Starting phenix.real_space_refine on Sun Sep 13 08:56:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n0d_24104/09_2026/7n0d_24104.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n0d_24104/09_2026/7n0d_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 { model { file = "/net/cci-nas-00/data/ceres_data/7n0d_24104/09_2026/7n0d_24104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n0d_24104/09_2026/7n0d_24104.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7n0d_24104/09_2026/7n0d_24104.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n0d_24104/09_2026/7n0d_24104.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n0d_24104/09_2026/7n0d_24104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n0d_24104/09_2026/7n0d_24104.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: 10 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: 10 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: 5.19, per 1000 atoms: 0.24 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: 1.38 Conformation dependent library (CDL) restraints added in 947.7 milliseconds 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: 2.69 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: 4.07 Time building geometry restraints manager: 1.91 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: 29906 2.25 - 4.50: 994 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: 11844 17.65 - 35.30: 914 35.30 - 52.94: 236 52.94 - 70.59: 50 70.59 - 88.24: 10 Dihedral angle restraints: 13054 sinusoidal: 5566 harmonic: 7488 Sorted by residual: dihedral pdb=" O5' G I 9 " pdb=" C5' G I 9 " pdb=" C4' G I 9 " pdb=" C3' G I 9 " ideal model delta sinusoidal sigma weight residual 180.00 127.39 52.61 3 6.40e+00 2.44e-02 5.02e+01 dihedral pdb=" O5' G T 9 " pdb=" C5' G T 9 " pdb=" C4' G T 9 " pdb=" C3' G T 9 " ideal model delta sinusoidal sigma weight residual 180.00 127.45 52.55 3 6.40e+00 2.44e-02 5.01e+01 dihedral pdb=" O5' A K 63 " pdb=" C5' A K 63 " pdb=" C4' A K 63 " pdb=" C3' A K 63 " ideal model delta sinusoidal sigma weight residual 60.00 16.46 43.54 3 6.40e+00 2.44e-02 4.30e+01 ... (remaining 13051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2999 0.083 - 0.166: 379 0.166 - 0.250: 95 0.250 - 0.333: 3 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: 0.00 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: 2.210 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.990 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 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 : 0.014 0.574 22640 Z= 0.529 Angle : 1.046 28.085 31092 Z= 0.542 Chirality : 0.063 0.416 3478 Planarity : 0.006 0.072 3688 Dihedral : 13.791 88.240 8246 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (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 ARG 0.006 0.000 ARG F 84 TYR 0.030 0.002 TYR A 76 PHE 0.015 0.002 PHE A 68 TRP 0.025 0.002 TRP B 348 HIS 0.016 0.002 HIS H 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.31 (22560) covalent geometry : angle 0.87281 / 0.53 (31028) hydrogen bonds : bond 0.18180 / 12.48 ( 680) hydrogen bonds : angle 7.50107 / 5.25 ( 1900) metal coordination : bond 0.21619 / 15.22 ( 80) metal coordination : angle 12.75392 / 9.36 ( 64) *********************** 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 : 0.666 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: 0.7695 (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: 0.8607 (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: 0.6283 time to fit residues: 220.1068 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 : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 0.3980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.0170 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 258 optimal weight: 3.9990 overall best weight: 1.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN B 246 GLN B 388 ASN D 22 GLN D 95 HIS D 246 GLN D 441 GLN D 499 ASN E 40 ASN F 246 GLN F 268 HIS F 388 ASN H 22 GLN H 95 HIS H 246 GLN H 441 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 = 0.3808 r_free = 0.3808 target = 0.130066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.085008 restraints weight = 30696.011| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.50 r_work: 0.3066 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22640 Z= 0.163 Angle : 0.623 13.153 31092 Z= 0.300 Chirality : 0.046 0.252 3478 Planarity : 0.004 0.055 3688 Dihedral : 9.876 78.939 3666 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.27 % Allowed : 9.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.15), residues: 2548 helix: -0.73 (0.19), residues: 644 sheet: -1.81 (0.27), residues: 316 loop : -1.06 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 476 TYR 0.018 0.001 TYR D 446 PHE 0.020 0.002 PHE F 350 TRP 0.011 0.001 TRP F 348 HIS 0.006 0.001 HIS F 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (22560) covalent geometry : angle 0.59283 / 0.30 (31028) hydrogen bonds : bond 0.03960 / 2.69 ( 680) hydrogen bonds : angle 5.01697 / 3.49 ( 1900) metal coordination : bond 0.01281 / 0.83 ( 80) metal coordination : angle 4.23824 / 3.02 ( 64) *********************** 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 261 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 233 time to evaluate : 0.832 Fit side-chains REVERT: A 43 LYS cc_start: 0.8145 (ttpt) cc_final: 0.7837 (tppp) REVERT: B 36 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7415 (tm-30) REVERT: B 77 GLU cc_start: 0.7887 (tt0) cc_final: 0.7083 (mp0) REVERT: B 168 GLN cc_start: 0.7129 (tp-100) cc_final: 0.6698 (tt0) REVERT: B 276 MET cc_start: 0.8382 (mtt) cc_final: 0.8147 (mtm) REVERT: B 302 GLU cc_start: 0.6674 (mt-10) cc_final: 0.6148 (mt-10) REVERT: B 304 LYS cc_start: 0.7940 (mttt) cc_final: 0.7704 (mtmm) REVERT: B 347 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7947 (tm-30) REVERT: B 350 PHE cc_start: 