Starting phenix.real_space_refine on Mon Jul 6 15:38:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mk9_23887/07_2026/7mk9_23887.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mk9_23887/07_2026/7mk9_23887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mk9_23887/07_2026/7mk9_23887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mk9_23887/07_2026/7mk9_23887.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7mk9_23887/07_2026/7mk9_23887.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mk9_23887/07_2026/7mk9_23887.cif" model { file = "/net/cci-nas-00/data/ceres_data/7mk9_23887/07_2026/7mk9_23887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mk9_23887/07_2026/7mk9_23887.cif" } resolution = 3.54 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 582 atoms to isotropic. 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 8 6.06 5 P 95 5.49 5 Mg 2 5.21 5 S 193 5.16 5 C 22459 2.51 5 N 6324 2.21 5 O 7041 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.03s 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: 36122 Number of models: 1 Model: "" Number of chains: 24 Chain: "N" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 822 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "O" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 827 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "A" Number of atoms: 11167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1425, 11167 Classifications: {'peptide': 1425} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 65, 'TRANS': 1354} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 9227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9227 Classifications: {'peptide': 1166} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 8} Link IDs: {'CIS': 11, 'PCIS': 1, 'PTRANS': 50, 'TRANS': 1103} Chain breaks: 7 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2086 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain: "D" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1331 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "G" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1335 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1080 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 2 Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 540 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 352 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "R" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 312 Classifications: {'RNA': 15} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 8} Link IDs: {'rna2p': 1, 'rna3p': 13} Chain: "Q" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1619 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 204} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 8, 'ASN:plan1': 2, 'GLN:plan1': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "M" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1106 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2465 SG CYS A 107 76.884 39.694 80.229 1.00250.70 S ATOM 2489 SG CYS A 110 74.935 39.636 79.670 1.00242.09 S ATOM 2794 SG CYS A 148 76.353 38.327 83.403 1.00294.76 S ATOM 2932 SG CYS A 167 75.584 36.362 79.575 1.00293.62 S ATOM 2160 SG CYS A 67 64.923 77.009 46.485 1.00231.64 S ATOM 2182 SG CYS A 70 62.738 76.249 48.734 1.00224.65 S ATOM 2235 SG CYS A 77 66.537 76.222 49.624 1.00202.98 S ATOM 21568 SG CYS B1163 57.581 70.370 62.684 1.00222.04 S ATOM 21586 SG CYS B1166 59.891 67.574 62.298 1.00229.02 S ATOM 21711 SG CYS B1182 59.359 69.468 59.216 1.00232.64 S ATOM 22690 SG CYS C 86 88.477 139.918 34.090 1.00323.13 S ATOM 22707 SG CYS C 88 88.685 136.498 32.435 1.00317.15 S ATOM 22740 SG CYS C 92 90.601 139.272 31.060 1.00296.54 S ATOM 22763 SG CYS C 95 91.735 137.791 34.343 1.00293.39 S ATOM 30385 SG CYS I 7 147.110 41.292 92.248 1.00276.12 S ATOM 30410 SG CYS I 10 144.714 41.504 89.078 1.00275.03 S ATOM 30576 SG CYS I 29 143.248 41.153 92.419 1.00273.60 S ATOM 30600 SG CYS I 32 145.484 38.340 91.078 1.00262.01 S ATOM 30927 SG CYS I 75 157.577 86.318 98.966 1.00273.06 S ATOM 30949 SG CYS I 78 159.188 86.143 97.907 1.00266.82 S ATOM 31185 SG CYS I 106 157.186 83.547 97.750 1.00279.11 S ATOM 31313 SG CYS J 7 115.754 130.004 54.667 1.00192.03 S ATOM 31336 SG CYS J 10 114.768 133.523 54.764 1.00191.68 S ATOM 31616 SG CYS J 45 116.352 132.348 57.916 1.00197.06 S ATOM 31622 SG CYS J 46 117.806 133.548 54.637 1.00203.76 S ATOM 