Starting phenix.real_space_refine on Mon Jul 6 12:45:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmd_38472/07_2026/8xmd_38472.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmd_38472/07_2026/8xmd_38472.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xmd_38472/07_2026/8xmd_38472.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmd_38472/07_2026/8xmd_38472.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xmd_38472/07_2026/8xmd_38472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmd_38472/07_2026/8xmd_38472.map" } resolution = 3.4 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= 0.001 sd= 0.051 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 9 6.06 5 P 55 5.49 5 Mg 1 5.21 5 S 219 5.16 5 C 22303 2.51 5 N 6177 2.21 5 O 6512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35276 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 8588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8588 Classifications: {'peptide': 1159} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1105} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 498 Unresolved non-hydrogen angles: 612 Unresolved non-hydrogen dihedrals: 401 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLU:plan': 25, 'ASN:plan1': 7, 'ASP:plan': 26, 'ARG:plan': 10, 'PHE:plan': 3, 'GLN:plan1': 6, 'TYR:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 315 Chain: "B" Number of atoms: 8056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8056 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 1020} Chain breaks: 9 Unresolved non-hydrogen bonds: 395 Unresolved non-hydrogen angles: 480 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASN:plan1': 5, 'GLU:plan': 35, 'ASP:plan': 22, 'GLN:plan1': 5, 'TYR:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 265 Chain: "C" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2111 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 12, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 14, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 101 Chain: "D" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 866 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1505 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 7, 'GLN:plan1': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "F" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 568 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 71} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "G" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1096 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 9, 'TRANS': 164} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 7, 'ASP:plan': 8, 'GLU:plan': 9, 'ARG:plan': 6, 'GLN:plan1': 2, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 187 Chain: "H" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 953 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 7, 'HIS:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "I" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 830 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 108} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "J" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 476 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 60} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "K" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 715 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 41 Chain: "L" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 312 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "M" Number of atoms: 8035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8035 Classifications: {'peptide': 1052} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 40, 'TRANS': 1011} Chain breaks: 3 Unresolved non-hydrogen bonds: 432 Unresolved non-hydrogen angles: 538 Unresolved non-hydrogen dihedrals: 351 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 19, 'ASP:plan': 12, 'ARG:plan': 11, 'ASN:plan1': 5, 'GLN:plan1': 8, 'TYR:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 278 Chain: "N" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 348 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "O" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 246 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 1} Link IDs: {'rna3p': 10} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 561 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" 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: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 334 SG CYS A 56 48.040 66.085 121.064 1.00229.43 S ATOM 352 SG CYS A 59 48.715 69.776 121.966 1.00214.33 S ATOM 399 SG CYS A 67 49.570 68.472 118.474 1.00245.40 S ATOM 6911 SG CYS A1031 144.077 71.081 85.306 1.00216.12 S ATOM 6980 SG CYS A1044 141.651 72.477 88.041 1.00179.34 S ATOM 625 SG CYS A 97 99.868 63.056 140.331 1.00289.25 S ATOM 16266 SG CYS B1108 57.240 80.709 133.104 1.00183.18 S ATOM 16288 SG CYS B1111 59.649 78.702 133.799 1.00179.00 S ATOM 16358 SG CYS B1133 55.704 77.223 133.507 1.00242.09 S ATOM 17311 SG CYS C 90 21.934 84.908 61.157 1.00180.40 S ATOM 17327 SG CYS C 93 21.548 81.421 62.612 1.00201.50 S ATOM 17360 SG CYS C 99 20.980 81.777 58.957 1.00176.61 S ATOM 17382 SG CYS C 102 24.412 82.189 60.076 1.00196.64 S ATOM 24284 SG CYS I 76 115.733 106.265 68.365 1.00173.01 S ATOM 24305 SG CYS I 79 112.074 106.208 67.203 1.00168.80 S ATOM 24483 SG CYS I 103 113.531 103.205 69.022 1.00178.05 S ATOM 24518 SG CYS I 108 114.610 104.088 65.471 1.00165.84 S ATOM 23790 SG CYS I 7 137.475 41.147 86.313 1.00196.09 S ATOM 23816 SG CYS I 10 134.865 38.736 87.404 1.00195.84 S ATOM 23950 SG CYS I 29 136.166 41.407 89.897 1.00206.69 S ATOM 23975 SG CYS I 32 138.149 38.417 89.143 1.00209.51 S ATOM 24649 SG CYS J 10 52.480 84.065 47.296 1.00149.24 S ATOM 24906 SG CYS J 44 55.799 83.082 47.287 1.00144.63 S ATOM 24912 SG CYS J 45 53.792 80.880 45.048 1.00158.39 S ATOM 25796 SG CYS L 12 44.917 41.042 69.330 1.00200.89 S ATOM 25814 SG CYS L 15 43.265 38.636 66.814 1.00184.57 S ATOM 25898 SG CYS L 29 42.654 38.278 70.565 1.00200.26 S ATOM 25914 SG CYS L 32 46.096 37.481 69.021 1.00213.08 S Time building chain proxies: 8.08, per 1000 atoms: 0.23 Number of scatterers: 35276 At special positions: 0 Unit cell: (184.8, 172.7, 189.2, 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 9 29.99 S 219 16.00 P 55 15.00 Mg 1 11.99 O 6512 8.00 N 6177 7.00 C 22303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 70 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 56 " pdb=" ZN A1503 " pdb="ZN ZN A1503 " - pdb=" ND1 HIS A 983 " pdb="ZN ZN A1503 " - pdb=" NE2 HIS A 985 " pdb="ZN ZN A1503 " - pdb=" SG CYS A1031 " pdb="ZN ZN A1503 " - pdb=" SG CYS A1044 " pdb=" ZN A1504 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 97 " pdb=" ZN B2001 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1108 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1133 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1111 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 99 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 102 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 93 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 90 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 108 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 79 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 76 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 7 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 32 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 12 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 15 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 29 " Number of angles added : 29 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8590 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 53 sheets defined 36.6% alpha, 18.3% beta 23 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 4.46 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 85 through 96 removed outlier: 3.571A pdb=" N LYS A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.552A pdb=" N THR A 125 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 126 " --> pdb=" O LEU A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 150 through 160 Processing helix chain 'A' and resid 166 through 171 removed outlier: 4.428A pdb=" N TRP A 170 " --> pdb=" O PRO A 167 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 171 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 201 removed outlier: 3.606A pdb=" N TYR A 197 " --> pdb=" O HIS A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 250 through 256 Processing helix chain 'A' and resid 262 through 275 removed outlier: 4.268A pdb=" N LEU A 266 " --> pdb=" O ASN A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 416 through 420 removed outlier: 3.707A pdb=" N LEU A 420 " --> pdb=" O GLN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.868A pdb=" N PHE A 444 " --> pdb=" O CYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 471 removed outlier: 3.648A pdb=" N GLU A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 removed outlier: 3.858A pdb=" N LEU A 477 " --> pdb=" O ASP A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 504 removed outlier: 3.550A pdb=" N GLU A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 518 removed outlier: 3.700A pdb=" N MET A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 548 removed outlier: 3.789A pdb=" N LEU A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 599 through 619 Processing helix chain 'A' and resid 623 through 629 removed outlier: 3.664A pdb=" N LEU A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 658 Processing helix chain 'A' and resid 659 through 660 No H-bonds generated for 'chain 'A' and resid 659 through 660' Processing helix chain 'A' and resid 661 through 663 No H-bonds generated for 'chain 'A' and resid 661 through 663' Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 675 through 682 removed outlier: 3.610A pdb=" N SER A 679 " --> pdb=" O LYS A 675 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 680 " --> pdb=" O GLU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 693 removed outlier: 4.316A pdb=" N CYS A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR A 688 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 713 removed outlier: 4.512A pdb=" N ASP A 710 " --> pdb=" O ASP A 706 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A 711 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 719 Processing helix chain 'A' and resid 723 through 732 Processing helix chain 'A' and resid 736 through 745 removed outlier: 3.580A pdb=" N LEU A 740 " --> pdb=" O ASN A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 770 removed outlier: 3.521A pdb=" N TRP A 769 " --> pdb=" O THR A 765 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN A 770 " --> pdb=" O CYS A 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 765 through 770' Processing helix chain 'A' and resid 805 through 817 Processing helix chain 'A' and resid 818 through 821 Processing helix chain 'A' and resid 825 through 840 removed outlier: 4.304A pdb=" N GLY A 829 " --> pdb=" O ALA A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 891 Processing helix chain 'A' and resid 903 through 913 removed outlier: 3.609A pdb=" N LEU A 908 " --> pdb=" O PRO A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 935 removed outlier: 3.953A pdb=" N LEU A 933 " --> pdb=" O