0.7817 (m-80) cc_final: 0.7552 (m-80) REVERT: B 382 CYS cc_start: 0.7763 (m) cc_final: 0.7317 (m) REVERT: B 391 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7930 (ttm-80) REVERT: B 485 ARG cc_start: 0.5748 (OUTLIER) cc_final: 0.5372 (mmp-170) REVERT: B 489 ASN cc_start: 0.7060 (p0) cc_final: 0.6831 (p0) REVERT: B 517 TYR cc_start: 0.7987 (t80) cc_final: 0.7496 (t80) REVERT: C 3 ASN cc_start: 0.8052 (t0) cc_final: 0.7664 (m110) REVERT: C 40 ASN cc_start: 0.8315 (t0) cc_final: 0.7555 (t0) REVERT: C 95 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.7025 (mttp) REVERT: D 77 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7082 (tt0) REVERT: D 331 ASP cc_start: 0.6590 (t0) cc_final: 0.6227 (t70) REVERT: D 476 ARG cc_start: 0.7437 (ptp-110) cc_final: 0.7118 (ttp-110) REVERT: E 63 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7900 (mmt) REVERT: F 36 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7397 (tm-30) REVERT: F 77 GLU cc_start: 0.7881 (tt0) cc_final: 0.7081 (mp0) REVERT: F 168 GLN cc_start: 0.7103 (tp-100) cc_final: 0.6655 (tt0) REVERT: F 276 MET cc_start: 0.8387 (mtt) cc_final: 0.8152 (mtm) REVERT: F 302 GLU cc_start: 0.6753 (mt-10) cc_final: 0.6269 (mt-10) REVERT: F 304 LYS cc_start: 0.7998 (mttt) cc_final: 0.7758 (mtmm) REVERT: F 347 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7806 (tm-30) REVERT: F 382 CYS cc_start: 0.7846 (m) cc_final: 0.7333 (m) REVERT: F 391 ARG cc_start: 0.8243 (ttp80) cc_final: 0.7812 (ttm-80) REVERT: F 485 ARG cc_start: 0.5618 (OUTLIER) cc_final: 0.5192 (mmp-170) REVERT: F 489 ASN cc_start: 0.7099 (p0) cc_final: 0.6877 (p0) REVERT: F 492 ARG cc_start: 0.7975 (mtt90) cc_final: 0.7765 (mtt90) REVERT: F 517 TYR cc_start: 0.7937 (t80) cc_final: 0.7410 (t80) REVERT: G 3 ASN cc_start: 0.8056 (t0) cc_final: 0.7668 (m110) REVERT: G 40 ASN cc_start: 0.8341 (t0) cc_final: 0.7588 (t0) REVERT: G 62 ASN cc_start: 0.5734 (m-40) cc_final: 0.5342 (m110) REVERT: G 95 LYS cc_start: 0.7241 (mptm) cc_final: 0.6959 (mttp) REVERT: H 61 LYS cc_start: 0.8354 (mtpt) cc_final: 0.7985 (mttm) REVERT: H 195 MET cc_start: 0.8948 (mtt) cc_final: 0.8699 (mtt) REVERT: H 331 ASP cc_start: 0.6659 (t0) cc_final: 0.6202 (t70) REVERT: H 476 ARG cc_start: 0.7425 (ptp-110) cc_final: 0.7109 (ttp-110) outliers start: 28 outliers final: 6 residues processed: 248 average time/residue: 0.6078 time to fit residues: 172.9412 Evaluate side-chains 222 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 211 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 340 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain G residue 57 VAL 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 6 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 204 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 268 HIS B 424 HIS C 105 ASN F 268 HIS F 424 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.129223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.084333 restraints weight = 30832.910| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.50 r_work: 0.3043 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22640 Z= 0.183 Angle : 0.597 10.535 31092 Z= 0.291 Chirality : 0.046 0.264 3478 Planarity : 0.004 0.052 3688 Dihedral : 9.563 78.983 3666 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.36 % Allowed : 12.12 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.16), residues: 2548 helix: -0.32 (0.20), residues: 664 sheet: -1.88 (0.27), residues: 308 loop : -0.81 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 492 TYR 0.020 0.001 TYR H 446 PHE 0.018 0.002 PHE H 444 TRP 0.010 0.001 TRP F 159 HIS 0.006 0.001 HIS B 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (22560) covalent geometry : angle 0.57598 / 0.29 (31028) hydrogen bonds : bond 0.03876 / 2.64 ( 680) hydrogen bonds : angle 4.78126 / 3.33 ( 1900) metal coordination : bond 0.01114 / 0.73 ( 80) metal coordination : angle 3.46981 / 2.49 ( 64) *********************** 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 260 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 0.872 Fit side-chains REVERT: A 63 MET cc_start: 0.8107 (mmt) cc_final: 0.7892 (mmt) REVERT: B 36 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7481 (tm-30) REVERT: B 77 GLU cc_start: 0.7779 (tt0) cc_final: 0.7002 (mp0) REVERT: B 168 GLN cc_start: 0.7158 (tp-100) cc_final: 0.6743 (tt0) REVERT: B 302 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6127 (mt-10) REVERT: B 304 LYS cc_start: 0.7983 (mttt) cc_final: 0.7746 (mtmm) REVERT: B 313 GLN cc_start: 0.7555 (tt0) cc_final: 0.7053 (tm-30) REVERT: B 324 ASP cc_start: 0.7632 (m-30) cc_final: 0.7212 (m-30) REVERT: B 325 LYS cc_start: 0.8409 (mppt) cc_final: 0.8053 (mppt) REVERT: B 340 CYS cc_start: 0.6824 (m) cc_final: 0.5436 (m) REVERT: B 347 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7611 (tm-30) REVERT: B 382 CYS cc_start: 0.7860 (m) cc_final: 0.7431 (m) REVERT: B 485 ARG cc_start: 0.5797 (OUTLIER) cc_final: 0.5262 (mmp-170) REVERT: B 489 ASN cc_start: 0.7112 (p0) cc_final: 0.6821 (p0) REVERT: B 492 ARG cc_start: 0.8016 (mtt90) cc_final: 0.7724 (mtt90) REVERT: B 517 TYR cc_start: 0.7923 (t80) cc_final: 0.7459 (t80) REVERT: C 40 ASN cc_start: 0.8343 (t0) cc_final: 0.7481 (t0) REVERT: C 95 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7223 (mttp) REVERT: D 61 LYS cc_start: 0.8407 (mtpt) cc_final: 0.8001 (mttm) REVERT: D 77 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7237 (tt0) REVERT: D 331 ASP cc_start: 0.6614 (t0) cc_final: 0.6196 (t70) REVERT: D 476 ARG cc_start: 0.7396 (ptp-110) cc_final: 0.7107 (ttp-110) REVERT: E 63 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7966 (mmt) REVERT: F 36 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7460 (tm-30) REVERT: F 77 GLU cc_start: 0.7785 (tt0) cc_final: 0.7006 (mp0) REVERT: F 168 GLN cc_start: 0.7141 (tp-100) cc_final: 0.6726 (tt0) REVERT: F 302 