32766 SG CYS L 31 113.611 99.946 19.816 1.00302.20 S ATOM 32890 SG CYS L 48 115.345 96.769 19.764 1.00309.77 S ATOM 32913 SG CYS L 51 118.040 99.250 20.018 1.00 30.00 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="ZN ZN A1801 " occ=0.95 Time building chain proxies: 7.04, per 1000 atoms: 0.19 Number of scatterers: 36122 At special positions: 0 Unit cell: (195.48, 172.8, 147.96, 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 8 29.99 S 193 16.00 P 95 15.00 Mg 2 11.99 O 7041 8.00 N 6324 7.00 C 22459 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: 2.93 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 31 " Number of angles added : 27 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8126 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 40 sheets defined 36.7% alpha, 16.3% beta 36 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 4.76 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.593A pdb=" N ILE A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 removed outlier: 3.541A pdb=" N PHE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 287 through 305 removed outlier: 4.034A pdb=" N GLU A 291 " --> pdb=" O HIS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 removed outlier: 3.657A pdb=" N GLY A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.775A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 removed outlier: 3.919A pdb=" N ARG A 498 " --> pdb=" O SER A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 511 removed outlier: 3.630A pdb=" N LEU A 509 " --> pdb=" O ALA A 506 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 511 " --> pdb=" O PRO A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.712A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 4.073A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 640 through 661 removed outlier: 3.660A pdb=" N LYS A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 4.016A pdb=" N THR A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 749 removed outlier: 3.557A pdb=" N GLN A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 809 through 845 removed outlier: 4.637A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 913 through 917 removed outlier: 4.613A pdb=" N SER A 917 " --> pdb=" O GLU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 960 through 972 Processing helix chain 'A' and resid 982 through 997 removed outlier: 3.919A pdb=" N LYS A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 3.508A pdb=" N GLN A1008 " --> pdb=" O ASN A1004 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1035 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1074 Processing helix chain 'A' and resid 1075 through 1077 No H-bonds generated for 'chain 'A' and resid 1075 through 1077' Processing helix chain 'A' and resid 1096 through 1106 removed outlier: 3.526A pdb=" N ARG A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1142 through 1146 removed outlier: 3.734A pdb=" N VAL A1146 " --> pdb=" O THR A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1142 through 1146' Processing helix chain 'A' and resid 1163 through 1166 Processing helix chain 'A' and resid 1167 through 1174 removed outlier: 3.610A pdb=" N GLN A1171 " --> pdb=" O GLU A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 removed outlier: 3.599A pdb=" N LYS A1205 " --> pdb=" O ALA A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1221 removed outlier: 3.644A pdb=" N VAL A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A1220 " --> pdb=" O ILE A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1271 removed outlier: 4.168A pdb=" N MET A1259 " --> pdb=" O GLU A1255 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A1271 " --> pdb=" O MET A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1339 removed outlier: 3.865A pdb=" N ILE A1335 " --> pdb=" O SER A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1358 Processing helix chain 'A' and resid 1364 through 1377 removed outlier: 4.069A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1453 removed outlier: 3.526A pdb=" N LEU A1450 " --> pdb=" O ASP A1446 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 29 through 42 removed outlier: 4.294A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 59 through 66 removed outlier: 4.017A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.676A pdb=" N GLU B 183 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 302 removed