SER A 930 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 934 " --> pdb=" O GLU A 931 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 935 " --> pdb=" O TYR A 932 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 930 through 935' Processing helix chain 'A' and resid 938 through 951 Processing helix chain 'A' and resid 957 through 959 No H-bonds generated for 'chain 'A' and resid 957 through 959' Processing helix chain 'A' and resid 988 through 995 Processing helix chain 'A' and resid 997 through 1012 removed outlier: 3.748A pdb=" N ARG A1012 " --> pdb=" O GLN A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1073 removed outlier: 4.286A pdb=" N ILE A1063 " --> pdb=" O GLU A1059 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE A1068 " --> pdb=" O ARG A1064 " (cutoff:3.500A) Proline residue: A1069 - end of helix Processing helix chain 'A' and resid 1121 through 1130 Processing helix chain 'A' and resid 1131 through 1134 Processing helix chain 'A' and resid 1150 through 1155 Processing helix chain 'A' and resid 1155 through 1175 Processing helix chain 'A' and resid 1179 through 1191 removed outlier: 3.880A pdb=" N LEU A1183 " --> pdb=" O LEU A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1211 Processing helix chain 'A' and resid 1215 through 1223 Processing helix chain 'A' and resid 1224 through 1236 Processing helix chain 'A' and resid 1243 through 1250 Processing helix chain 'B' and resid 27 through 46 removed outlier: 3.768A pdb=" N LEU B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 62 through 71 removed outlier: 3.545A pdb=" N ASN B 66 " --> pdb=" O HIS B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 125 Processing helix chain 'B' and resid 191 through 197 removed outlier: 3.836A pdb=" N LYS B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 286 Processing helix chain 'B' and resid 290 through 298 Processing helix chain 'B' and resid 304 through 322 Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 349 through 357 removed outlier: 3.592A pdb=" N LEU B 354 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N HIS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 384 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 405 through 431 removed outlier: 3.846A pdb=" N GLU B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER B 431 " --> pdb=" O GLN B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.655A pdb=" N TYR B 442 " --> pdb=" O PRO B 438 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 438 through 443' Processing helix chain 'B' and resid 446 through 459 Processing helix chain 'B' and resid 482 through 491 removed outlier: 3.573A pdb=" N THR B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 490 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 514 Processing helix chain 'B' and resid 548 through 556 removed outlier: 3.728A pdb=" N PHE B 553 " --> pdb=" O VAL B 549 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA B 554 " --> pdb=" O GLU B 550 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N CYS B 555 " --> pdb=" O LYS B 551 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 600 Processing helix chain 'B' and resid 649 through 656 Processing helix chain 'B' and resid 664 through 668 removed outlier: 3.938A pdb=" N GLU B 668 " --> pdb=" O ILE B 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 664 through 668' Processing helix chain 'B' and resid 675 through 682 removed outlier: 3.598A pdb=" N LYS B 681 " --> pdb=" O LYS B 677 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU B 682 " --> pdb=" O GLN B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.565A pdb=" N PHE B 695 " --> pdb=" O ASP B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 703 removed outlier: 4.062A pdb=" N VAL B 703 " --> pdb=" O VAL B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 711 through 721 Processing helix chain 'B' and resid 721 through 726 Processing helix chain 'B' and resid 755 through 762 Processing helix chain 'B' and resid 763 through 767 removed outlier: 4.118A pdb=" N LEU B 766 " --> pdb=" O LYS B 763 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE B 767 " --> pdb=" O GLU B 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 763 through 767' Processing helix chain 'B' and resid 792 through 797 Processing helix chain 'B' and resid 929 through 933 Processing helix chain 'B' and resid 949 through 955 removed outlier: 3.932A pdb=" N SER B 953 " --> pdb=" O HIS B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 971 Processing helix chain 'B' and resid 996 through 1007 Processing helix chain 'B' and resid 1076 through 1087 Processing helix chain 'B' and resid 1088 through 1097 removed outlier: 3.809A pdb=" N LEU B1092 " --> pdb=" O ALA B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1148 through 1162 removed outlier: 3.503A pdb=" N LYS B1152 " --> pdb=" O PRO B1148 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.662A pdb=" N ALA C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 removed outlier: 3.533A pdb=" N LEU C 73 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 133 removed outlier: 3.913A pdb=" N THR C 133 " --> pdb=" O PRO C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 216 removed outlier: 3.593A pdb=" N ILE C 210 " --> pdb=" O ASP C 206 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.563A pdb=" N ALA C 237 " --> pdb=" O ASP C 234 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR C 238 " --> pdb=" O PRO C 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 234 through 238' Processing helix chain 'C' and resid 243 through 252 Processing helix chain 'C' and resid 277 through 297 Processing helix chain 'D' and resid 94 through 109 removed outlier: 3.802A pdb=" N PHE D 98 " --> pdb=" O ASP D 94 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY D 103 " --> pdb=" O GLN D 99 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 128 removed outlier: 3.547A pdb=" N ASP D 124 " --> pdb=" O PRO D 120 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 152 removed outlier: 3.572A pdb=" N LYS D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Proline residue: D 148 - end of helix Processing helix chain 'D' and resid 155 through 166 removed outlier: 3.703A pdb=" N CYS D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 removed outlier: 4.146A pdb=" N ILE D 177 " --> pdb=" O VAL D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 181 removed outlier: 3.655A pdb=" N LYS D 181 " --> pdb=" O PRO D 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 178 through 181' Processing helix chain 'D' and resid 187 through 202 removed outlier: 3.733A pdb=" N LEU D 191 " --> pdb=" O ILE D 187 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 78 through 93 Processing helix chain 'E' and resid 106 through 116 Processing helix chain 'E' and resid 147 through 159 Processing helix chain 'E' and resid 172 through 179 Processing helix chain 'F' and resid 66 through 83 Processing helix chain 'F' and resid 96 through 107 Processing helix chain 'G' and resid 20 through 22 No H-bonds generated for 'chain 'G' and resid 20 through 22' Processing helix chain 'G' and resid 23 through 40 removed outlier: 4.025A pdb=" N ALA G 27 " --> pdb=" O MET G 23 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE G 36 " --> pdb=" O LEU G 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 135 removed outlier: 4.288A pdb=" N TYR G 134 " --> pdb=" O MET G 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.628A pdb=" N ARG J 46 " --> pdb=" O ARG J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.539A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 removed outlier: 3.640A pdb=" N ALA K 110 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 34 Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'M' and resid 246 through 252 removed outlier: 3.520A pdb=" N ILE M 250 " --> pdb=" O THR M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 292 through 305 removed outlier: 3.548A pdb=" N LEU M 296 " --> pdb=" O PRO M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 314 Processing helix chain 'M' and resid 315 through 324 removed outlier: 3.757A pdb=" N ILE M 319 " --> pdb=" O ASP M 315 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY M 324 " --> pdb=" O LYS M 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 326 through 339 Processing helix chain 'M' and resid 346 through 355 removed outlier: 3.525A pdb=" N PHE M 350 " --> pdb=" O ASP M 346 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET M 355 " --> pdb=" O VAL M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 377 Processing helix chain 'M' and resid 429 through 433 removed outlier: 3.520A pdb=" N LEU M 433 " --> pdb=" O ALA M 430 " (cutoff:3.500A) Processing helix chain 'M' and resid 448 through 461 removed outlier: 3.557A pdb=" N ASN M 452 " --> pdb=" O THR M 448 " (cutoff:3.500A) Processing helix chain 'M' and resid 475 through 480 removed outlier: 3.579A pdb=" N ARG M 480 " --> pdb=" O ALA M 476 " (cutoff:3.500A) Processing helix chain 'M' and resid 494 through 503 removed outlier: 3.536A pdb=" N GLY M 503 " --> pdb=" O ARG M 499 " (cutoff:3.500A) Processing helix chain 'M' and resid 510 through 520 Processing helix chain 'M' and resid 561 through 569 removed outlier: 3.514A pdb=" N ALA M 565 " --> pdb=" O SER M 561 " (cutoff:3.500A) Processing helix chain 'M' and resid 632 through 640 removed outlier: 3.606A pdb=" N ILE M 636 " --> pdb=" O ASN M 632 " (cutoff:3.500A) Processing helix chain 'M' and resid 645 through 662 removed outlier: 4.427A pdb=" N PHE M 649 " --> pdb=" O GLU M 645 " (cutoff:3.500A) Processing helix chain 'M' and resid 666 through 678 removed outlier: 3.736A pdb=" N ALA M 670 " --> pdb=" O ASP M 666 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU M 671 " --> pdb=" O ARG M 667 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN M 672 " --> pdb=" O ASP M 668 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER M 678 " --> pdb=" O LEU M 674 " (cutoff:3.500A) Processing helix chain 'M' and resid 684 through 692 removed outlier: 3.767A pdb=" N LEU M 691 " --> pdb=" O VAL M 687 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN M 692 " --> pdb=" O LYS M 688 " (cutoff:3.500A) Processing helix chain 'M' and resid 699 through 720 removed outlier: 3.709A pdb=" N MET M 705 " --> pdb=" O TYR M 701 " (cutoff:3.500A) Processing helix chain 'M' and resid 753 through 759 Processing helix chain 'M' and resid 788 through 792 removed outlier: 3.784A pdb=" N ILE M 792 " --> pdb=" O PRO M 789 " (cutoff:3.500A) Processing helix chain 'M' and resid 800 through 807 removed outlier: 3.607A pdb=" N LYS M 806 " --> pdb=" O HIS M 802 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY M 807 " --> pdb=" O PHE M 803 " (cutoff:3.500A) Processing helix chain 'M' and resid 821 through 826 Processing helix chain 'M' and resid 870 through 879 Processing helix chain 'M' and resid 884 through 899 removed outlier: 3.591A pdb=" N ILE M 888 " --> pdb=" O THR M 884 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER M 889 " --> pdb=" O LEU M 885 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR M 890 " --> pdb=" O GLY M 886 " (cutoff:3.500A) Processing helix chain 'M' and resid 905 through 920 removed outlier: 3.594A pdb=" N LEU M 909 " --> pdb=" O SER M 905 " (cutoff:3.500A) Processing helix chain 'M' and resid 955 through 969 Processing helix chain 'M' and resid 999 