GLU cc_start: 0.6600 (mt-10) cc_final: 0.6109 (mt-10) REVERT: F 304 LYS cc_start: 0.7971 (mttt) cc_final: 0.7736 (mtmm) REVERT: F 313 GLN cc_start: 0.7554 (tt0) cc_final: 0.7061 (tm-30) REVERT: F 324 ASP cc_start: 0.7713 (m-30) cc_final: 0.7279 (m-30) REVERT: F 325 LYS cc_start: 0.8561 (mppt) cc_final: 0.7806 (mppt) REVERT: F 340 CYS cc_start: 0.6833 (m) cc_final: 0.5484 (m) REVERT: F 382 CYS cc_start: 0.7873 (m) cc_final: 0.7321 (m) REVERT: F 485 ARG cc_start: 0.5818 (OUTLIER) cc_final: 0.5281 (mmp-170) REVERT: F 489 ASN cc_start: 0.7088 (p0) cc_final: 0.6818 (p0) REVERT: F 517 TYR cc_start: 0.7923 (t80) cc_final: 0.7427 (t80) REVERT: G 40 ASN cc_start: 0.8324 (t0) cc_final: 0.7478 (t0) REVERT: G 95 LYS cc_start: 0.7478 (mptm) cc_final: 0.7175 (mttp) REVERT: H 61 LYS cc_start: 0.8387 (mtpt) cc_final: 0.7978 (mttm) REVERT: H 331 ASP cc_start: 0.6613 (t0) cc_final: 0.6254 (t70) REVERT: H 476 ARG cc_start: 0.7361 (ptp-110) cc_final: 0.7050 (ttp-110) outliers start: 30 outliers final: 9 residues processed: 243 average time/residue: 0.6124 time to fit residues: 170.8644 Evaluate side-chains 227 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 213 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 340 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain G residue 57 VAL 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 107 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 214 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 242 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 252 ASN B 268 HIS F 252 ASN F 268 HIS G 62 ASN G 105 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.129315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.084447 restraints weight = 30682.767| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.49 r_work: 0.3052 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22640 Z= 0.178 Angle : 0.582 9.464 31092 Z= 0.285 Chirality : 0.046 0.262 3478 Planarity : 0.004 0.050 3688 Dihedral : 9.296 80.163 3666 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.08 % Allowed : 13.11 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.16), residues: 2548 helix: 0.04 (0.21), residues: 640 sheet: -1.62 (0.26), residues: 348 loop : -0.67 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 492 TYR 0.027 0.001 TYR D 446 PHE 0.021 0.002 PHE H 444 TRP 0.011 0.001 TRP F 292 HIS 0.007 0.001 HIS F 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (22560) covalent geometry : angle 0.56748 / 0.28 (31028) hydrogen bonds : bond 0.03701 / 2.51 ( 680) hydrogen bonds : angle 4.65781 / 3.26 ( 1900) metal coordination : bond 0.01016 / 0.68 ( 80) metal coordination : angle 2.89347 / 2.06 ( 64) *********************** 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 272 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 0.870 Fit side-chains REVERT: A 43 LYS cc_start: 0.8256 (ttpt) cc_final: 0.8029 (tttt) REVERT: A 63 MET cc_start: 0.8211 (mmt) cc_final: 0.8007 (mmt) REVERT: B 36 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7573 (tm-30) REVERT: B 77 GLU cc_start: 0.7805 (tt0) cc_final: 0.7106 (mp0) REVERT: B 168 GLN cc_start: 0.7168 (tp-100) cc_final: 0.6771 (tt0) REVERT: B 304 LYS cc_start: 0.7965 (mttt) cc_final: 0.7736 (mtmm) REVERT: B 313 GLN cc_start: 0.7707 (tt0) cc_final: 0.7132 (tm-30) REVERT: B 325 LYS cc_start: 0.8408 (mppt) cc_final: 0.8072 (mppt) REVERT: B 340 CYS cc_start: 0.6811 (m) cc_final: 0.5460 (m) REVERT: B 347 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7828 (tm-30) REVERT: B 382 CYS cc_start: 0.7884 (m) cc_final: 0.7552 (m) REVERT: B 391 ARG cc_start: 0.8307 (ttp80) cc_final: 0.7907 (ttm-80) REVERT: B 489 ASN cc_start: 0.7150 (p0) cc_final: 0.6839 (p0) REVERT: B 492 ARG cc_start: 0.8037 (mtt90) cc_final: 0.7763 (mtt90) REVERT: B 517 TYR cc_start: 0.7891 (t80) cc_final: 0.7376 (t80) REVERT: C 40 ASN cc_start: 0.8225 (t0) cc_final: 0.7344 (t0) REVERT: C 95 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7125 (mttm) REVERT: D 61 LYS cc_start: 0.8421 (mtpt) cc_final: 0.8027 (mttm) REVERT: D 77 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7293 (tt0) REVERT: D 331 ASP cc_start: 0.6533 (t0) cc_final: 0.6190 (t70) REVERT: D 476 ARG cc_start: 0.7568 (ptp-110) cc_final: 0.7211 (ttp-110) REVERT: E 43 LYS cc_start: 0.8318 (ttpt) cc_final: 0.8097 (tttt) REVERT: E 63 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8040 (mmt) REVERT: F 36 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7533 (tm-30) REVERT: F 77 GLU cc_start: 0.7828 (tt0) cc_final: 0.7055 (mp0) REVERT: F 168 GLN cc_start: 0.7137 (tp-100) cc_final: 0.6746 (tt0) REVERT: F 304 LYS cc_start: 0.7915 (mttt) cc_final: 0.7691 (mtmm) REVERT: F 313 GLN cc_start: 0.7701 (tt0) cc_final: 0.7132 (tm-30) REVERT: F 325 LYS cc_start: 0.8488 (mppt) cc_final: 0.7841 (mppt) REVERT: F 340 CYS cc_start: 0.6837 (m) cc_final: 0.5492 (m) REVERT: F 382 CYS cc_start: 0.7860 (m) cc_final: 0.7520 (m) REVERT: F 492 ARG cc_start: 0.7966 (mtt90) cc_final: 0.7371 (mtt90) REVERT: F 517 TYR cc_start: 0.7898 (t80) cc_final: 0.7405 (t80) REVERT: G 40 ASN cc_start: 0.8232 (t0) cc_final: 0.7361 (t0) REVERT: H 61 LYS cc_start: 0.8390 (mtpt) cc_final: 0.7994 (mttm) REVERT: H 331 ASP cc_start: 0.6533 (t0) cc_final: 0.6169 (t70) REVERT: H 476 ARG cc_start: 0.7557 (ptp-110) cc_final: 0.7204 (ttp-110) outliers start: 46 outliers final: 15 residues processed: 251 average time/residue: 0.5906 time to fit residues: 171.1663 Evaluate side-chains 225 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 207 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 83 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 E residue 63 MET Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 160 ASN 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 18 optimal weight: 0.8980 chunk 63 optimal weight: 0.0870 chunk 191 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 217 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 157 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 221 optimal weight: 7.