outlier: 3.561A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 332 Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.588A pdb=" N CYS B 388 " --> pdb=" O ARG B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 430 Processing helix chain 'B' and resid 444 through 464 removed outlier: 3.853A pdb=" N ILE B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.503A pdb=" N LEU B 495 " --> pdb=" O THR B 491 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 606 removed outlier: 4.165A pdb=" N LEU B 596 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 667 removed outlier: 3.673A pdb=" N ILE B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 removed outlier: 4.561A pdb=" N GLU B 687 " --> pdb=" O SER B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.664A pdb=" N GLU B 699 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.940A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 755 removed outlier: 3.592A pdb=" N SER B 754 " --> pdb=" O GLY B 750 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 750 through 755' Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.713A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.332A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 787 removed outlier: 4.308A pdb=" N ASN B 786 " --> pdb=" O THR B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 812 removed outlier: 4.342A pdb=" N TYR B 811 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 889 through 893 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.404A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1039 Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.758A pdb=" N ILE B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1103 removed outlier: 3.752A pdb=" N LYS B1102 " --> pdb=" O MET B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1174 through 1178 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 68 Processing helix chain 'C' and resid 92 through 96 removed outlier: 3.741A pdb=" N SER C 96 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'D' and resid 51 through 76 removed outlier: 3.870A pdb=" N LYS D 60 " --> pdb=" O ARG D 56 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU D 61 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 134 removed outlier: 3.850A pdb=" N GLU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 152 removed outlier: 3.593A pdb=" N PHE D 151 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.672A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 195 through 202 removed outlier: 3.575A pdb=" N ILE D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 4.184A pdb=" N GLU D 213 " --> pdb=" O ARG D 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 26 removed outlier: 4.413A pdb=" N ARG E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.877A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 31 through 36' Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.549A pdb=" N MET E 58 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER E 59 " --> pdb=" O ARG E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 59' Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.553A pdb=" N ILE E 69 " --> pdb=" O THR E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 103 Processing helix chain 'E' and resid 117 through 121 Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 17 through 25 removed outlier: 3.522A pdb=" N LEU J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 44 through 53 removed outlier: 4.208A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.738A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 9 removed outlier: 3.597A pdb=" N GLU K 8 " --> pdb=" O ASP K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.819A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 112 Processing helix chain 'Q' and resid 23 through 35 removed outlier: 3.657A pdb=" N MET Q 27 " --> pdb=" O LYS Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 112 removed outlier: 3.748A pdb=" N GLU Q 112 " --> pdb=" O LYS Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 133 Processing helix chain 'Q' and resid 152 through 164 Processing helix chain 'Q' and resid 336 through 347 Processing helix chain 'Q' and resid 405 through 414 Processing helix chain 'Q' and resid 423 through 432 Processing helix chain 'Q' and resid 436 through 447 Processing helix chain 'M' and resid 61 through 65 removed outlier: 3.796A pdb=" N