) cc_final: 0.7629 (p0) REVERT: F 489 ASN cc_start: 0.7129 (p0) cc_final: 0.6838 (p0) REVERT: F 492 ARG cc_start: 0.7965 (mtt90) cc_final: 0.7672 (mtt90) REVERT: F 517 TYR cc_start: 0.7635 (t80) cc_final: 0.7168 (t80) REVERT: G 40 ASN cc_start: 0.8285 (t0) cc_final: 0.7521 (t0) REVERT: G 95 LYS cc_start: 0.7419 (mptm) cc_final: 0.7126 (mttp) REVERT: H 61 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7988 (mttm) REVERT: H 331 ASP cc_start: 0.6437 (t0) cc_final: 0.6134 (t70) REVERT: H 476 ARG cc_start: 0.7511 (ptp-110) cc_final: 0.7167 (ttp-110) outliers start: 30 outliers final: 15 residues processed: 242 average time/residue: 1.2253 time to fit residues: 344.3686 Evaluate side-chains 223 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 207 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 326 PHE Chi-restraints excluded: chain H residue 341 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.5428 > 50: distance: 37 - 210: 4.403 distance: 40 - 207: 10.387 distance: 50 - 196: 16.103 distance: 53 - 193: 10.638 distance: 101 - 224: 7.955 distance: 129 - 151: 3.438 distance: 133 - 159: 10.190 distance: 144 - 167: 4.195 distance: 148 - 173: 6.512 distance: 151 - 152: 4.077 distance: 152 - 153: 3.248 distance: 152 - 155: 10.463 distance: 153 - 159: 5.130 distance: 155 - 156: 5.837 distance: 156 - 157: 9.172 distance: 157 - 158: 8.585 distance: 159 - 160: 6.174 distance: 160 - 161: 4.335 distance: 161 - 162: 8.524 distance: 161 - 167: 5.268 distance: 163 - 164: 11.587 distance: 163 - 165: 18.423 distance: 164 - 166: 4.490 distance: 167 - 168: 3.325 distance: 168 - 169: 3.648 distance: 168 - 171: 5.341 distance: 169 - 173: 5.558 distance: 171 - 172: 5.972 distance: 174 - 175: 5.498 distance: 174 - 177: 5.103 distance: 175 - 176: 3.872 distance: 175 - 178: 3.516 distance: 179 - 180: 3.180 distance: 180 - 181: 4.421 distance: 180 - 182: 3.618 distance: 183 - 184: 8.034 distance: 183 - 186: 4.328 distance: 184 - 185: 3.703 distance: 184 - 193: 7.258 distance: 186 - 187: 4.352 distance: 187 - 188: 4.571 distance: 188 - 190: 5.926 distance: 189 - 191: 3.265 distance: 190 - 192: 4.314 distance: 193 - 194: 6.740 distance: 194 - 195: 6.642 distance: 194 - 197: 9.076 distance: 195 - 196: 13.897 distance: 195 - 199: 15.269 distance: 197 - 198: 8.817 distance: 199 - 200: 31.930 distance: 200 - 201: 17.224 distance: 200 - 203: 19.640 distance: 201 - 202: 7.231 distance: 201 - 207: 15.163 distance: 203 - 204: 32.714 distance: 204 - 205: 36.196 distance: 204 - 206: 18.045 distance: 207 - 208: 9.589 distance: 208 - 211: 3.848 distance: 209 - 210: 3.993 distance: 211 - 212: 9.093 distance: 212 - 213: 7.260 distance: 213 - 215: 3.892 distance: 214 - 216: 7.090 distance: 214 - 217: 6.332 distance: 215 - 216: 7.648 distance: 218 - 220: 6.816 distance: 219 - 220: 5.237 distance: 221 - 222: 3.560 distance: 225 - 226: 7.117 distance: 225 - 227: 3.744