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 245 GLN B 268 HIS B 354 GLN C 105 ASN D 82 HIS D 108 GLN D 518 ASN F 245 GLN F 268 HIS H 82 HIS H 108 GLN H 518 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.131937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.087652 restraints weight = 30441.716| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.49 r_work: 0.3115 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 22640 Z= 0.104 Angle : 0.533 10.275 31092 Z= 0.260 Chirality : 0.044 0.250 3478 Planarity : 0.004 0.047 3688 Dihedral : 9.003 80.759 3666 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.63 % Allowed : 13.92 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.16), residues: 2548 helix: 0.23 (0.20), residues: 664 sheet: -1.45 (0.30), residues: 292 loop : -0.61 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 492 TYR 0.014 0.001 TYR H 446 PHE 0.021 0.001 PHE H 444 TRP 0.011 0.001 TRP F 292 HIS 0.009 0.001 HIS F 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (22560) covalent geometry : angle 0.52444 / 0.26 (31028) hydrogen bonds : bond 0.03116 / 2.11 ( 680) hydrogen bonds : angle 4.49345 / 3.14 ( 1900) metal coordination : bond 0.00653 / 0.45 ( 80) metal coordination : angle 2.17370 / 1.55 ( 64) *********************** 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 273 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8283 (mt0) cc_final: 0.7827 (mm-40) REVERT: B 36 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7558 (tm-30) REVERT: B 77 GLU cc_start: 0.7775 (tt0) cc_final: 0.7121 (mp0) REVERT: B 165 LYS cc_start: 0.8342 (mtpt) cc_final: 0.8113 (mtpp) REVERT: B 168 GLN cc_start: 0.7087 (tp-100) cc_final: 0.6726 (tt0) REVERT: B 304 LYS cc_start: 0.7886 (mttt) cc_final: 0.7683 (mtmm) REVERT: B 313 GLN cc_start: 0.7626 (tt0) cc_final: 0.7091 (tm-30) REVERT: B 325 LYS cc_start: 0.8385 (mppt) cc_final: 0.8053 (mppt) REVERT: B 340 CYS cc_start: 0.6743 (m) cc_final: 0.5371 (m) REVERT: B 347 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7853 (tm-30) REVERT: B 382 CYS cc_start: 0.7790 (m) cc_final: 0.7298 (m) REVERT: B 408 ASN cc_start: 0.8202 (m-40) cc_final: 0.7659 (p0) REVERT: B 489 ASN cc_start: 0.7067 (p0) cc_final: 0.6798 (p0) REVERT: B 492 ARG cc_start: 0.7919 (mtt90) cc_final: 0.7640 (mtt90) REVERT: B 517 TYR cc_start: 0.7705 (t80) cc_final: 0.7231 (t80) REVERT: C 40 ASN cc_start: 0.8192 (t0) cc_final: 0.7362 (t0) REVERT: C 95 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.7050 (mttm) REVERT: D 61 LYS cc_start: 0.8404 (mtpt) cc_final: 0.8013 (mttm) REVERT: D 76 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7423 (ttm170) REVERT: D 77 GLU cc_start: 0.7573 (pt0) cc_final: 0.7253 (tt0) REVERT: D 331 ASP cc_start: 0.6393 (t0) cc_final: 0.6082 (t70) REVERT: D 476 ARG cc_start: 0.7553 (ptp-110) cc_final: 0.7229 (ttp-110) REVERT: E 43 LYS cc_start: 0.8287 (ttpt) cc_final: 0.8086 (tttt) REVERT: E 53 GLN cc_start: 0.8291 (mt0) cc_final: 0.7818 (mm-40) REVERT: E 63 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7969 (mmt) REVERT: F 36 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7518 (tm-30) REVERT: F 77 GLU cc_start: 0.7787 (tt0) cc_final: 0.7132 (mp0) REVERT: F 165 LYS cc_start: 0.8341 (mtpt) cc_final: 0.8111 (mtpp) REVERT: F 168 GLN cc_start: 0.7074 (tp-100) cc_final: 0.6717 (tt0) REVERT: F 304 LYS cc_start: 0.7903 (mttt) cc_final: 0.7702 (mtmm) REVERT: F 313 GLN cc_start: 0.7646 (tt0) cc_final: 0.7089 (tm-30) REVERT: F 325 LYS cc_start: 0.8533 (mppt) cc_final: 0.7893 (mppt) REVERT: F 340 CYS cc_start: 0.6687 (m) cc_final: 0.5345 (m) REVERT: F 382 CYS cc_start: 0.7794 (m) cc_final: 0.7368 (m) REVERT: F 408 ASN cc_start: 0.8209 (m-40) cc_final: 0.7661 (p0) REVERT: F 492 ARG cc_start: 0.7922 (mtt90) cc_final: 0.7607 (mtt90) REVERT: F 517 TYR cc_start: 0.7708 (t80) cc_final: 0.7227 (t80) REVERT: G 40 ASN cc_start: 0.8209 (t0) cc_final: 0.7352 (t0) REVERT: G 95 LYS cc_start: 0.7470 (mptm) cc_final: 0.7191 (mttp) REVERT: H 61 LYS cc_start: 0.8399 (mtpt) cc_final: 0.8011 (mttm) REVERT: H 331 ASP cc_start: 0.6360 (t0) cc_final: 0.6053 (t70) REVERT: H 476 ARG cc_start: 0.7544 (ptp-110) cc_final: 0.7207 (ttp-110) outliers start: 36 outliers final: 13 residues processed: 262 average time/residue: 0.6178 time to fit residues: 185.3367 Evaluate side-chains 228 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LYS 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 341 VAL Chi-restraints excluded: chain E residue 63 MET 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 105 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 249 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 201 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 232 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 268 HIS B 354 GLN C 62 ASN D 188 HIS F 252 ASN F 268 HIS F 354 GLN G 105 ASN H 188 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.131572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.087070 restraints weight = 30447.309| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.50 r_work: 0.3097 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22640 Z= 0.115 Angle : 0.538 13.122 31092 Z= 0.262 Chirality : 0.045 0.223 3478 Planarity : 0.003 0.047 3688 Dihedral : 8.871 81.511 3666 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.54 % Allowed : 14.83 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.17), residues: 2548 helix: 0.34 (0.21), residues: 660 sheet: -1.31 (0.30), residues: 292 loop : -0.52 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 492 TYR 0.012 0.001 TYR D 446 PHE 0.012 0.001 PHE A 68 TRP 0.011 0.001 TRP F 292 HIS 0.007 0.001 HIS F 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (22560) covalent geometry : angle 0.53046 / 0.26 (31028) hydrogen bonds : bond 0.03144 / 2.14 ( 680) hydrogen bonds : angle 4.42155 / 3.08 ( 1900) metal coordination : bond 0.00636 / 0.44 ( 80) metal coordination : angle 2.04202 / 1.45 ( 64) *********************** 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 260 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8271 (mt0) cc_final: 0.7815 (mm-40) REVERT: B 36 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7502 (tm-30) REVERT: B 77 GLU cc_start: 0.7783 (tt0) cc_final: 0.7134 (mp0) REVERT: B 168 GLN cc_start: 0.7109 (tp-100) cc_final: 0.6744 (tt0) REVERT: B 304 LYS cc_start: 0.7919 (mttt) cc_final: 0.7651 (mtpt) REVERT: B 313 GLN cc_start: 0.7657 (tt0) cc_final: 0.7093 (tm-30) REVERT: B 325 LYS cc_start: 0.8366 (mppt) cc_final: 0.8038 (mppt) REVERT: B 340 CYS cc_start: 0.6770 (m) cc_final: 0.5383 (m) REVERT: B 382 CYS cc_start: 0.7817 (m) cc_final: 0.7329 (m) REVERT: B 469 LYS cc_start: 0.7506 (mmtt) cc_final: 0.7250 (tptt) REVERT: B 489 ASN cc_start: 0.7094 (p0) cc_final: 0.6826 (p0) REVERT: B 492 ARG cc_start: 0.7924 (mtt90) cc_final: 0.7648 (mtt90) REVERT: B 517 TYR cc_start: 0.7633 (t80) cc_final: 0.7196 (t80) REVERT: C 40 ASN cc_start: 0.8316 (t0) cc_final: 0.7511 (t0) REVERT: C 95 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7150 (mttm) REVERT: C 122 MET cc_start: 0.6012 (OUTLIER) cc_final: 0.5802 (pmm) REVERT: D 61 LYS cc_start: 0.8314 (mtpt) cc_final: 0.7962 (mttm) REVERT: D 76 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7422 (ttm170) REVERT: D 77 GLU cc_start: 0.7507 (pt0) cc_final: 0.7211 (tt0) REVERT: D 195 MET cc_start: 0.8887 (mtp) cc_final: 0.8589 (mtp) REVERT: D 331 ASP cc_start: 0.6318 (t0) cc_final: 0.6020 (t70) REVERT: D 476 ARG cc_start: 0.7497 (ptp-110) cc_final: 0.7150 (ttp-110) REVERT: E 43 LYS cc_start: 0.8316 (ttpt) cc_final: 0.8007 (tttt) REVERT: E 63 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8006 (mmt) REVERT: F 36 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7493 (tm-30) REVERT: F 77 GLU cc_start: 0.7795 (tt0) cc_final: 0.7144 (mp0) REVERT: F 168 GLN cc_start: 0.7122 (tp-100) cc_final: 0.6738 (tt0) REVERT: F 304 LYS cc_start: 0.7925 (mttt) cc_final: 0.7655 (mtpt) REVERT: F 313 GLN cc_start: 0.7630 (tt0) cc_final: 0.7068 (tm-30) REVERT: F 325 LYS cc_start: 0.8550 (mppt) cc_final: 0.7916 (mppt) REVERT: F 340 CYS cc_start: 0.6750 (m) cc_final: 0.5386 (m) REVERT: F 382 CYS cc_start: 0.7830 (m) cc_final: 0.7407 (m) REVERT: F 408 ASN cc_start: 0.8198 (m-40) cc_final: 0.7672 (p0) REVERT: F 492 ARG cc_start: 0.7962 (mtt90) cc_final: 0.7653 (mtt90) REVERT: F 517 TYR cc_start: 0.7644 (t80) cc_final: 0.7164 (t80) REVERT: G 40 ASN cc_start: 0.8322 (t0) cc_final: 0.7512 (t0) REVERT: G 95 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.7138 (mttp) REVERT: H 61 LYS cc_start: 0.8328 (mtpt) cc_final: 0.7978 (mttm) REVERT: H 76 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7529 (ttm170) REVERT: H 154 TYR cc_start: 0.8550 (m-80) cc_final: 0.8309 (m-80) REVERT: H 331 ASP cc_start: 0.6300 (t0) cc_final: 0.5997 (t70) REVERT: H 476 ARG cc_start: 0.7517 (ptp-110) cc_final: 0.7254 (ttp-110) outliers start: 34 outliers final: 19 residues processed: 250 average time/residue: 0.5848 time to fit residues: 168.2285 Evaluate side-chains 238 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 95 LYS Chi-restraints excluded: chain C residue 122 MET 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 169 MET Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 76 ARG 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 241 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 178 optimal weight: 0.0770 chunk 72 optimal weight: 20.0000 chunk 249 optimal weight: 0.3980 chunk 124 optimal weight: 5.9990 chunk 111 optimal weight: 0.2980 chunk 87 optimal weight: 4.9990 chunk 202 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 chunk 117 optimal weight: 0.0670 chunk 234 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 268 HIS C 105 ASN F 268 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.132781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.088510 restraints weight = 30400.563| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.51 r_work: 0.3126 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22640 Z= 0.099 Angle : 0.530 12.106 31092 Z= 0.255 Chirality : 0.044 0.216 3478 Planarity : 0.003 0.046 3688 Dihedral : 8.764 81.617 3666 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.45 % Allowed : 15.33 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.17), residues: 2548 helix: 0.54 (0.21), residues: 640 sheet: -1.14 (0.28), residues: 332 loop : -0.47 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 492 TYR 0.012 0.001 TYR D 446 PHE 0.022 0.001 PHE H 444 TRP 0.011 0.001 TRP B 292 HIS 0.009 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (22560) covalent geometry : angle 0.51720 / 0.25 (31028) hydrogen bonds : bond 0.02974 / 2.01 ( 680) hydrogen bonds : angle 4.36598 / 3.03 ( 1900) metal coordination : bond 0.00548 / 0.34 ( 80) metal coordination : angle 2.57369 / 1.90 ( 64) *********************** REFINEMENT MACRO_CYCLE 7 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 251 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 219 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8206 (mt0) cc_final: 0.7752 (mm-40) REVERT: B 36 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7582 (tm-30) REVERT: B 77 GLU cc_start: 0.7780 (tt0) cc_final: 0.7138 (mp0) REVERT: B 168 GLN cc_start: 0.7120 (tp-100) cc_final: 0.6742 (tt0) REVERT: B 313 GLN cc_start: 0.7631 (tt0) cc_final: 0.7071 (tm-30) REVERT: B 325 LYS cc_start: 0.8396 (mppt) cc_final: 0.8054 (mppt) REVERT: B 340 CYS cc_start: 0.6711 (m) cc_final: 0.5330 (m) REVERT: B 382 CYS cc_start: 0.7777 (m) cc_final: 0.7268 (m) REVERT: B 408 ASN cc_start: 0.8234 (m-40) cc_final: 0.7650 (p0) REVERT: B 489 ASN cc_start: 0.7087 (p0) cc_final: 0.6831 (p0) REVERT: B 492 ARG cc_start: 0.7895 (mtt90) cc_final: 0.7623 (mtt90) REVERT: B 517 TYR cc_start: 0.7642 (t80) cc_final: 0.7204 (t80) REVERT: C 40 ASN cc_start: 0.8336 (t0) cc_final: 0.7549 (t0) REVERT: C 95 LYS cc_start: 0.7326 (mttm) cc_final: 0.7067 (mttm) REVERT: D 61 LYS cc_start: 0.8310 (mtpt) cc_final: 0.7936 (mttm) REVERT: D 76 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7525 (ttm170) REVERT: D 77 GLU cc_start: 0.7522 (pt0) cc_final: 0.7220 (tt0) REVERT: D 154 TYR cc_start: 0.8473 (m-80) cc_final: 0.8221 (m-80) REVERT: D 331 ASP cc_start: 0.6339 (t0) cc_final: 0.6054 (t70) REVERT: D 476 ARG cc_start: 0.7515 (ptp-110) cc_final: 0.7277 (ttp-110) REVERT: E 53 GLN cc_start: 0.8195 (mt0) cc_final: 0.7730 (mm-40) REVERT: F 36 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7526 (tm-30) REVERT: F 77 GLU cc_start: 0.7778 (tt0) cc_final: 0.7143 (mp0) REVERT: F 168 GLN cc_start: 0.7122 (tp-100) cc_final: 0.6741 (tt0) REVERT: F 313 GLN cc_start: 0.7633 (tt0) cc_final: 0.7069 (tm-30) REVERT: F 325 LYS cc_start: 0.8542 (mppt) cc_final: 0.7945 (mppt) REVERT: F 340 CYS cc_start: 0.6640 (m) cc_final: 0.5265 (m) REVERT: F 382 CYS cc_start: 0.7748 (m) cc_final: 0.7304 (m) REVERT: F 408 ASN cc_start: 0.8202 (m-40) cc_final: 0.7699 (p0) REVERT: F 492 ARG cc_start: 0.7931 (mtt90) cc_final: 0.7618 (mtt90) REVERT: F 517 TYR cc_start: 0.7708 (t80) cc_final: 0.7232 (t80) REVERT: G 40 ASN cc_start: 0.8322 (t0) cc_final: 0.7521 (t0) REVERT: G 95 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.7077 (mttp) REVERT: H 61 LYS cc_start: 0.8319 (mtpt) cc_final: 0.7946 (mttm) REVERT: H 76 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7554 (ttm170) REVERT: H 154 TYR cc_start: 0.8478 (m-80) cc_final: 0.8240 (m-80) REVERT: H 195 MET cc_start: 0.8972 (mtp) cc_final: 0.8467 (mtp) REVERT: H 331 ASP cc_start: 0.6368 (t0) cc_final: 0.6085 (t70) REVERT: H 476 ARG cc_start: 0.7504 (ptp-110) cc_final: 0.7271 (ttp-110) outliers start: 32 outliers final: 20 residues processed: 240 average time/residue: 0.5988 time to fit residues: 165.3374 Evaluate side-chains 233 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain C residue 38 ILE 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 169 MET 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 G residue 95 LYS Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 76 ARG 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 321 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 109 optimal weight: 10.0000 chunk 214 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 217 optimal weight: 4.9990 chunk 193 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 268 HIS F 268 HIS G 105 ASN ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.132124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.087648 restraints weight = 30446.249| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.51 r_work: 0.3104 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22640 Z= 0.120 Angle : 0.539 11.876 31092 Z= 0.262 Chirality : 0.045 0.202 3478 Planarity : 0.003 0.047 3688 Dihedral : 8.754 81.815 3666 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.36 % Allowed : 15.33 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.17), residues: 2548 helix: 0.53 (0.21), residues: 640 sheet: -1.16 (0.27), residues: 332 loop : -0.45 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 492 TYR 0.011 0.001 TYR D 446 PHE 0.036 0.001 PHE D 377 TRP 0.012 0.001 TRP B 292 HIS 0.008 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (22560) covalent geometry : angle 0.52979 / 0.26 (31028) hydrogen bonds : bond 0.03093 / 2.10 ( 680) hydrogen bonds : angle 4.36996 / 3.03 ( 1900) metal coordination : bond 0.00652 / 0.42 ( 80) metal coordination : angle 2.26476 / 1.66 ( 64) *********************** REFINEMENT MACRO_CYCLE 8 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 246 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7569 (tm-30) REVERT: B 77 GLU cc_start: 0.7794 (tt0) cc_final: 0.7146 (mp0) REVERT: B 168 GLN cc_start: 0.7148 (tp-100) cc_final: 0.6762 (tt0) REVERT: B 313 GLN cc_start: 0.7677 (tt0) cc_final: 0.7113 (tm-30) REVERT: B 340 CYS cc_start: 0.6729 (m) cc_final: 0.5364 (m) REVERT: B 382 CYS cc_start: 0.7822 (m) cc_final: 0.7353 (m) REVERT: B 408 ASN cc_start: 0.8216 (m-40) cc_final: 0.7663 (p0) REVERT: B 489 ASN cc_start: 0.7097 (p0) cc_final: 0.6829 (p0) REVERT: B 492 ARG cc_start: 0.7939 (mtt90) cc_final: 0.7667 (mtt90) REVERT: B 517 TYR cc_start: 0.7637 (t80) cc_final: 0.7163 (t80) REVERT: C 40 ASN cc_start: 0.8354 (t0) cc_final: 0.7555 (t0) REVERT: C 95 LYS cc_start: 0.7438 (mttm) cc_final: 0.7179 (mttm) REVERT: D 61 LYS cc_start: 0.8319 (mtpt) cc_final: 0.7959 (mttm) REVERT: D 76 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7528 (ttm170) REVERT: D 77 GLU cc_start: 0.7598 (pt0) cc_final: 0.7296 (tt0) REVERT: D 154 TYR cc_start: 0.8500 (m-80) cc_final: 0.8229 (m-80) REVERT: D 331 ASP cc_start: 0.6463 (t0) cc_final: 0.6167 (t70) REVERT: E 63 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7930 (mmt) REVERT: F 36 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7575 (tm-30) REVERT: F 77 GLU cc_start: 0.7794 (tt0) cc_final: 0.7147 (mp0) REVERT: F 168 GLN cc_start: 0.7132 (tp-100) cc_final: 0.6748 (tt0) REVERT: F 313 GLN cc_start: 0.7665 (tt0) cc_final: 0.7105 (tm-30) REVERT: F 325 LYS cc_start: 0.8541 (mppt) cc_final: 0.7942 (mppt) REVERT: F 340 CYS cc_start: 0.6649 (m) cc_final: 0.5287 (m) REVERT: F 347 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7563 (tp30) REVERT: F 382 CYS cc_start: 0.7779 (m) cc_final: 0.7362 (m) REVERT: F 408 ASN cc_start: 0.8209 (m-40) cc_final: 0.7694 (p0) REVERT: F 492 ARG cc_start: 0.7931 (mtt90) cc_final: 0.7620 (mtt90) REVERT: F 517 TYR cc_start: 0.7700 (t80) cc_final: 0.7242 (t80) REVERT: G 40 ASN cc_start: 