SER M 64 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN M 65 " --> pdb=" O GLU M 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 65' Processing helix chain 'M' and resid 74 through 82 removed outlier: 3.503A pdb=" N LYS M 80 " --> pdb=" O PHE M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 113 Processing helix chain 'M' and resid 234 through 243 removed outlier: 3.503A pdb=" N GLU M 238 " --> pdb=" O HIS M 234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 removed outlier: 3.606A pdb=" N VAL A 17 " --> pdb=" O ASP A1419 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 90 removed outlier: 10.202A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 177 removed outlier: 3.757A pdb=" N THR A 173 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345 removed outlier: 4.100A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.553A pdb=" N ALA A 349 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N SER A 354 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 379 Processing sheet with id=AA8, first strand: chain 'A' and resid 588 through 589 removed outlier: 7.087A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.574A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 879 through 882 removed outlier: 3.610A pdb=" N GLN A 881 " --> pdb=" O TRP A 954 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1283 through 1292 removed outlier: 3.548A pdb=" N TYR A1328 " --> pdb=" O THR A1117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.356A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N SER A1150 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ARG I 45 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ILE A1152 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 48 through 49 removed outlier: 3.974A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 48 through 49 removed outlier: 3.974A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER G 37 " --> pdb=" O ILE G 45 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 68 through 70 removed outlier: 5.512A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AB8, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AB9, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AC1, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.523A pdb=" N GLN B 224 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR B 268 " --> pdb=" O TYR B 259 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 544 through 547 removed outlier: 6.538A pdb=" N CYS B 544 " --> pdb=" O VAL B 633 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B 633 " --> pdb=" O CYS B 544 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER B 546 " --> pdb=" O GLY B 631 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.328A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AC5, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.518A pdb=" N ALA B 793 " --> pdb=" O PHE B 856 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 795 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 4.466A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA B 826 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 981 " --> pdb=" O GLN B1093 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1158 through 1162 Processing sheet with id=AC8, first strand: chain 'C' and resid 8 through 13 removed outlier: 6.800A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN C 231 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.144A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.856A pdb=" N GLN C 73 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.986A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AD4, first strand: chain 'E' and resid 78 through 80 removed outlier: 6.358A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.503A pdb=" N ARG E 200 " --> pdb=" O TYR E 208 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 86 through 93 removed outlier: 5.430A pdb=" N VAL G 91 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN G 102 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER G 93 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 121 through 122 removed outlier: 3.895A pdb=" N SER G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 54 through 58 removed outlier: 3.782A pdb=" N ASP H 8 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU H 111 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU H 106 