through 1017 Processing helix chain 'M' and resid 1021 through 1027 removed outlier: 3.728A pdb=" N ILE M1025 " --> pdb=" O ASN M1021 " (cutoff:3.500A) Processing helix chain 'M' and resid 1041 through 1071 removed outlier: 3.807A pdb=" N CYS M1070 " --> pdb=" O PHE M1066 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU M1071 " --> pdb=" O GLU M1067 " (cutoff:3.500A) Processing helix chain 'M' and resid 1072 through 1089 Processing helix chain 'M' and resid 1090 through 1093 Processing sheet with id=AA1, first strand: chain 'A' and resid 1238 through 1239 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 81 removed outlier: 4.246A pdb=" N GLY A 72 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR A 221 " --> pdb=" O PHE A 76 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N TYR A 78 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLY A 219 " --> pdb=" O TYR A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 134 removed outlier: 3.541A pdb=" N ARG A 133 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 147 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG A 189 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 316 through 318 removed outlier: 3.578A pdb=" N LYS A 316 " --> pdb=" O PHE B1075 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 318 " --> pdb=" O ILE B1073 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE B1073 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 removed outlier: 3.554A pdb=" N THR A 324 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N VAL A 434 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 325 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU A 436 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL A 327 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 340 removed outlier: 3.554A pdb=" N THR A 324 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 Processing sheet with id=AA8, first strand: chain 'A' and resid 528 through 529 removed outlier: 3.775A pdb=" N ILE A 529 " --> pdb=" O GLN A 540 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 557 through 559 removed outlier: 6.497A pdb=" N VAL A 565 " --> pdb=" O LEU A 572 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 748 through 751 Processing sheet with id=AB2, first strand: chain 'A' and resid 842 through 844 removed outlier: 6.443A pdb=" N ASN A 852 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU A 858 " --> pdb=" O ASN A 852 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 927 through 928 removed outlier: 7.095A pdb=" N GLU A1106 " --> pdb=" O TRP A1089 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N TRP A1089 " --> pdb=" O GLU A1106 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR A1108 " --> pdb=" O ILE A1087 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE A1087 " --> pdb=" O TYR A1108 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS A1110 " --> pdb=" O VAL A1085 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL A1085 " --> pdb=" O LYS A1110 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR A1112 " --> pdb=" O LYS A1083 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 954 through 955 removed outlier: 6.678A pdb=" N LEU A 954 " --> pdb=" O VAL A1076 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1023 through 1028 removed outlier: 3.711A pdb=" N ASP A1024 " --> pdb=" O THR A1048 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A 962 " --> pdb=" O HIS A 985 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR I 44 " --> pdb=" O ILE A 965 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1261 through 1264 Processing sheet with id=AB7, first strand: chain 'B' and resid 94 through 102 removed outlier: 6.202A pdb=" N VAL B 95 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N GLU B 139 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE B 97 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN B 137 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLU B 99 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN B 135 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ALA B 130 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER B 175 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE B 132 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 173 " --> pdb=" O ILE B 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AB9, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AC1, first strand: chain 'B' and resid 398 through 401 removed outlier: 5.872A pdb=" N ALA B 219 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 229 through 231 removed outlier: 3.842A pdb=" N TRP B 235 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 539 through 540 removed outlier: 3.544A pdb=" N GLU B 660 " --> pdb=" O LEU B 631 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 539 through 540 Processing sheet with id=AC5, first strand: chain 'B' and resid 558 through 559 removed outlier: 7.354A pdb=" N VAL B 574 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU B 583 " --> pdb=" O HIS B 572 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS B 572 " --> pdb=" O LEU B 583 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS B 573 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE B 620 " --> pdb=" O LYS B 573 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU B 575 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 617 " --> pdb=" O ASP B 612 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP B 612 " --> pdb=" O GLU B 617 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 742 through 745 removed outlier: 3.564A pdb=" N SER B 802 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS B 885 " --> pdb=" O SER B 901 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG B 903 " --> pdb=" O VAL B 883 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL B 883 " --> pdb=" O ARG B 903 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N VAL B 905 " --> pdb=" O GLY B 881 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N GLY B 881 " --> pdb=" O VAL B 905 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 742 through 745 removed outlier: 3.564A pdb=" N SER B 802 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS B 885 " --> pdb=" O SER B 901 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG B 903 " --> pdb=" O VAL B 883 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL B 883 " --> pdb=" O ARG B 903 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N VAL B 905 " --> pdb=" O GLY B 881 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N GLY B 881 " --> pdb=" O VAL B 905 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N VAL B 886 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1014 through 1015 removed outlier: 7.099A pdb=" N ILE B 788 " --> pdb=" O GLY B 925 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU B 927 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N MET B 790 " --> pdb=" O LEU B 927 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE B 944 " --> pdb=" O ASN B 771 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE B 773 " --> pdb=" O ILE B 944 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE B 946 " --> pdb=" O ILE B 773 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA B 775 " --> pdb=" O ILE B 946 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE B1031 " --> pdb=" O VAL B 776 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 859 through 861 removed outlier: 3.627A pdb=" N ILE B 861 " --> pdb=" O ILE B 873 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1103 through 1108 removed outlier: 3.554A pdb=" N VAL B1147 " --> pdb=" O SER B1103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 11 through 17 removed outlier: 6.850A pdb=" N LYS C 23 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU C 17 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLU C 271 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N THR C 185 " --> pdb=" O GLU C 271 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 126 through 127 removed outlier: 5.258A pdb=" N CYS C 112 " --> pdb=" O GLN C 161 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLN C 161 " --> pdb=" O CYS C 112 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N GLU C 162 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN C 58 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS C 164 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 52 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARG C 170 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE C 50 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY C 172 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL C 48 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.507A pdb=" N VAL C 155 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 193 through 196 removed outlier: 3.653A pdb=" N ASP C 193 " --> pdb=" O SER C 260 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER C 260 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 221 through 224 removed outlier: 3.611A pdb=" N GLN C 229 " --> pdb=" O ASP C 224 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 55 through 58 removed outlier: 3.639A pdb=" N THR E 55 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG E 96 " --> pdb=" O GLN E 66 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.869A pdb=" N GLU E 142 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG E 202 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 6 through 14 removed outlier: 3.940A pdb=" N PHE G 75 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL G 11 " --> pdb=" O PHE G 71 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN G 76 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU G 54 " --> pdb=" O ASN G 76 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 6 through 14 removed outlier: 3.940A pdb=" N PHE G 75 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL G 11 " --> pdb=" O PHE G 71 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU G 68 " --> pdb=" O LYS G 63 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 87 through 92 removed outlier: 3.524A pdb=" N TYR G 111 " --> pdb=" O ALA G 162 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER G 165 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL G 147 " --> pdb=" O SER G 165 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 8 through 17 removed outlier: 6.905A pdb=" N GLU H 31 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU H 17 " --> pdb=" O ARG H 29 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARG H 29 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP H 44 " --> pdb=" O LEU H 120 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N TYR H 113 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE H 8 " --> pdb=" O MET H 62 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 15 through 18 removed outlier: 3.723A pdb=" N TYR I 15 " --> pdb=" O ALA I 28 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA I 28 " --> pdb=" O TYR I 15 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AE6, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.870A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N HIS K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 39 through 43 Processing sheet with id=AE8, first strand: chain 'M' and resid 218 through 221 removed outlier: 4.205A pdb=" N MET M 218 " --> pdb=" O VAL M 195 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N