0.8338 (t0) cc_final: 0.7578 (t0) REVERT: G 95 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7156 (mttp) REVERT: H 61 LYS cc_start: 0.8331 (mtpt) cc_final: 0.7971 (mttm) REVERT: H 76 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7557 (ttm170) REVERT: H 154 TYR cc_start: 0.8523 (m-80) cc_final: 0.8270 (m-80) REVERT: H 331 ASP cc_start: 0.6482 (t0) cc_final: 0.6263 (t70) outliers start: 30 outliers final: 19 residues processed: 236 average time/residue: 0.5998 time to fit residues: 163.3633 Evaluate side-chains 240 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain C residue 38 ILE 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 169 MET 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 E residue 63 MET Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 347 GLU Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 321 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 140 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 135 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 189 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 268 HIS C 105 ASN F 268 HIS H 314 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.132057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.087540 restraints weight = 30563.364| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.51 r_work: 0.3101 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22640 Z= 0.120 Angle : 0.542 11.776 31092 Z= 0.263 Chirality : 0.045 0.208 3478 Planarity : 0.004 0.047 3688 Dihedral : 8.734 81.946 3666 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.31 % Allowed : 15.73 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.17), residues: 2548 helix: 0.57 (0.21), residues: 640 sheet: -1.18 (0.27), residues: 332 loop : -0.40 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 476 TYR 0.012 0.001 TYR D 446 PHE 0.030 0.001 PHE H 377 TRP 0.014 0.001 TRP F 292 HIS 0.008 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (22560) covalent geometry : angle 0.53477 / 0.26 (31028) hydrogen bonds : bond 0.03097 / 2.10 ( 680) hydrogen bonds : angle 4.36176 / 3.02 ( 1900) metal coordination : bond 0.00663 / 0.43 ( 80) metal coordination : angle 2.06679 / 1.50 ( 64) *********************** REFINEMENT MACRO_CYCLE 9 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 245 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7611 (tm-30) REVERT: B 77 GLU cc_start: 0.7814 (tt0) cc_final: 0.7158 (mp0) REVERT: B 154 TYR cc_start: 0.7238 (m-80) cc_final: 0.6864 (m-80) REVERT: B 168 GLN cc_start: 0.7140 (tp-100) cc_final: 0.6760 (tt0) REVERT: B 313 GLN cc_start: 0.7713 (tt0) cc_final: 0.7190 (tm-30) REVERT: B 326 PHE cc_start: 0.7450 (m-10) cc_final: 0.7220 (m-10) REVERT: B 340 CYS cc_start: 0.6695 (m) cc_final: 0.5434 (m) REVERT: B 382 CYS cc_start: 0.7875 (m) cc_final: 0.7419 (m) REVERT: B 408 ASN cc_start: 0.8192 (m-40) cc_final: 0.7668 (p0) REVERT: B 469 LYS cc_start: 0.7468 (mmtt) cc_final: 0.7197 (tptt) REVERT: B 489 ASN cc_start: 0.7098 (p0) cc_final: 0.6828 (p0) REVERT: B 492 ARG cc_start: 0.7933 (mtt90) cc_final: 0.7664 (mtt90) REVERT: B 517 TYR cc_start: 0.7609 (t80) cc_final: 0.7178 (t80) REVERT: C 40 ASN cc_start: 0.8389 (t0) cc_final: 0.7641 (t0) REVERT: C 85 ASN cc_start: 0.6977 (t0) cc_final: 0.6585 (p0) REVERT: C 95 LYS cc_start: 0.7361 (mttm) cc_final: 0.7095 (mttm) REVERT: D 61 LYS cc_start: 0.8343 (mtpt) cc_final: 0.7999 (mttm) REVERT: D 76 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7546 (ttm170) REVERT: D 77 GLU cc_start: 0.7595 (pt0) cc_final: 0.7294 (tt0) REVERT: D 331 ASP cc_start: 0.6463 (t0) cc_final: 0.6176 (t70) REVERT: E 63 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7957 (mmt) REVERT: F 36 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7606 (tm-30) REVERT: F 77 GLU cc_start: 0.7794 (tt0) cc_final: 0.7153 (mp0) REVERT: F 168 GLN cc_start: 0.7124 (tp-100) cc_final: 0.6746 (tt0) REVERT: F 313 GLN cc_start: 0.7693 (tt0) cc_final: 0.7175 (tm-30) REVERT: F 340 CYS cc_start: 0.6747 (m) cc_final: 0.5440 (m) REVERT: F 347 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7552 (tp30) REVERT: F 382 CYS cc_start: 0.7846 (m) cc_final: 0.7551 (m) REVERT: F 408 ASN cc_start: 0.8216 (m-40) cc_final: 0.7707 (p0) REVERT: F 492 ARG cc_start: 0.7931 (mtt90) cc_final: 0.7623 (mtt90) REVERT: F 517 TYR cc_start: 0.7582 (t80) cc_final: 0.7100 (t80) REVERT: G 40 ASN cc_start: 0.8376 (t0) cc_final: 0.7622 (t0) REVERT: G 44 MET cc_start: 0.7533 (mmm) cc_final: 0.7167 (mmm) REVERT: G 95 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.7091 (mttp) REVERT: H 61 LYS cc_start: 0.8349 (mtpt) cc_final: 0.8006 (mttm) REVERT: H 76 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7545 (ttm170) REVERT: H 154 TYR cc_start: 0.8522 (m-80) cc_final: 0.8259 (m-80) REVERT: H 331 ASP cc_start: 0.6571 (t0) cc_final: 0.6281 (t70) outliers start: 29 outliers final: 16 residues processed: 238 average time/residue: 0.6093 time to fit residues: 168.7366 Evaluate side-chains 236 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 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 169 MET 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 E residue 63 MET Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 347 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 326 PHE Chi-restraints excluded: chain H residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 256 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 chunk 133 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 8 optimal weight: 0.0770 chunk 94 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 202 optimal weight: 20.0000 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 268 HIS D 314 HIS F 268 HIS G 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.133569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.089325 restraints weight = 