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 14 through 18 Processing sheet with id=AE1, first strand: chain 'I' and resid 84 through 87 Processing sheet with id=AE2, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE3, first strand: chain 'Q' and resid 102 through 104 removed outlier: 4.148A pdb=" N GLY M 93 " --> pdb=" O LEU Q 103 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE M 104 " --> pdb=" O LEU M 122 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLU M 221 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL M 68 " --> pdb=" O CYS M 219 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLU M 221 " --> pdb=" O VAL M 68 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU M 70 " --> pdb=" O GLU M 221 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLN M 223 " --> pdb=" O LEU M 70 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG M 72 " --> pdb=" O GLN M 223 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N MET M 225 " --> pdb=" O ARG M 72 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN M 67 " --> pdb=" O VAL Q 378 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL Q 378 " --> pdb=" O GLN M 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 102 through 104 removed outlier: 4.148A pdb=" N GLY M 93 " --> pdb=" O LEU Q 103 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE M 104 " --> pdb=" O LEU M 122 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLU M 221 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL M 134 " --> pdb=" O VAL M 215 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR M 217 " --> pdb=" O GLU M 132 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLU M 132 " --> pdb=" O THR M 217 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR Q 116 " --> pdb=" O LYS Q 391 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N TYR Q 393 " --> pdb=" O THR Q 116 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LEU Q 118 " --> pdb=" O TYR Q 393 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE Q 395 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS Q 120 " --> pdb=" O PHE Q 395 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA Q 397 " --> pdb=" O LYS Q 120 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLN Q 122 " --> pdb=" O ALA Q 397 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR Q 360 " --> pdb=" O ARG Q 398 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TRP Q 350 " --> pdb=" O GLY Q 363 " (cutoff:3.500A) 1341 hydrogen bonds defined for protein. 3753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 85 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 9.25 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11531 1.34 - 1.46: 8046 1.46 - 1.58: 16884 1.58 - 1.71: 185 1.71 - 1.83: 312 Bond restraints: 36958 Sorted by residual: bond pdb=" O3' C R 15 " pdb=" P C R 16 " ideal model delta sigma weight residual 1.607 1.666 -0.059 1.50e-02 4.44e+03 1.56e+01 bond pdb=" C3' DT O -21 " pdb=" C2' DT O -21 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DT O -23 " pdb=" C2' DT O -23 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" O3' U R 13 " pdb=" P C R 14 " ideal model delta sigma weight residual 1.607 1.655 -0.048 1.50e-02 4.44e+03 1.03e+01 bond pdb=" C3' DA N 22 " pdb=" C2' DA N 22 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.55e+00 ... (remaining 36953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 49278 2.44 - 4.89: 952 4.89 - 7.33: 73 7.33 - 9.77: 21 9.77 - 12.21: 2 Bond angle restraints: 50326 Sorted by residual: angle pdb=" N PRO Q 421 " pdb=" CA PRO Q 421 " pdb=" CB PRO Q 421 " ideal model delta sigma weight residual 103.27 110.16 -6.89 9.00e-01 1.23e+00 5.87e+01 angle pdb=" C THR B 79 " pdb=" N GLU B 80 " pdb=" CA GLU B 80 " ideal model delta sigma weight residual 121.70 133.32 -11.62 1.80e+00 3.09e-01 4.17e+01 angle pdb=" C ILE B 918 " pdb=" N SER B 919 " pdb=" CA SER B 919 " ideal model delta sigma weight residual 121.70 131.16 -9.46 1.80e+00 3.09e-01 2.76e+01 angle pdb=" C VAL A1107 " pdb=" N ALA A1108 " pdb=" CA ALA A1108 " ideal model delta sigma weight residual 121.70 130.85 -9.15 1.80e+00 3.09e-01 2.58e+01 angle pdb=" C4' A R 12 " pdb=" C3' A R 12 " pdb=" O3' A R 12 " ideal model delta sigma weight residual 113.00 105.70 7.30 1.50e+00 4.44e-01 2.37e+01 ... (remaining 50321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 21621 35.82 - 71.63: 730 71.63 - 107.45: 43 107.45 - 143.27: 