CYS M 153 " --> pdb=" O ARG M 194 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N TRP M 148 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N GLY M 131 " --> pdb=" O TRP M 148 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ILE M 109 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ARG M 133 " --> pdb=" O ASP M 107 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASP M 107 " --> pdb=" O ARG M 133 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU M 165 " --> pdb=" O LYS M 184 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ARG M 258 " --> pdb=" O ILE M 164 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR M 166 " --> pdb=" O ARG M 258 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP M 260 " --> pdb=" O THR M 166 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER M 168 " --> pdb=" O ASP M 260 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 123 through 125 removed outlier: 6.799A pdb=" N PHE M 123 " --> pdb=" O VAL M 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'M' and resid 391 through 400 removed outlier: 6.681A pdb=" N ARG M 383 " --> pdb=" O LEU M 394 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N CYS M 381 " --> pdb=" O PRO M 396 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU M 398 " --> pdb=" O MET M 379 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N MET M 379 " --> pdb=" O LEU M 398 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE M 415 " --> pdb=" O SER M 380 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN M 382 " --> pdb=" O PHE M 415 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N TRP M 485 " --> pdb=" O LEU M 472 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE M 462 " --> pdb=" O PHE M 469 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 435 through 438 removed outlier: 3.538A pdb=" N SER M 437 " --> pdb=" O LYS M 444 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 526 through 530 removed outlier: 3.596A pdb=" N VAL M 620 " --> pdb=" O ARG M 526 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU M 618 " --> pdb=" O THR M 528 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASN M 619 " --> pdb=" O ARG M 584 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG M 584 " --> pdb=" O ASN M 619 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE M 581 " --> pdb=" O ILE M 592 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE M 592 " --> pdb=" O PHE M 581 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 543 through 546 Processing sheet with id=AF5, first strand: chain 'M' and resid 627 through 631 removed outlier: 4.421A pdb=" N MET M 627 " --> pdb=" O ILE M 730 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLY M 728 " --> pdb=" O CYS M 629 " (cutoff:3.500A) removed outlier: 11.488A pdb=" N LEU M 631 " --> pdb=" O PRO M 726 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 733 through 735 Processing sheet with id=AF7, first strand: chain 'M' and resid 745 through 746 removed outlier: 3.658A pdb=" N VAL M 746 " --> pdb=" O ASP M 796 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 748 through 751 removed outlier: 4.724A pdb=" N VAL M 748 " --> pdb=" O VAL M 775 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL M 750 " --> pdb=" O SER M 773 " (cutoff:3.500A) 1399 hydrogen bonds defined for protein. 3957 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 10.04 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11308 1.34 - 1.46: 5842 1.46 - 1.58: 18460 1.58 - 1.70: 108 1.70 - 1.82: 333 Bond restraints: 36051 Sorted by residual: bond pdb=" C3' DA N 39 " pdb=" C2' DA N 39 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.94e+00 bond pdb=" C3' DT N 40 " pdb=" C2' DT N 40 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.50e+00 bond pdb=" C1' DC Q 19 " pdb=" N1 DC Q 19 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.18e+00 bond pdb=" C1' DT Q 20 " pdb=" N1 DT Q 20 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.67e+00 bond pdb=" C3' DC Q 23 " pdb=" C2' DC Q 23 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.20e+00 ... (remaining 36046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 48621 1.65 - 3.31: 458 3.31 - 4.96: 32 4.96 - 6.62: 6 6.62 - 8.27: 2 Bond angle restraints: 49119 Sorted by residual: angle pdb=" N3 DT N 44 " pdb=" C4 DT N 44 " pdb=" O4 DT N 44 " ideal model delta sigma weight residual 119.90 122.84 -2.94 6.00e-01 2.78e+00 2.40e+01 angle pdb=" O4 DT N 44 " pdb=" C4 DT N 44 " pdb=" C5 DT N 44 " ideal model delta sigma weight residual 124.90 121.78 3.12 7.00e-01 2.04e+00 1.99e+01 angle pdb=" N3 DT Q 29 " pdb=" C4 DT Q 29 " pdb=" O4 DT Q 29 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT N 34 " pdb=" C4 DT N 34 " pdb=" O4 DT N 34 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT Q 4 " pdb=" C4 DT Q 4 " pdb=" O4 DT Q 4 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 ... (remaining 49114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.34: 21268 31.34 - 62.69: 305 62.69 - 94.03: 23 94.03 - 125.38: 0 125.38 - 156.72: 3 Dihedral angle restraints: 21599 sinusoidal: 8354 harmonic: 13245 Sorted by residual: dihedral pdb=" C4' DT N 40 " pdb=" C3' DT N 40 " pdb=" O3' DT N 40 " pdb=" P DC N 41 " ideal model delta sinusoidal sigma weight residual 220.00 63.28 156.72 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C4' DG N 43 " pdb=" C3' DG N 43 " pdb=" O3' DG N 43 " pdb=" P DT N 44 " ideal model delta sinusoidal sigma weight residual 220.00 66.62 153.38 1 3.50e+01 8.16e-04 1.48e+01 dihedral pdb=" C4' DT Q 24 " pdb=" C3' DT Q 24 " pdb=" O3' DT Q 24 " pdb=" P DC Q 25 " ideal model delta sinusoidal sigma weight residual 220.00 75.05 144.95 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 21596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3654 0.028 - 0.056: 1312 0.056 - 0.083: 329 0.083 - 0.111: 352 0.111 - 0.139: 63 Chirality restraints: 5710 Sorted by residual: chirality pdb=" CA ILE M 539 " pdb=" N ILE M 539 " pdb=" C ILE M 539 " pdb=" CB ILE M 539 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE H 11 " pdb=" N ILE H 11 " pdb=" C ILE H 11 " pdb=" CB ILE H 11 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA ILE J 3 " pdb=" N ILE J 3 " pdb=" C ILE J 3 " pdb=" CB ILE J 3 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 5707 not shown) Planarity restraints: 6081 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 903 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO A 904 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 904 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 904 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 978 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.50e+00 pdb=" N PRO A 979 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 979 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 979 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE M 939 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO M 940 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO M 940 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO M 940 " -0.017 5.00e-02 4.00e+02 ... (remaining 6078 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 486 2.68 - 3.23: 31577 3.23 - 3.79: 51898 3.79 - 4.34: 68323 4.34 - 4.90: 115298 Nonbonded interactions: 267582 Sorted by model distance: nonbonded pdb=" OD1 ASP A 449 " pdb="MG MG A1502 " model vdw 2.119 2.170 nonbonded pdb=" OD1 ASP A 447 " pdb="MG MG A1502 " model vdw 2.126 2.170 nonbonded pdb=" OP1 G O 11 " pdb="MG MG A1502 " model vdw 2.208 2.170 nonbonded pdb=" OD2 ASP H 10 " pdb=" OG SER H 34 " model vdw 2.228 3.040 nonbonded pdb=" OD2 ASP B 845 " pdb=" OH TYR L 10 " model vdw 2.236 3.040 ... (remaining 267577 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.690 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 44.450 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 36082 Z= 0.138 Angle : 0.410 8.270 49148 Z= 0.253 Chirality : 0.039 0.139 5710 Planarity : 0.003 0.031 6081 Dihedral : 10.561 156.721 13009 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.41 % Allowed : 2.69 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.53 (0.12), residues: 4483 helix: 1.04 (0.14), residues: 1459 sheet: 0.06 (0.21), residues: 658 loop : -1.42 (0.11), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 70 TYR 0.009 0.001 TYR K 87 PHE 0.008 0.001 PHE J 8 TRP 0.007 0.001 TRP B 119 HIS 0.003 0.000 HIS A 743 Details of bonding type rmsd/Z covalent geometry : bond 0.00181 / 0.14 (36051) covalent geometry : angle 0.40171 / 0.25 (49119) hydrogen bonds : bond 0.20322 / 13.96 ( 1413) hydrogen bonds : angle 6.76768 / 4.79 ( 4071) metal coordination : bond 0.00269 / 0.18 ( 31) metal coordination : angle 3.37102 / 2.11 ( 29) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 4038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 407 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8796 (tpp) cc_final: 0.8414 (tpp) REVERT: A 130 MET cc_start: 0.7087 (mmm) cc_final: 0.6886 (pmm) REVERT: A 191 ILE cc_start: 0.8785 (mm) cc_final: 0.8584 (mm) REVERT: A 271 MET cc_start: 0.8773 (tpt) cc_final: 0.8005 (ppp) REVERT: A 402 MET cc_start: 0.8309 (ptp) cc_final: 0.8058 (ptt) REVERT: A 745 MET cc_start: 0.9121 (mtm) cc_final: 0.8826 (mtm) REVERT: A 836 MET cc_start: 0.9580 (mmm) cc_final: 0.9128 (tpp) REVERT: A 841 ASP cc_start: 0.9150 (m-30) cc_final: 0.8805 (m-30) REVERT: A 1135 ASP cc_start: 0.9185 (m-30) cc_final: 0.8529 (p0) REVERT: B 557 MET cc_start: 0.8748 (ttp) cc_final: 0.8262 (tmm) REVERT: B 854 MET cc_start: 0.9154 (mmm) cc_final: 0.8951 (mmm) REVERT: C 82 MET cc_start: 0.8683 (mmm) cc_final: 0.8425 (tpp) REVERT: E 18 MET cc_start: 0.9547 (mmt) cc_final: 0.9285 (mmm) REVERT: E 35 MET cc_start: 0.9122 (ttm) cc_final: 0.8880 (tpp) REVERT: E 123 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8459 (mp0) REVERT: E 144 GLN cc_start: 0.8704 (tt0) cc_final: 0.8313 (tm-30) REVERT: E 187 LYS cc_start: 0.8814 (tttm) cc_final: 0.8557 (ttmm) REVERT: G 9 TRP cc_start: 0.8398 (m100) cc_final: 0.8180 (m100) REVERT: G 25 GLN cc_start: 0.8888 (mp10) cc_final: 0.8651 (pm20) REVERT: G 75 PHE cc_start: 0.7393 (p90) cc_final: 0.7041 (p90) REVERT: G 80 PHE cc_start: -0.4059 (m-80) cc_final: -0.5035 (t80) REVERT: G 146 PHE cc_start: 0.7630 (p90) cc_final: 0.7125 (p90) REVERT: H 99 LYS cc_start: 0.9613 (ttpt) cc_final: 0.9277 (ttpp) REVERT: I 77 SER cc_start: 0.9541 (m) cc_final: 0.9248 (p) REVERT: I 83 GLU cc_start: 0.8920 (tt0) cc_final: 0.8679 (tt0) REVERT: I 97 MET cc_start: 0.8972 (mmt) cc_final: 0.8440 (mmp) REVERT: J 61 ASN cc_start: 0.9252 (m-40) cc_final: 0.8941 (m110) REVERT: L 49 GLU cc_start: 0.8953 (tt0) cc_final: 0.8296 (tm-30) REVERT: M 22 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.7907 (t) REVERT: M 43 GLU cc_start: 0.9149 (tt0) cc_final: 0.8916 (tm-30) REVERT: M 438 LYS cc_start: 0.9603 (tttt) cc_final: 0.9380 (tppt) REVERT: M 604 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7135 (tp) REVERT: M 738 MET cc_start: 0.6797 (mmm) cc_final: 0.6580 (ptt) REVERT: M 874 LYS cc_start: 0.9254 (mmtt) cc_final: 0.9030 (mmtm) REVERT: M 923 LYS cc_start: 0.9403 (mtpt) cc_final: 0.9143 (mtmm) outliers start: 14 outliers final: 4 residues processed: 420 average time/residue: 0.2435 time to fit residues: 159.3820 Evaluate side-chains 246 residues out of total 4038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 240 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain L residue 15 CYS Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 604 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 0.0170 overall best weight: 3.