30664.965| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.53 r_work: 0.3139 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22640 Z= 0.097 Angle : 0.531 11.475 31092 Z= 0.255 Chirality : 0.044 0.224 3478 Planarity : 0.004 0.045 3688 Dihedral : 8.646 81.818 3666 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.08 % Allowed : 16.18 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.17), residues: 2548 helix: 0.65 (0.21), residues: 640 sheet: -1.14 (0.27), residues: 332 loop : -0.35 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 476 TYR 0.011 0.001 TYR D 446 PHE 0.026 0.001 PHE H 377 TRP 0.014 0.001 TRP H 348 HIS 0.008 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (22560) covalent geometry : angle 0.52302 / 0.25 (31028) hydrogen bonds : bond 0.02873 / 1.94 ( 680) hydrogen bonds : angle 4.29761 / 2.98 ( 1900) metal coordination : bond 0.00503 / 0.33 ( 80) metal coordination : angle 2.04109 / 1.50 ( 64) ********************** REFINEMENT MACRO_CYCLE 10 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 251 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8165 (mt0) cc_final: 0.7700 (mm-40) REVERT: B 36 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7634 (tm-30) REVERT: B 77 GLU cc_start: 0.7787 (tt0) cc_final: 0.7146 (mp0) REVERT: B 147 LYS cc_start: 0.8759 (ptmt) cc_final: 0.8106 (ttmt) REVERT: B 154 TYR cc_start: 0.7215 (m-80) cc_final: 0.6797 (m-80) REVERT: B 168 GLN cc_start: 0.7212 (tp-100) cc_final: 0.6866 (tt0) REVERT: B 313 GLN cc_start: 0.7643 (tt0) cc_final: 0.7097 (tm-30) REVERT: B 340 CYS cc_start: 0.6634 (m) cc_final: 0.5268 (m) REVERT: B 382 CYS cc_start: 0.7810 (m) cc_final: 0.7356 (m) REVERT: B 408 ASN cc_start: 0.8136 (m-40) cc_final: 0.7654 (p0) REVERT: B 469 LYS cc_start: 0.7475 (mmtt) cc_final: 0.7212 (tptt) REVERT: B 489 ASN cc_start: 0.7091 (p0) cc_final: 0.6833 (p0) REVERT: B 492 ARG cc_start: 0.7918 (mtt90) cc_final: 0.7635 (mtt90) REVERT: B 517 TYR cc_start: 0.7583 (t80) cc_final: 0.7075 (t80) REVERT: C 40 ASN cc_start: 0.8351 (t0) cc_final: 0.7609 (t0) REVERT: C 44 MET cc_start: 0.7544 (mmm) cc_final: 0.7235 (mmm) REVERT: C 85 ASN cc_start: 0.6936 (t0) cc_final: 0.6585 (p0) REVERT: C 91 ASP cc_start: 0.8794 (m-30) cc_final: 0.8561 (m-30) REVERT: C 95 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.7135 (mttm) REVERT: D 61 LYS cc_start: 0.8327 (mtpt) cc_final: 0.7957 (mttm) REVERT: D 76 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7607 (ttm170) REVERT: D 77 GLU cc_start: 0.7529 (pt0) cc_final: 0.7251 (tt0) REVERT: D 331 ASP cc_start: 0.6547 (t0) cc_final: 0.6285 (t70) REVERT: F 36 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7635 (tm-30) REVERT: F 77 GLU cc_start: 0.7773 (tt0) cc_final: 0.7139 (mp0) REVERT: F 147 LYS cc_start: 0.8763 (ptmt) cc_final: 0.8121 (ttmt) REVERT: F 154 TYR cc_start: 0.7308 (m-80) cc_final: 0.6812 (m-80) REVERT: F 168 GLN cc_start: 0.7204 (tp-100) cc_final: 0.6911 (tt0) REVERT: F 313 GLN cc_start: 0.7621 (tt0) cc_final: 0.7072 (tm-30) REVERT: F 340 CYS cc_start: 0.6645 (m) cc_final: 0.5257 (m) REVERT: F 347 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7544 (tp30) REVERT: F 382 CYS cc_start: 0.7812 (m) cc_final: 0.7392 (m) REVERT: F 408 ASN cc_start: 0.8218 (m-40) cc_final: 0.7748 (p0) REVERT: F 492 ARG cc_start: 0.7935 (mtt90) cc_final: 0.7629 (mtt90) REVERT: F 517 TYR cc_start: 0.7580 (t80) cc_final: 0.7041 (t80) REVERT: G 40 ASN cc_start: 0.8350 (t0) cc_final: 0.7600 (t0) REVERT: G 85 ASN cc_start: 0.7033 (t0) cc_final: 0.6640 (p0) REVERT: G 95 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7144 (mttp) REVERT: H 61 LYS cc_start: 0.8324 (mtpt) cc_final: 0.7956 (mttp) REVERT: H 76 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7511 (ttm170) REVERT: H 154 TYR cc_start: 0.8446 (m-80) cc_final: 0.8198 (m-80) REVERT: H 331 ASP cc_start: 0.6564 (t0) cc_final: 0.6331 (t70) outliers start: 24 outliers final: 15 residues processed: 244 average time/residue: 0.5932 time to fit residues: 166.4345 Evaluate side-chains 236 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain C residue 95 LYS 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 169 MET Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 347 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 326 PHE Chi-restraints excluded: chain H residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 74 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 60 optimal weight: 0.0770 chunk 169 optimal weight: 1.9990 chunk 219 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 91 optimal weight: 0.0870 chunk 239 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 268 HIS C 36 GLN C 105 ASN D 314 HIS F 268 HIS G 36 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.134466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.090253 restraints weight = 30561.761| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.53 r_work: 0.3154 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22640 Z= 0.093 Angle : 0.527 11.319 31092 Z= 0.253 Chirality : 0.044 0.236 3478 Planarity : 0.004 0.046 3688 Dihedral : 8.576 81.725 3666 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.99 % Allowed : 16.59 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.17), residues: 2548 helix: 0.63 (0.21), residues: 660 sheet: -1.17 (0.30), residues: 284 loop : -0.32 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 476 TYR 0.010 0.001 TYR D 446 PHE 0.024 0.001 PHE D 444 TRP 0.013 0.001 TRP F 292 HIS 0.009 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 (22560) covalent geometry : angle 0.52030 / 0.25 (31028) hydrogen bonds : bond 0.02806 / 1.90 ( 680) hydrogen bonds : angle 4.25132 / 2.95 ( 1900) metal coordination : bond 0.00475 / 0.31 ( 80) metal coordination : angle 1.89065 / 1.40 ( 64) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9930.62 seconds wall clock time: 169 minutes 31.32 seconds (10171.32 seconds total)