3 143.27 - 179.08: 1 Dihedral angle restraints: 22398 sinusoidal: 9858 harmonic: 12540 Sorted by residual: dihedral pdb=" CA HIS B 363 " pdb=" C HIS B 363 " pdb=" N ILE B 364 " pdb=" CA ILE B 364 " ideal model delta harmonic sigma weight residual -180.00 -133.31 -46.69 0 5.00e+00 4.00e-02 8.72e+01 dihedral pdb=" CA LYS B 510 " pdb=" C LYS B 510 " pdb=" N PRO B 511 " pdb=" CA PRO B 511 " ideal model delta harmonic sigma weight residual -180.00 -134.49 -45.51 0 5.00e+00 4.00e-02 8.28e+01 dihedral pdb=" CA PHE A 252 " pdb=" C PHE A 252 " pdb=" N ASN A 253 " pdb=" CA ASN A 253 " ideal model delta harmonic sigma weight residual 180.00 138.65 41.35 0 5.00e+00 4.00e-02 6.84e+01 ... (remaining 22395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4951 0.073 - 0.146: 680 0.146 - 0.220: 33 0.220 - 0.293: 1 0.293 - 0.366: 1 Chirality restraints: 5666 Sorted by residual: chirality pdb=" C3' DG O -7 " pdb=" C4' DG O -7 " pdb=" O3' DG O -7 " pdb=" C2' DG O -7 " both_signs ideal model delta sigma weight residual False -2.73 -2.36 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CB VAL C 243 " pdb=" CA VAL C 243 " pdb=" CG1 VAL C 243 " pdb=" CG2 VAL C 243 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB VAL A 474 " pdb=" CA VAL A 474 " pdb=" CG1 VAL A 474 " pdb=" CG2 VAL A 474 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 5663 not shown) Planarity restraints: 6198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 510 " 0.065 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO B 511 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO B 511 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 511 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA O -3 " -0.005 2.00e-02 2.50e+03 1.59e-02 6.98e+00 pdb=" N9 DA O -3 " 0.034 2.00e-02 2.50e+03 pdb=" C8 DA O -3 " -0.031 2.00e-02 2.50e+03 pdb=" N7 DA O -3 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA O -3 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA O -3 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA O -3 " 0.003 2.00e-02 2.50e+03 pdb=" N1 DA O -3 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA O -3 " -0.023 2.00e-02 2.50e+03 pdb=" N3 DA O -3 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA O -3 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 82 " -0.043 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO F 83 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO F 83 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 83 " -0.036 5.00e-02 4.00e+02 ... (remaining 6195 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 2 1.97 - 2.71: 1923 2.71 - 3.44: 57123 3.44 - 4.17: 87417 4.17 - 4.90: 146697 Nonbonded interactions: 293162 Sorted by model distance: nonbonded pdb=" OP1 U R 13 " pdb="MG MG R 101 " model vdw 1.243 2.170 nonbonded pdb=" SG CYS B1185 " pdb=" NZ LYS D 16 " model vdw 1.793 3.480 nonbonded pdb=" O CYS A 67 " pdb="ZN ZN A1802 " model vdw 2.000 2.230 nonbonded pdb=" N GLY A1395 " pdb="MG MG A1803 " model vdw 2.011 2.250 nonbonded pdb=" O2' C R 14 " pdb=" O2 C R 14 " model vdw 2.025 3.040 ... (remaining 293157 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=0.95 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 40.980 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.245 36987 Z= 0.297 Angle : 0.894 57.086 50353 Z= 0.507 Chirality : 0.047 0.366 5666 Planarity : 0.004 0.097 6198 Dihedral : 16.705 179.082 14272 Min Nonbonded Distance : 1.243 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.33 % Favored : 89.55 % Rotamer: Outliers : 0.19 % Allowed : 0.48 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 1.08 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.13), residues: 4259 helix: 0.55 (0.14), residues: 1359 sheet: -0.68 (0.20), residues: 685 loop : -2.01 (0.13), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 135 TYR 0.016 0.002 TYR B 679 PHE 0.022 0.002 PHE A 81 TRP 0.015 0.002 TRP A 954 HIS 0.011 0.002 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.30 (36958) covalent geometry : angle 0.81297 / 0.50 (50326) hydrogen bonds : bond 0.19418 / 21.29 ( 1400) hydrogen bonds : angle 7.49755 / 8.21 ( 3923) metal coordination : bond 0.05343 / 2.85 ( 29) metal coordination : angle 16.08870 / 28.44 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 993 time to evaluate : 1.017 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: 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 