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 ASN A 410 ASN A 459 GLN A 481 GLN A 491 GLN A 562 ASN A 634 GLN A 657 GLN A 742 GLN ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1219 GLN B 220 GLN B 222 GLN B 316 HIS B 355 HIS B 417 HIS B 441 HIS B 477 ASN B 543 GLN B 577 ASN B 600 GLN B 642 GLN B 711 HIS B 718 GLN B 724 GLN B 749 GLN B 771 ASN B 779 HIS B 804 GLN B1003 GLN B1091 ASN B1106 HIS C 280 GLN E 126 GLN ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 GLN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 GLN I 50 HIS I 80 GLN K 76 HIS K 89 GLN K 104 GLN L 17 GLN L 28 GLN L 47 GLN M 84 HIS M 85 ASN M 298 GLN M 304 HIS M 339 GLN M 865 HIS M 873 HIS M 913 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.062402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.043973 restraints weight = 221791.321| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 4.72 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 36082 Z= 0.187 Angle : 0.570 9.750 49148 Z= 0.294 Chirality : 0.041 0.213 5710 Planarity : 0.004 0.073 6081 Dihedral : 11.234 161.250 5550 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.28 % Allowed : 6.45 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.18 (0.12), residues: 4483 helix: 1.44 (0.14), residues: 1514 sheet: -0.02 (0.20), residues: 723 loop : -1.27 (0.12), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 43 TYR 0.016 0.001 TYR M 951 PHE 0.021 0.001 PHE M 649 TRP 0.008 0.001 TRP A 541 HIS 0.013 0.001 HIS B 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 (36051) covalent geometry : angle 0.56336 / 0.29 (49119) hydrogen bonds : bond 0.04655 / 3.23 ( 1413) hydrogen bonds : angle 5.15724 / 3.65 ( 4071) metal coordination : bond 0.00839 / 0.58 ( 31) metal coordination : angle 3.53441 / 2.18 ( 29) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 4038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 239 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8758 (tpp) cc_final: 0.8533 (tpp) REVERT: A 130 MET cc_start: 0.7157 (mmm) cc_final: 0.6579 (pmm) REVERT: A 214 MET cc_start: 0.6625 (mtt) cc_final: 0.6260 (mtp) REVERT: A 271 MET cc_start: 0.8680 (tpt) cc_final: 0.8042 (ppp) REVERT: A 402 MET cc_start: 0.8242 (ptp) cc_final: 0.8009 (ptt) REVERT: A 499 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9315 (mm) REVERT: A 706 ASP cc_start: 0.8983 (m-30) cc_final: 0.8740 (p0) REVERT: A 836 MET cc_start: 0.9458 (mmm) cc_final: 0.9240 (mmt) REVERT: A 841 ASP cc_start: 0.9059 (m-30) cc_final: 0.8775 (m-30) REVERT: A 1134 MET cc_start: 0.9063 (mmm) cc_final: 0.8525 (mmm) REVERT: A 1135 ASP cc_start: 0.9240 (m-30) cc_final: 0.8675 (p0) REVERT: B 557 MET cc_start: 0.8905 (ttp) cc_final: 0.8339 (tmm) REVERT: B 628 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8828 (pp) REVERT: B 854 MET cc_start: 0.9063 (mmm) cc_final: 0.8856 (mmm) REVERT: B 929 GLU cc_start: 0.7541 (mp0) cc_final: 0.7321 (mp0) REVERT: B 1029 MET cc_start: 0.8847 (mtp) cc_final: 0.8524 (mtp) REVERT: B 1032 MET cc_start: 0.9004 (mtp) cc_final: 0.8708 (ttm) REVERT: C 82 MET cc_start: 0.8774 (mmm) cc_final: 0.8557 (tpp) REVERT: E 18 MET cc_start: 0.9519 (mmt) cc_final: 0.9232 (mmm) REVERT: E 127 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8272 (mp0) REVERT: E 130 MET cc_start: 0.9426 (mmm) cc_final: 0.9072 (mmm) REVERT: E 144 GLN cc_start: 0.8841 (tt0) cc_final: 0.8306 (tm-30) REVERT: G 9 TRP cc_start: 0.8469 (m100) cc_final: 0.8071 (m-10) REVERT: G 80 PHE cc_start: -0.3919 (m-80) cc_final: -0.4793 (t80) REVERT: G 146 PHE cc_start: 0.7608 (p90) cc_final: 0.7097 (p90) REVERT: H 41 MET cc_start: 0.9342 (ttt) cc_final: 0.8872 (tmm) REVERT: H 62 MET cc_start: 0.8823 (mtp) cc_final: 0.8498 (mmm) REVERT: I 75 ARG cc_start: 0.7820 (tpp80) cc_final: 0.7553 (tpp80) REVERT: I 77 SER cc_start: 0.9349 (m) cc_final: 0.9137 (p) REVERT: I 97 MET cc_start: 0.8783 (mmt) cc_final: 0.8342 (mmp) REVERT: J 61 ASN cc_start: 0.9151 (m-40) cc_final: 0.8831 (m110) REVERT: K 97 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8681 (tt0) REVERT: L 49 GLU cc_start: 0.8835 (tt0) cc_final: 0.8153 (tm-30) REVERT: M 43 GLU cc_start: 0.9050 (tt0) cc_final: 0.8781 (tm-30) REVERT: M 325 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7896 (mtm) REVERT: M 379 MET cc_start: 0.9473 (ptm) cc_final: 0.8881 (ptm) REVERT: M 416 MET cc_start: 0.9121 (ttp) cc_final: 0.8502 (tpp) REVERT: M 438 LYS cc_start: 0.9567 (tttt) cc_final: 0.9316 (tppt) REVERT: M 735 MET cc_start: 0.6397 (ttp) cc_final: 0.6193 (tpp) REVERT: M 738 MET cc_start: 0.6686 (mmm) cc_final: 0.6432 (ptt) REVERT: M 874 LYS cc_start: 0.9363 (mmtt) cc_final: 0.9064 (mmtm) REVERT: M 923 LYS cc_start: 0.9449 (mtpt) cc_final: 0.9184 (mtmm) REVERT: M 929 GLU cc_start: 0.8211 (tp30) cc_final: 0.7828 (tp30) outliers start: 44 outliers final: 18 residues processed: 273 average time/residue: 0.2009 time to fit residues: 91.5341 Evaluate side-chains 245 residues out of total 4038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 1107 ILE Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain H residue 39 MET Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 15 CYS Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 325 MET Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 1012 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 350 optimal weight: 4.9990 chunk 55 optimal weight: 0.0980 chunk 312 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 232 optimal weight: 9.9990 chunk 324 optimal weight: 9.9990 chunk 373 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 285 optimal weight: 5.9990 chunk 313 optimal weight: 0.0980 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 164 GLN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 HIS M 653 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.061558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.042869 restraints weight = 222857.551| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 4.71 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 36082 Z= 0.159 Angle : 0.515 10.845 49148 Z= 0.267 Chirality : 0.040 0.226 5710 Planarity : 0.003 0.045 6081 Dihedral : 11.201 160.939 5545 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.37 % Allowed : 6.74 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.04 (0.13), residues: 4483 helix: 1.68 (0.14), residues: 1521 sheet: -0.05 (0.19), residues: 756 loop : -1.17 (0.12), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 709 TYR 0.012 0.001 TYR M 451 PHE 0.021 0.001 PHE G 36 TRP 0.007 0.001 TRP M 219 HIS 0.009 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (36051) covalent geometry : angle 0.50867 / 0.27 (49119) hydrogen bonds : bond 0.03798 / 2.64 ( 1413) hydrogen bonds : angle 4.70296 / 3.33 ( 4071) metal coordination : bond 0.00742 / 0.52 ( 31) metal coordination : angle 3.28689 / 2.10 ( 29) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 4038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 226 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8748 (tpp) cc_final: 0.8519 (tpp) REVERT: A 130 MET cc_start: 0.7343 (mmm) cc_final: 0.7140 (pmm) REVERT: A 214 MET cc_start: 0.6830 (mtt) cc_final: 0.6502 (mtp) REVERT: A 271 MET cc_start: 0.8688 (tpt) cc_final: 0.8299 (ppp) REVERT: A 402 MET cc_start: 0.8244 (ptp) cc_final: 0.7998 (ptt) REVERT: A 499 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9319 (mm) REVERT: A 837 PHE cc_start: 0.9425 (OUTLIER) cc_final: 0.8721 (t80) REVERT: A 841 ASP cc_start: 0.9166 (m-30) cc_final: 0.8906 (m-30) REVERT: A 925 MET cc_start: 0.8673 (mmt) cc_final: 0.8449 (mmm) REVERT: A 1130 CYS cc_start: 0.9507 (OUTLIER) cc_final: 0.8348 (p) REVERT: A 1135 ASP cc_start: 0.9243 (m-30) cc_final: 0.8696 (p0) REVERT: B 557 MET cc_start: 0.8956 (ttp) cc_final: 0.8218 (tmm) REVERT: B 854 MET cc_start: 0.9152 (mmm) cc_final: 0.8802 (mmm) REVERT: B 929 GLU cc_start: 0.7784 (mp0) cc_final: 0.7543 (mp0) REVERT: B 1029 MET cc_start: 0.8919 (mtp) cc_final: 0.8608 (mtp) REVERT: B 1032 MET cc_start: 0.9009 (mtp) cc_final: 0.8753 (ttm) REVERT: C 82 MET cc_start: 0.8770 (mmm) cc_final: 0.8533 (tpp) REVERT: E 18 MET cc_start: 0.9504 (mmt) cc_final: 0.9216 (mmm) REVERT: E 130 MET cc_start: 0.9484 (mmm) cc_final: 0.9125 (mmm) REVERT: E 144 GLN cc_start: 0.8963 (tt0) cc_final: 0.8394 (tm-30) REVERT: F 102 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8861 (tmm) REVERT: G 9 TRP cc_start: 0.8478 (m100) cc_final: 0.8035 (m-10) REVERT: G 36 PHE cc_start: 0.7832 (p90) cc_final: 0.7042 (p90) REVERT: G 80 PHE cc_start: -0.4208 (m-80) cc_final: -0.4836 (t80) REVERT: G 146 PHE cc_start: 0.7591 (p90) cc_final: 0.7116 (p90) REVERT: H 23 LYS cc_start: 0.9006 (tppt) cc_final: 0.8789 (mmmt) REVERT: H 41 MET cc_start: 0.9399 (ttt) cc_final: 0.8686 (tmm) REVERT: H 111 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: I 75 ARG cc_start: 0.7729 (tpp80) cc_final: 0.7517 (tpp80) REVERT: I 77 SER cc_start: 0.9382 (m) cc_final: 0.9132 (p) REVERT: I 97 MET cc_start: 0.8723 (mmt) cc_final: 0.8207 (mmp) REVERT: J 61 ASN cc_start: 0.9123 (m-40) cc_final: 0.8833 (m110) REVERT: K 97 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8636 (tp30) REVERT: L 49 GLU cc_start: 0.8836 (tt0) cc_final: 0.8139 (tm-30) REVERT: M 43 GLU cc_start: 0.9052 (tt0) cc_final: 0.8828 (tm-30) REVERT: M 379 MET cc_start: 0.9542 (ptm) cc_final: 0.8987 (ptt) REVERT: M 416 MET cc_start: 0.9053 (ttp) cc_final: 0.8475 (tpp) REVERT: M 438 LYS cc_start: 0.9533 (tttt) cc_final: 0.9268 (tppt) REVERT: M 735 MET cc_start: 0.6352 (ttp) cc_final: 0.6032 (tpp) REVERT: M 853 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.7778 (mtm) REVERT: M 874 LYS cc_start: 0.9373 (mmtt) cc_final: 0.9084 (mmtm) REVERT: M 923 LYS cc_start: 0.9457 (mtpt) cc_final: 0.9197 (mtmm) REVERT: M 929 GLU cc_start: 0.8360 (tp30) cc_final: 0.7884 (tp30) outliers start: 47 outliers final: 18 residues processed: 260 average time/residue: 0.2192 time to fit residues: 95.0612 Evaluate side-chains 242 residues out of total 4038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 217 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 1107 ILE Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 15 CYS Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 853 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 365 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 386 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 428 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 306 optimal weight: 8.9990 chunk 141 optimal weight: 0.0050 overall best weight: 5.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN A 476 GLN A 895 GLN ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.059510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.040839 restraints weight = 226435.252| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 4.61 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 36082 Z= 0.250 Angle : 0.621 13.247 49148 Z= 0.313 Chirality : 0.042 0.224 5710 Planarity : 0.004 0.038 6081 Dihedral : 11.347 161.777 5544 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.87 % Allowed : 6.95 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.07 (0.13), residues: 4483 helix: 1.70 (0.14), residues: 1520 sheet: -0.08 (0.19), residues: 732 loop : -1.10 (0.12), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 903 TYR 0.016 0.001 TYR E 85 PHE 0.019 0.001 PHE C 268 TRP 0.017 0.001 TRP M 219 HIS 0.009 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.25 (36051) covalent geometry : angle 0.61448 / 0.31 (49119) hydrogen bonds : bond 0.04132 / 2.89 ( 1413) hydrogen bonds : angle 4.69209 / 3.32 ( 4071) metal coordination : bond 0.01362 / 0.96 ( 31) metal coordination : angle 3.77709 / 2.40 ( 29) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 4038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 220 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.7163 (mtt) cc_final: 0.6601 (tpp) REVERT: A 271 MET cc_start: 0.9017 (tpt) cc_final: 0.8453 (tmm) REVERT: A 402 MET cc_start: 0.8128 (ptp) cc_final: 0.7894 (ptt) REVERT: A 499 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9331 (mm) REVERT: A 660 MET cc_start: 0.9528 (mmt) cc_final: 0.9306 (mmp) REVERT: A 706 ASP cc_start: 0.9024 (m-30) cc_final: 0.8749 (p0) REVERT: A 906 LEU cc_start: 0.9771 (OUTLIER) cc_final: 0.9481 (mm) REVERT: A 925 MET cc_start: 0.8754 (mmt) cc_final: 0.8522 (mmm) REVERT: A 1130 CYS cc_start: 0.9406 (OUTLIER) cc_final: 0.8535 (p) REVERT: A 1134 MET cc_start: 0.9063 (mmm) cc_final: 0.7903 (mmm) REVERT: A 1136 MET cc_start: 0.9052 (mmm) cc_final: 0.8784 (mmp) REVERT: B 223 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7647 (mmm) REVERT: B 557 MET cc_start: 0.8997 (ttp) cc_final: 0.8302 (tmm) REVERT: B 854 MET cc_start: 0.9152 (mmm) cc_final: 0.8930 (mmm) REVERT: B 929 GLU cc_start: 0.8042 (mp0) cc_final: 0.7821 (mp0) REVERT: B 1029 MET cc_start: 0.8950 (mtp) cc_final: 0.8715 (mtp) REVERT: B 1032 MET cc_start: 0.9119 (mtp) cc_final: 0.8917 (ttm) REVERT: C 82 MET cc_start: 0.8783 (mmm) cc_final: 0.8561 (tpp) REVERT: E 18 MET cc_start: 0.9489 (mmt) cc_final: 0.8999 (mmm) REVERT: E 19 GLN cc_start: 0.9446 (mm-40) cc_final: 0.9145 (mm-40) REVERT: E 130 MET cc_start: 0.9522 (mmm) cc_final: 0.9194 (mmm) REVERT: E 144 GLN cc_start: 0.8926 (tt0) cc_final: 0.8351 (tm-30) REVERT: F 102 MET cc_start: 0.9199 (tmm) cc_final: 0.8898 (tmm) REVERT: G 9 TRP cc_start: 0.8600 (m100) cc_final: 0.8186 (m-10) REVERT: G 36 PHE cc_start: 0.7985 (p90) cc_final: 0.7215 (p90) REVERT: H 41 MET cc_start: 0.9490 (ttt) cc_final: 0.8769 (tmm) REVERT: H 62 MET cc_start: 0.8893 (mmm) cc_final: 0.8627 (mmm) REVERT: H 111 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: I 75 ARG cc_start: 0.7884 (tpp80) cc_final: 0.7607 (tpp80) REVERT: I 77 SER cc_start: 0.9412 (m) cc_final: 0.9197 (p) REVERT: I 97 MET cc_start: 0.8768 (mmt) cc_final: 0.8152 (mmp) REVERT: J 48 MET cc_start: 0.8906 (tpp) cc_final: 0.8609 (mtt) REVERT: K 97 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8480 (tp30) REVERT: L 49 GLU cc_start: 0.8796 (tt0) cc_final: 0.8054 (tm-30) REVERT: M 43 GLU cc_start: 0.9105 (tt0) cc_final: 0.8860 (tm-30) REVERT: M 416 MET cc_start: 0.9037 (ttp) cc_final: 0.8393 (tpp) REVERT: M 438 LYS cc_start: 0.9543 (tttt) cc_final: 0.9154 (tppt) REVERT: M 738 MET cc_start: 0.6992 (ptt) cc_final: 0.6619 (ppp) REVERT: M 923 LYS cc_start: 0.9479 (mtpt) cc_final: 0.9237 (mtmm) REVERT: M 929 GLU cc_start: 0.8560 (tp30) cc_final: 0.8218 (tp30) REVERT: M 1012 SER cc_start: 0.9280 (OUTLIER) cc_final: 0.8872 (p) outliers start: 64 outliers final: 31 residues processed: 268 average time/residue: 0.2188 time to fit residues: 98.6931 Evaluate side-chains 249 residues out of total 4038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1107 ILE Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 853 MET Chi-restraints excluded: chain M residue 1012 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 453 optimal weight: 30.0000 chunk 4 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 418 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 273 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 406 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 246 optimal weight: 2.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.063149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.044844 restraints weight = 220742.668| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 4.67 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36082 Z= 0.160 Angle : 0.530 12.135 49148 Z= 0.271 Chirality : 0.041 0.236 5710 Planarity : 0.003 0.057 6081 Dihedral : 11.338 161.008 5543 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.43 % Allowed : 7.91 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.15 (0.13), residues: 4483 helix: 1.86 (0.14), residues: 1526 sheet: -0.10 (0.19), residues: 745 loop : -1.13 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 917 TYR 0.013 0.001 TYR M 451 PHE 0.020 0.001 PHE A1256 TRP 0.008 0.001 TRP M 219 HIS 0.009 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (36051) covalent geometry : angle 0.52412 / 0.27 (49119) hydrogen bonds : bond 0.03480 / 2.44 ( 1413) hydrogen bonds : angle 4.47611 / 3.16 ( 4071) metal coordination : bond 0.00839 / 0.56 ( 31) metal coordination : angle 3.35715 / 2.18 ( 29) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 4038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 214 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.7350 (mtt) cc_final: 0.7083 (tpp) REVERT: A 271 MET cc_start: 0.9090 (tpt) cc_final: 0.8507 (ppp) REVERT: A 402 MET cc_start: 0.8126 (ptp) cc_final: 0.7889 (ptt) REVERT: A 499 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9326 (mm) REVERT: A 706 ASP cc_start: 0.8982 (m-30) cc_final: 0.8701 (p0) REVERT: A 925 MET cc_start: 0.8815 (mmt) cc_final: 0.8573 (mmm) REVERT: A 1130 CYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9108 (t) REVERT: A 1136 MET cc_start: 0.9091 (mmm) cc_final: 0.8751 (mmp) REVERT: B 557 MET cc_start: 0.8956 (ttp) cc_final: 0.8281 (tmm) REVERT: B 917 MET cc_start: 0.9295 (mmm) cc_final: 0.9094 (tpp) REVERT: B 1029 MET cc_start: 0.8902 (mtp) cc_final: 0.8683 (mtp) REVERT: B 1032 MET cc_start: 0.9058 (mtp) cc_final: 0.8827 (ttm) REVERT: C 82 MET cc_start: 0.8829 (mmm) cc_final: 0.8589 (tpp) REVERT: E 18 MET cc_start: 0.9448 (mmt) cc_final: 0.9230 (mmm) REVERT: E 19 GLN cc_start: 0.9467 (mm-40) cc_final: 0.9062 (tp-100) REVERT: E 51 GLU cc_start: 0.9323 (mm-30) cc_final: 0.9068 (mm-30) REVERT: E 82 MET cc_start: 0.9172 (tmm) cc_final: 0.8948 (ttt) REVERT: E 130 MET cc_start: 0.9498 (mmm) cc_final: 0.9156 (mmm) REVERT: E 144 GLN cc_start: 0.8925 (tt0) cc_final: 0.8328 (tm-30) REVERT: F 102 MET cc_start: 0.9244 (tmm) cc_final: 0.8903 (tmm) REVERT: G 9 TRP cc_start: 0.8622 (m100) cc_final: 0.8258 (m-10) REVERT: G 36 PHE cc_start: 0.8000 (p90) cc_final: 0.7202 (p90) REVERT: G 52 THR cc_start: 0.5929 (p) cc_final: 0.5719 (p) REVERT: H 41 MET cc_start: 0.9446 (ttt) cc_final: 0.8635 (tmm) REVERT: H 62 MET cc_start: 0.8843 (mmm) cc_final: 0.8585 (mmm) REVERT: H 111 GLU cc_start: 0.8127 (pm20) cc_final: 0.7913 (mp0) REVERT: I 75 ARG cc_start: 0.7909 (tpp80) cc_final: 0.7595 (tpp80) REVERT: I 77 SER cc_start: 0.9399 (m) cc_final: 0.9164 (p) REVERT: I 83 GLU cc_start: 0.9167 (tt0) cc_final: 0.8964 (tp30) REVERT: I 97 MET cc_start: 0.8738 (mmt) cc_final: 0.8123 (mmp) REVERT: J 48 MET cc_start: 0.8976 (tpp) cc_final: 0.8521 (mtt) REVERT: J 61 ASN cc_start: 0.9262 (m-40) cc_final: 0.9012 (m110) REVERT: K 97 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8443 (tp30) REVERT: L 49 GLU cc_start: 0.8767 (tt0) cc_final: 0.8045 (tm-30) REVERT: M 379 MET cc_start: 0.9646 (ptm) cc_final: 0.9343 (ptm) REVERT: M 416 MET cc_start: 0.8962 (ttp) cc_final: 0.8403 (tpp) REVERT: M 438 LYS cc_start: 0.9480 (tttt) cc_final: 0.9161 (tppt) REVERT: M 735 MET cc_start: 0.5886 (ttp) cc_final: 0.5625 (tpp) REVERT: M 738 MET cc_start: 0.7013 (ptt) cc_final: 0.6662 (ppp) REVERT: M 853 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7398 (mtm) REVERT: M 923 LYS cc_start: 0.9468 (mtpt) cc_final: 0.9236 (mtmm) REVERT: M 929 GLU cc_start: 0.8707 (tp30) cc_final: 0.8268 (tp30) REVERT: M 1012 SER cc_start: 0.9233 (OUTLIER) cc_final: 0.8817 (p) outliers start: 49 outliers final: 29 residues processed: 252 average time/residue: 0.2156 time to fit residues: 92.0833 Evaluate side-chains 248 residues out of total 4038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 1107 ILE Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 853 MET Chi-restraints excluded: chain M residue 911 LEU Chi-restraints excluded: chain M residue 1012 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 50 optimal weight: 6.9990 chunk 232 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 HIS ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS B 652 HIS C 284 ASN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.058659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.040115 restraints weight = 226882.519| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 4.50 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 36082 Z= 0.284 Angle : 0.665 14.929 49148 Z= 0.334 Chirality : 0.042 0.229 5710 Planarity : 0.004 0.038 6081 Dihedral : 11.526 161.379 5543 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.84 % Allowed : 8.06 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.01 (0.13), residues: 4483 helix: 1.64 (0.14), residues: 1528 sheet: -0.25 (0.19), residues: 736 loop : -1.11 (0.13), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 392 TYR 0.016 0.002 TYR A 127 PHE 0.021 0.002 PHE C 268 TRP 0.017 0.001 TRP B 229 HIS 0.008 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.28 (36051) covalent geometry : angle 0.65783 / 0.33 (49119) hydrogen bonds : bond 0.04407 / 3.11 ( 1413) hydrogen bonds : angle 4.74107 / 3.35 ( 4071) metal coordination : bond 0.01519 / 1.05 ( 31) metal coordination : angle 4.04211 / 2.54 ( 29) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 4038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 212 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.7955 (mtt) cc_final: 0.7366 (tpp) REVERT: A 271 MET cc_start: 0.8954 (tpt) cc_final: 0.8395 (tmm) REVERT: A 324 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8807 (p) REVERT: A 402 MET cc_start: 0.8083 (ptp) cc_final: 0.7830 (ptt) REVERT: A 423 MET cc_start: 0.9127 (mtp) cc_final: 0.8400 (mtp) REVERT: A 499 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9305 (mm) REVERT: A 906 LEU cc_start: 0.9754 (OUTLIER) cc_final: 0.9452 (mm) REVERT: A 925 MET cc_start: 0.8969 (mmt) cc_final: 0.8656 (mmm) REVERT: A 1130 CYS cc_start: 0.9403 (OUTLIER) cc_final: 0.8735 (p) REVERT: B 557 MET cc_start: 0.9009 (ttp) cc_final: 0.8394 (tmm) REVERT: B 854 MET cc_start: 0.9190 (mmm) cc_final: 0.8938 (mmt) REVERT: B 929 GLU cc_start: 0.8248 (mp0) cc_final: 0.8047 (mp0) REVERT: B 1079 GLU cc_start: 0.9401 (mp0) cc_final: 0.8920 (mp0) REVERT: E 18 MET cc_start: 0.9456 (mmt) cc_final: 0.9233 (mmm) REVERT: E 19 GLN cc_start: 0.9485 (mm-40) cc_final: 0.9089 (tp-100) REVERT: E 82 MET cc_start: 0.9184 (tmm) cc_final: 0.8908 (ttt) REVERT: E 130 MET cc_start: 0.9533 (mmm) cc_final: 0.9232 (mmm) REVERT: E 144 GLN cc_start: 0.8934 (tt0) cc_final: 0.8201 (tm-30) REVERT: F 102 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8870 (tmm) REVERT: G 9 TRP cc_start: 0.8621 (m100) cc_final: 0.8178 (m-10) REVERT: G 36 PHE cc_start: 0.8413 (p90) cc_final: 0.7657 (p90) REVERT: H 41 MET cc_start: 0.9484 (ttt) cc_final: 0.8655 (tmm) REVERT: H 111 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8001 (mp0) REVERT: I 75 ARG cc_start: 0.8139 (tpp80) cc_final: 0.7735 (tpp80) REVERT: I 77 SER cc_start: 0.9456 (m) cc_final: 0.9220 (p) REVERT: I 83 GLU cc_start: 0.9155 (tt0) cc_final: 0.8876 (tp30) REVERT: I 97 MET cc_start: 0.8808 (mmt) cc_final: 0.8360 (mmp) REVERT: K 97 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8413 (tp30) REVERT: L 49 GLU cc_start: 0.8759 (tt0) cc_final: 0.7962 (tm-30) REVERT: M 218 MET cc_start: 0.9106 (mmm) cc_final: 0.8512 (tpp) REVERT: M 416 MET cc_start: 0.8916 (ttp) cc_final: 0.8215 (tpp) REVERT: M 438 LYS cc_start: 0.9453 (tttt) cc_final: 0.9148 (tppt) REVERT: M 735 MET cc_start: 0.6568 (ttp) cc_final: 0.6215 (tpp) REVERT: M 738 MET cc_start: 0.7519 (ptt) cc_final: 0.7006 (ppp) REVERT: M 792 ILE cc_start: 0.8928 (mm) cc_final: 0.8692 (mp) REVERT: M 923 LYS cc_start: 0.9504 (mtpt) cc_final: 0.9257 (mtmm) REVERT: M 929 GLU cc_start: 0.8778 (tp30) cc_final: 0.8523 (tp30) outliers start: 63 outliers final: 37 residues processed: 262 average time/residue: 0.1986 time to fit residues: 88.7447 Evaluate side-chains 250 residues out of total 4038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 206 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 1107 ILE Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 443 VAL Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 748 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 322 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 340 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 299 optimal weight: 30.0000 chunk 362 optimal weight: 0.0570 chunk 449 optimal weight: 7.9990 chunk 342 optimal weight: 10.0000 chunk 395 optimal weight: 7.9990 chunk 413 optimal weight: 10.0000 overall best weight: 5.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 GLN D 164 ASN G 65 GLN M 339 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.058148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.039601 restraints weight = 225339.769| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 4.55 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 36082 Z= 0.222 Angle : 0.585 11.122 49148 Z= 0.298 Chirality : 0.042 0.240 5710 Planarity : 0.003 0.039 6081 Dihedral : 11.519 160.748 5543 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.72 % Allowed : 8.93 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.06 (0.13), residues: 4483 helix: 1.75 (0.14), residues: 1535 sheet: -0.25 (0.19), residues: 743 loop : -1.11 (0.13), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 917 TYR 0.012 0.001 TYR A 605 PHE 0.018 0.001 PHE J 8 TRP 0.017 0.001 TRP A1089 HIS 0.009 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.22 (36051) covalent geometry : angle 0.57770 / 0.30 (49119) hydrogen bonds : bond 0.03813 / 2.69 ( 1413) hydrogen bonds : angle 4.58533 / 3.23 ( 4071) metal coordination : bond 0.01151 / 0.79 ( 31) metal coordination : angle 3.74307 / 2.34 ( 29) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 4038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 213 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.7890 (tt) REVERT: A 214 MET cc_start: 0.8158 (mtt) cc_final: 0.7507 (tpp) REVERT: A 271 MET cc_start: 0.9046 (tpt) cc_final: 0.8451 (ppp) REVERT: A 402 MET cc_start: 0.8053 (ptp) cc_final: 0.7794 (ptt) REVERT: A 423 MET cc_start: 0.9086 (mtp) cc_final: 0.8360 (mtp) REVERT: A 499 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9295 (mm) REVERT: A 706 ASP cc_start: 0.8988 (m-30) cc_final: 0.8703 (p0) REVERT: A 906 LEU cc_start: 0.9763 (OUTLIER) cc_final: 0.9489 (mm) REVERT: A 925 MET cc_start: 0.8964 (mmt) cc_final: 0.8632 (mmm) REVERT: A 1130 CYS cc_start: 0.9392 (OUTLIER) cc_final: 0.8759 (p) REVERT: B 557 MET cc_start: 0.9011 (ttp) cc_final: 0.8408 (tmm) REVERT: B 1079 GLU cc_start: 0.9398 (mp0) cc_final: 0.8907 (mp0) REVERT: D 93 MET cc_start: 0.3753 (mtp) cc_final: 0.1766 (mmm) REVERT: D 159 MET cc_start: 0.1251 (tmm) cc_final: 0.0913 (tmm) REVERT: E 18 MET cc_start: 0.9434 (mmt) cc_final: 0.8859 (mmm) REVERT: E 19 GLN cc_start: 0.9481 (mm-40) cc_final: 0.9082 (tp-100) REVERT: E 130 MET cc_start: 0.9554 (mmm) cc_final: 0.9282 (mmm) REVERT: E 144 GLN cc_start: 0.8919 (tt0) cc_final: 0.8219 (tm-30) REVERT: F 102 MET cc_start: 0.9232 (tmm) cc_final: 0.8881 (tmm) REVERT: G 9 TRP cc_start: 0.8611 (m100) cc_final: 0.8202 (m-10) REVERT: G 36 PHE cc_start: 0.8478 (p90) cc_final: 0.7693 (p90) REVERT: H 41 MET cc_start: 0.9463 (ttt) cc_final: 0.8649 (tmm) REVERT: H 62 MET cc_start: 0.8934 (mmm) cc_final: 0.8641 (mmm) REVERT: H 111 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: I 75 ARG cc_start: 0.8219 (tpp80) cc_final: 0.7787 (tpp80) REVERT: I 77 SER cc_start: 0.9449 (m) cc_final: 0.9208 (p) REVERT: I 97 MET cc_start: 0.8923 (mmt) cc_final: 0.8374 (mmp) REVERT: J 61 ASN cc_start: 0.9225 (m-40) cc_final: 0.8988 (m110) REVERT: K 97 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8453 (tp30) REVERT: L 49 GLU cc_start: 0.8741 (tt0) cc_final: 0.7947 (tm-30) REVERT: M 218 MET cc_start: 0.9085 (mmm) cc_final: 0.8718 (tpp) REVERT: M 379 MET cc_start: 0.9534 (ptm) cc_final: 0.9097 (ptm) REVERT: M 416 MET cc_start: 0.8922 (ttp) cc_final: 0.8280 (tpp) REVERT: M 438 LYS cc_start: 0.9447 (tttt) cc_final: 0.9156 (tppt) REVERT: M 663 MET cc_start: 0.7890 (mpp) cc_final: 0.7425 (mpp) REVERT: M 735 MET cc_start: 0.6601 (ttp) cc_final: 0.6319 (tpp) REVERT: M 738 MET cc_start: 0.7589 (ptt) cc_final: 0.7307 (ppp) REVERT: M 792 ILE cc_start: 0.8993 (mm) cc_final: 0.8720 (mp) REVERT: M 923 LYS cc_start: 0.9493 (mtpt) cc_final: 0.9276 (mtmm) REVERT: M 929 GLU cc_start: 0.8699 (tp30) cc_final: 0.8481 (tp30) REVERT: M 1012 SER cc_start: 0.9198 (OUTLIER) cc_final: 0.8783 (p) outliers start: 59 outliers final: 38 residues processed: 262 average time/residue: 0.2098 time to fit residues: 93.6098 Evaluate side-chains 256 residues out of total 4038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1107 ILE Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 443 VAL Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 748 VAL Chi-restraints excluded: chain M residue 911 LEU Chi-restraints excluded: chain M residue 1012 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 351 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 246 optimal weight: 6.9990 chunk 347 optimal weight: 10.0000 chunk 391 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 420 optimal weight: 20.0000 chunk 176 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS ** M 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.058110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.039590 restraints weight = 225438.920| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 4.53 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 36082 Z= 0.198 Angle : 0.577 12.618 49148 Z= 0.292 Chirality : 0.041 0.235 5710 Planarity : 0.003 0.038 6081 Dihedral : 11.523 161.050 5543 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.58 % Allowed : 9.20 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.10 (0.13), residues: 4483 helix: 1.81 (0.14), residues: 1535 sheet: -0.24 (0.19), residues: 741 loop : -1.10 (0.13), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 917 TYR 0.011 0.001 TYR A 605 PHE 0.020 0.001 PHE J 8 TRP 0.010 0.001 TRP A1089 HIS 0.008 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (36051) covalent geometry : angle 0.57094 / 0.29 (49119) hydrogen bonds : bond 0.03673 / 2.59 ( 1413) hydrogen bonds : angle 4.51529 / 3.18 ( 4071) metal coordination : bond 0.01054 / 0.72 ( 31) metal coordination : angle 3.47526 / 2.19 ( 29) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 4038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 210 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.7799 (tt) REVERT: A 214 MET cc_start: 0.8237 (mtt) cc_final: 0.7659 (tpp) REVERT: A 271 MET cc_start: 0.9064 (tpt) cc_final: 0.8464 (ppp) REVERT: A 402 MET cc_start: 0.8077 (ptp) cc_final: 0.7812 (ptt) REVERT: A 423 MET cc_start: 0.9078 (mtp) cc_final: 0.8314 (mtp) REVERT: A 499 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9313 (mm) REVERT: A 513 MET cc_start: 0.9413 (mmm) cc_final: 0.9022 (ttm) REVERT: A 706 ASP cc_start: 0.8972 (m-30) cc_final: 0.8683 (p0) REVERT: A 762 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.7943 (ptm-80) REVERT: A 925 MET cc_start: 0.8957 (mmt) cc_final: 0.8624 (mmm) REVERT: A 1130 CYS cc_start: 0.9386 (OUTLIER) cc_final: 0.8690 (p) REVERT: A 1134 MET cc_start: 0.8797 (mmm) cc_final: 0.8433 (mmm) REVERT: B 557 MET cc_start: 0.8963 (ttp) cc_final: 0.8436 (tmm) REVERT: B 1029 MET cc_start: 0.8867 (mtp) cc_final: 0.8666 (mtp) REVERT: B 1079 GLU cc_start: 0.9433 (mp0) cc_final: 0.8996 (mp0) REVERT: C 251 MET cc_start: 0.8934 (tpp) cc_final: 0.8569 (ttt) REVERT: D 93 MET cc_start: 0.3667 (mtp) cc_final: 0.1718 (mmm) REVERT: D 159 MET cc_start: 0.1252 (tmm) cc_final: 0.0912 (tmm) REVERT: E 7 LEU cc_start: 0.9806 (OUTLIER) cc_final: 0.9567 (mm) REVERT: E 18 MET cc_start: 0.9409 (mmt) cc_final: 0.8824 (mmm) REVERT: E 19 GLN cc_start: 0.9472 (mm-40) cc_final: 0.9070 (tp-100) REVERT: E 130 MET cc_start: 0.9530 (mmm) cc_final: 0.9286 (mmm) REVERT: E 144 GLN cc_start: 0.8908 (tt0) cc_final: 0.8212 (tm-30) REVERT: F 102 MET cc_start: 0.9225 (tmm) cc_final: 0.8859 (tmm) REVERT: G 9 TRP cc_start: 0.8591 (m100) cc_final: 0.8171 (m-10) REVERT: G 36 PHE cc_start: 0.8579 (p90) cc_final: 0.7862 (p90) REVERT: H 41 MET cc_start: 0.9461 (ttt) cc_final: 0.8650 (tmm) REVERT: H 62 MET cc_start: 0.8966 (mmm) cc_final: 0.8636 (mmm) REVERT: H 111 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: I 75 ARG cc_start: 0.8287 (tpp80) cc_final: 0.7797 (tpp80) REVERT: I 77 SER cc_start: 0.9469 (m) cc_final: 0.9194 (p) REVERT: I 97 MET cc_start: 0.8928 (mmt) cc_final: 0.8381 (mmp) REVERT: J 48 MET cc_start: 0.9052 (tpp) cc_final: 0.8798 (tpp) REVERT: J 61 ASN cc_start: 0.9262 (m-40) cc_final: 0.9011 (m110) REVERT: K 97 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8373 (tp30) REVERT: L 49 GLU cc_start: 0.8716 (tt0) cc_final: 0.7930 (tm-30) REVERT: M 218 MET cc_start: 0.9055 (mmm) cc_final: 0.8684 (tpp) REVERT: M 416 MET cc_start: 0.8914 (ttp) cc_final: 0.8272 (tpp) REVERT: M 663 MET cc_start: 0.8145 (mpp) cc_final: 0.7755 (mpp) REVERT: M 735 MET cc_start: 0.6679 (ttp) cc_final: 0.6401 (tpp) REVERT: M 738 MET cc_start: 0.7582 (ptt) cc_final: 0.7333 (ppp) REVERT: M 792 ILE cc_start: 0.9038 (mm) cc_final: 0.8757 (mp) REVERT: M 853 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7969 (mpp) REVERT: M 923 LYS cc_start: 0.9474 (mtpt) cc_final: 0.9268 (mtmm) REVERT: M 929 GLU cc_start: 0.8786 (tp30) cc_final: 0.8493 (tp30) REVERT: M 1012 SER cc_start: 0.9168 (OUTLIER) cc_final: 0.8748 (p) outliers start: 54 outliers final: 34 residues processed: 258 average time/residue: 0.2096 time to fit residues: 91.7701 Evaluate side-chains 249 residues out of total 4038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 206 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 1107 ILE Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 8 PHE Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 484 VAL Chi-restraints excluded: chain M residue 748 VAL Chi-restraints excluded: chain M residue 853 MET Chi-restraints excluded: chain M residue 911 LEU Chi-restraints excluded: chain M residue 1012 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 98 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 276 optimal weight: 0.5980 chunk 337 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 274 optimal weight: 4.9990 chunk 451 optimal weight: 30.0000 chunk 308 optimal weight: 0.9980 chunk 348 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 ASN ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN ** M 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.058919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.040301 restraints weight = 223939.059| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 4.58 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 36082 Z= 0.101 Angle : 0.536 13.476 49148 Z= 0.271 Chirality : 0.041 0.239 5710 Planarity : 0.003 0.039 6081 Dihedral : 11.469 160.509 5543 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.23 % Allowed : 9.61 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.25 (0.13), residues: 4483 helix: 1.93 (0.14), residues: 1539 sheet: -0.02 (0.19), residues: 719 loop : -1.07 (0.13), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 917 TYR 0.011 0.001 TYR K 87 PHE 0.015 0.001 PHE J 8 TRP 0.012 0.001 TRP A1089 HIS 0.008 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (36051) covalent geometry : angle 0.53098 / 0.27 (49119) hydrogen bonds : bond 0.03171 / 2.22 ( 1413) hydrogen bonds : angle 4.32349 / 3.03 ( 4071) metal coordination : bond 0.00437 / 0.26 ( 31) metal coordination : angle 3.13968 / 2.04 ( 29) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 4038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 207 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8263 (mtt) cc_final: 0.7801 (tpp) REVERT: A 271 MET cc_start: 0.9027 (tpt) cc_final: 0.8431 (ppp) REVERT: A 402 MET cc_start: 0.8082 (ptp) cc_final: 0.7806 (ptt) REVERT: A 423 MET cc_start: 0.8981 (mtp) cc_final: 0.8154 (mtp) REVERT: A 499 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9310 (mm) REVERT: A 513 MET cc_start: 0.9430 (mmm) cc_final: 0.8994 (ttm) REVERT: A 706 ASP cc_start: 0.8977 (m-30) cc_final: 0.8679 (p0) REVERT: A 745 MET cc_start: 0.9254 (mtm) cc_final: 0.8985 (pmm) REVERT: A 762 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.7940 (ptm-80) REVERT: A 925 MET cc_start: 0.8939 (mmt) cc_final: 0.8614 (mmm) REVERT: B 557 MET cc_start: 0.8906 (ttp) cc_final: 0.8492 (tmm) REVERT: B 1029 MET cc_start: 0.8856 (mtp) cc_final: 0.8622 (mtp) REVERT: B 1079 GLU cc_start: 0.9434 (mp0) cc_final: 0.9029 (mp0) REVERT: D 93 MET cc_start: 0.3540 (mtp) cc_final: 0.1584 (mmm) REVERT: D 159 MET cc_start: 0.1386 (tmm) cc_final: 0.1054 (tmm) REVERT: E 7 LEU cc_start: 0.9776 (OUTLIER) cc_final: 0.9569 (mm) REVERT: E 18 MET cc_start: 0.9355 (mmt) cc_final: 0.8801 (mmm) REVERT: E 82 MET cc_start: 0.9092 (tmm) cc_final: 0.8824 (ttt) REVERT: E 130 MET cc_start: 0.9467 (mmm) cc_final: 0.9198 (mmm) REVERT: E 144 GLN cc_start: 0.8889 (tt0) cc_final: 0.8224 (tm-30) REVERT: F 102 MET cc_start: 0.9188 (tmm) cc_final: 0.8815 (tmm) REVERT: G 9 TRP cc_start: 0.8621 (m100) cc_final: 0.8199 (m-10) REVERT: G 36 PHE cc_start: 0.8542 (p90) cc_final: 0.7836 (p90) REVERT: G 112 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.5949 (tp) REVERT: G 146 PHE cc_start: 0.8051 (p90) cc_final: 0.7023 (p90) REVERT: H 41 MET cc_start: 0.9402 (ttt) cc_final: 0.8614 (tmm) REVERT: H 62 MET cc_start: 0.9008 (mmm) cc_final: 0.8743 (mmm) REVERT: H 111 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: I 75 ARG cc_start: 0.8313 (tpp80) cc_final: 0.8028 (tpp80) REVERT: I 77 SER cc_start: 0.9474 (m) cc_final: 0.9227 (p) REVERT: I 83 GLU cc_start: 0.8863 (tp30) cc_final: 0.8592 (tp30) REVERT: I 97 MET cc_start: 0.8898 (mmt) cc_final: 0.8341 (mmp) REVERT: J 61 ASN cc_start: 0.9316 (m-40) cc_final: 0.9055 (m110) REVERT: K 97 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8446 (tp30) REVERT: L 49 GLU cc_start: 0.8678 (tt0) cc_final: 0.7891 (tm-30) REVERT: M 218 MET cc_start: 0.9045 (mmm) cc_final: 0.8673 (tpp) REVERT: M 379 MET cc_start: 0.9594 (ptm) cc_final: 0.9314 (ptm) REVERT: M 416 MET cc_start: 0.8859 (ttp) cc_final: 0.8217 (tpp) REVERT: M 438 LYS cc_start: 0.9416 (tttt) cc_final: 0.9146 (tppt) REVERT: M 663 MET cc_start: 0.8106 (mpp) cc_final: 0.7764 (mpp) REVERT: M 735 MET cc_start: 0.6733 (ttp) cc_final: 0.6342 (tpp) REVERT: M 738 MET cc_start: 0.7571 (ptt) cc_final: 0.7262 (ppp) REVERT: M 792 ILE cc_start: 0.9032 (mm) cc_final: 0.8727 (mp) REVERT: M 853 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7919 (mpp) REVERT: M 923 LYS cc_start: 0.9481 (mtpt) cc_final: 0.9254 (mtmm) REVERT: M 1012 SER cc_start: 0.9143 (OUTLIER) cc_final: 0.8722 (p) outliers start: 42 outliers final: 31 residues processed: 241 average time/residue: 0.2060 time to fit residues: 84.3119 Evaluate side-chains 242 residues out of total 4038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 1107 ILE Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 101 PHE Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 8 PHE Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 484 VAL Chi-restraints excluded: chain M residue 748 VAL Chi-restraints excluded: chain M residue 853 MET Chi-restraints excluded: chain M residue 911 LEU Chi-restraints excluded: chain M residue 1012 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 261 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 398 optimal weight: 50.0000 chunk 340 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 417 optimal weight: 8.9990 chunk 324 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 270 optimal weight: 9.9990 chunk 329 optimal weight: 3.9990 chunk 333 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1006 ASN ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN ** M 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.058188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.039727 restraints weight = 228907.426| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 4.47 r_work: 0.2641 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 36082 Z= 0.300 Angle : 0.681 12.594 49148 Z= 0.339 Chirality : 0.043 0.222 5710 Planarity : 0.004 0.069 6081 Dihedral : 11.573 163.532 5543 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.34 % Allowed : 9.61 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.07 (0.13), residues: 4483 helix: 1.78 (0.14), residues: 1539 sheet: -0.34 (0.19), residues: 755 loop : -1.09 (0.13), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 22 TYR 0.013 0.001 TYR A 605 PHE 0.016 0.002 PHE B 34 TRP 0.010 0.001 TRP I 112 HIS 0.007 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.30 (36051) covalent geometry : angle 0.67520 / 0.34 (49119) hydrogen bonds : bond 0.04117 / 2.92 ( 1413) hydrogen bonds : angle 4.61524 / 3.24 ( 4071) metal coordination : bond 0.01445 / 1.02 ( 31) metal coordination : angle 3.62382 / 2.19 ( 29) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 4038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.7981 (mtt) cc_final: 0.7609 (tpp) REVERT: A 271 MET cc_start: 0.8979 (tpt) cc_final: 0.8397 (ppp) REVERT: A 402 MET cc_start: 0.8505 (ptp) cc_final: 0.8262 (ptt) REVERT: A 423 MET cc_start: 0.9304 (mtp) cc_final: 0.8654 (mtp) REVERT: A 499 LEU cc_start: 0.9678 (OUTLIER) cc_final: 0.9402 (mm) REVERT: A 762 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.7988 (ptm-80) REVERT: A 925 MET cc_start: 0.9332 (mmt) cc_final: 0.8973 (mmm) REVERT: A 1098 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8313 (mtm-85) REVERT: A 1134 MET cc_start: 0.9052 (mmm) cc_final: 0.8839 (mmm) REVERT: B 557 MET cc_start: 0.9139 (ttp) cc_final: 0.8606 (tmm) REVERT: B 917 MET cc_start: 0.9561 (mmm) cc_final: 0.9329 (tpp) REVERT: B 1079 GLU cc_start: 0.9567 (mp0) cc_final: 0.9185 (mp0) REVERT: C 82 MET cc_start: 0.9057 (mmm) cc_final: 0.8754 (tpp) REVERT: D 93 MET cc_start: 0.3455 (mtp) cc_final: 0.1419 (mmm) REVERT: E 7 LEU cc_start: 0.9806 (OUTLIER) cc_final: 0.9573 (mm) REVERT: E 18 MET cc_start: 0.9617 (mmt) cc_final: 0.9139 (mmm) REVERT: E 82 MET cc_start: 0.9301 (tmm) cc_final: 0.9055 (ttt) REVERT: E 130 MET cc_start: 0.9660 (mmm) cc_final: 0.9436 (mmm) REVERT: E 144 GLN cc_start: 0.9167 (tt0) cc_final: 0.8413 (tm-30) REVERT: F 102 MET cc_start: 0.9334 (tmm) cc_final: 0.9002 (tmm) REVERT: G 9 TRP cc_start: 0.8497 (m100) cc_final: 0.8106 (m-10) REVERT: G 36 PHE cc_start: 0.8726 (p90) cc_final: 0.7972 (p90) REVERT: G 112 LEU cc_start: 0.6319 (OUTLIER) cc_final: 0.5600 (tt) REVERT: G 146 PHE cc_start: 0.7969 (p90) cc_final: 0.6868 (p90) REVERT: H 41 MET cc_start: 0.9686 (ttt) cc_final: 0.9027 (tmm) REVERT: H 62 MET cc_start: 0.9289 (mmm) cc_final: 0.8947 (mmm) REVERT: H 111 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: I 75 ARG cc_start: 0.8436 (tpp80) cc_final: 0.8054 (tpp80) REVERT: I 97 MET cc_start: 0.9087 (mmt) cc_final: 0.8403 (mmm) REVERT: K 97 GLU cc_start: 0.9329 (OUTLIER) cc_final: 0.8735 (tp30) REVERT: L 49 GLU cc_start: 0.9149 (tt0) cc_final: 0.8306 (tm-30) REVERT: M 218 MET cc_start: 0.9269 (mmm) cc_final: 0.8942 (tpp) REVERT: M 379 MET cc_start: 0.9538 (ptm) cc_final: 0.9223 (ptm) REVERT: M 416 MET cc_start: 0.8970 (ttp) cc_final: 0.8211 (tpp) REVERT: M 663 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7826 (mpp) REVERT: M 735 MET cc_start: 0.7207 (ttp) cc_final: 0.6779 (tpp) REVERT: M 738 MET cc_start: 0.8066 (ptt) cc_final: 0.6598 (ppp) REVERT: M 792 ILE cc_start: 0.9174 (mm) cc_final: 0.8935 (mp) REVERT: M 853 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7724 (mpp) outliers start: 46 outliers final: 31 residues processed: 240 average time/residue: 0.1973 time to fit residues: 80.1514 Evaluate side-chains 238 residues out of total 4038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 198 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1098 ARG Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 484 VAL Chi-restraints excluded: chain M residue 663 MET Chi-restraints excluded: chain M residue 748 VAL Chi-restraints excluded: chain M residue 853 MET Chi-restraints excluded: chain M residue 911 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 422 optimal weight: 40.0000 chunk 312 optimal weight: 2.9990 chunk 250 optimal weight: 30.0000 chunk 232 optimal weight: 9.9990 chunk 282 optimal weight: 20.0000 chunk 440 optimal weight: 9.9990 chunk 344 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 416 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.057631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.039050 restraints weight = 227549.406| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 4.52 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 36082 Z= 0.225 Angle : 0.617 14.459 49148 Z= 0.310 Chirality : 0.042 0.230 5710 Planarity : 0.004 0.063 6081 Dihedral : 11.594 163.492 5543 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.52 % Allowed : 9.64 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.09 (0.13), residues: 4483 helix: 1.79 (0.14), residues: 1532 sheet: -0.37 (0.19), residues: 759 loop : -1.05 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1016 TYR 0.012 0.001 TYR A 605 PHE 0.045 0.001 PHE J 8 TRP 0.010 0.001 TRP B 229 HIS 0.009 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 (36051) covalent geometry : angle 0.61058 / 0.31 (49119) hydrogen bonds : bond 0.03710 / 2.62 ( 1413) hydrogen bonds : angle 4.55164 / 3.19 ( 4071) metal coordination : bond 0.01105 / 0.75 ( 31) metal coordination : angle 3.56687 / 2.21 ( 29) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7202.95 seconds wall clock time: 124 minutes 37.49 seconds (7477.49 seconds total)