92 HIS cc_start: 0.8136 (t-90) cc_final: 0.6797 (t-90) REVERT: A 95 PHE cc_start: 0.9282 (m-80) cc_final: 0.8559 (m-80) REVERT: A 117 GLU cc_start: 0.9604 (tt0) cc_final: 0.9375 (tm-30) REVERT: A 225 ASN cc_start: 0.8861 (t0) cc_final: 0.8515 (t0) REVERT: A 234 MET cc_start: 0.9210 (ttm) cc_final: 0.8826 (ttm) REVERT: A 247 ARG cc_start: 0.8725 (ptt90) cc_final: 0.8202 (ptt-90) REVERT: A 445 ASN cc_start: 0.8527 (t0) cc_final: 0.8112 (t0) REVERT: A 450 LEU cc_start: 0.9151 (mm) cc_final: 0.8810 (tp) REVERT: A 456 MET cc_start: 0.8661 (mpp) cc_final: 0.7988 (mpp) REVERT: A 463 ILE cc_start: 0.9227 (mm) cc_final: 0.8897 (mm) REVERT: A 478 TYR cc_start: 0.7872 (m-80) cc_final: 0.6907 (m-80) REVERT: A 505 CYS cc_start: 0.9166 (m) cc_final: 0.8693 (m) REVERT: A 521 MET cc_start: 0.8737 (mmm) cc_final: 0.8170 (mmm) REVERT: A 535 THR cc_start: 0.8666 (m) cc_final: 0.8453 (t) REVERT: A 549 MET cc_start: 0.9141 (ptp) cc_final: 0.8874 (ptm) REVERT: A 662 PHE cc_start: 0.8432 (t80) cc_final: 0.7939 (t80) REVERT: A 696 GLU cc_start: 0.9163 (tt0) cc_final: 0.8887 (tp30) REVERT: A 741 ASN cc_start: 0.8541 (t0) cc_final: 0.8325 (t0) REVERT: A 786 HIS cc_start: 0.8452 (m-70) cc_final: 0.7735 (m-70) REVERT: A 846 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8450 (mt-10) REVERT: A 847 ASP cc_start: 0.8112 (p0) cc_final: 0.7624 (p0) REVERT: A 1063 MET cc_start: 0.8329 (mmp) cc_final: 0.8099 (mmm) REVERT: A 1120 LEU cc_start: 0.9641 (mt) cc_final: 0.9234 (tp) REVERT: A 1147 THR cc_start: 0.9381 (m) cc_final: 0.9144 (p) REVERT: A 1309 ASP cc_start: 0.9069 (t70) cc_final: 0.8292 (p0) REVERT: A 1364 ASN cc_start: 0.8585 (t0) cc_final: 0.8317 (t0) REVERT: B 239 GLU cc_start: 0.8068 (tt0) cc_final: 0.7405 (tm-30) REVERT: B 258 LEU cc_start: 0.9133 (tp) cc_final: 0.8924 (tp) REVERT: B 292 ILE cc_start: 0.9092 (mt) cc_final: 0.8852 (mm) REVERT: B 296 GLU cc_start: 0.9348 (mm-30) cc_final: 0.8971 (mp0) REVERT: B 361 LEU cc_start: 0.9026 (tp) cc_final: 0.8649 (tt) REVERT: B 396 ASP cc_start: 0.7756 (m-30) cc_final: 0.7373 (m-30) REVERT: B 404 LYS cc_start: 0.9228 (mttt) cc_final: 0.8828 (mttt) REVERT: B 566 LEU cc_start: 0.9364 (mt) cc_final: 0.9090 (mt) REVERT: B 576 ASP cc_start: 0.9197 (p0) cc_final: 0.8888 (t70) REVERT: B 610 ASN cc_start: 0.8715 (t0) cc_final: 0.8468 (t0) REVERT: B 705 MET cc_start: 0.7655 (mmm) cc_final: 0.6798 (mmm) REVERT: B 767 ASN cc_start: 0.8107 (m110) cc_final: 0.7859 (m110) REVERT: B 809 MET cc_start: 0.8155 (pmm) cc_final: 0.7839 (pmm) REVERT: B 834 ASN cc_start: 0.8727 (p0) cc_final: 0.8114 (p0) REVERT: B 846 ILE cc_start: 0.9647 (mm) cc_final: 0.9338 (tt) REVERT: B 847 ASP cc_start: 0.8844 (m-30) cc_final: 0.8525 (m-30) REVERT: B 860 MET cc_start: 0.8554 (ppp) cc_final: 0.7799 (ppp) REVERT: B 963 PHE cc_start: 0.8588 (t80) cc_final: 0.7822 (t80) REVERT: B 980 PHE cc_start: 0.8527 (m-10) cc_final: 0.8274 (m-10) REVERT: B 1069 PHE cc_start: 0.8782 (m-10) cc_final: 0.8444 (m-10) REVERT: B 1082 MET cc_start: 0.9052 (tpt) cc_final: 0.8691 (tpt) REVERT: B 1133 MET cc_start: 0.9181 (mtp) cc_final: 0.8759 (mtm) REVERT: B 1152 MET cc_start: 0.8178 (mmm) cc_final: 0.7549 (mmm) REVERT: B 1168 LEU cc_start: 0.8802 (mm) cc_final: 0.8588 (mm) REVERT: B 1183 LYS cc_start: 0.6857 (OUTLIER) cc_final: 0.6548 (mmmt) REVERT: B 1206 GLU cc_start: 0.9245 (mp0) cc_final: 0.9011 (mp0) REVERT: C 15 LYS cc_start: 0.9151 (tttm) cc_final: 0.8907 (tmtt) REVERT: C 16 ASP cc_start: 0.9122 (p0) cc_final: 0.8633 (p0) REVERT: C 46 ILE cc_start: 0.9253 (mt) cc_final: 0.8688 (tp) REVERT: C 52 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8752 (tm-30) REVERT: C 77 ILE cc_start: 0.9257 (tp) cc_final: 0.9048 (mm) REVERT: C 157 CYS cc_start: 0.9349 (m) cc_final: 0.9111 (m) REVERT: C 165 LYS cc_start: 0.9045 (tttt) cc_final: 0.8688 (tttt) REVERT: C 228 PHE cc_start: 0.8622 (m-10) cc_final: 0.8149 (m-10) REVERT: C 233 GLU cc_start: 0.8888 (tt0) cc_final: 0.8023 (tt0) REVERT: E 7 ARG cc_start: 0.9075 (ptm-80) cc_final: 0.8657 (ttp80) REVERT: E 18 THR cc_start: 0.8663 (p) cc_final: 0.8427 (p) REVERT: E 75 MET cc_start: 0.7567 (mpp) cc_final: 0.7352 (mpp) REVERT: E 140 LEU cc_start: 0.9530 (tp) cc_final: 0.9299 (tp) REVERT: F 81 THR cc_start: 0.9032 (m) cc_final: 0.8529 (p) REVERT: F 88 TYR cc_start: 0.7871 (m-10) cc_final: 0.7577 (m-10) REVERT: F 109 VAL cc_start: 0.8708 (p) cc_final: 0.8494 (p) REVERT: G 32 GLU cc_start: 0.8758 (mp0) cc_final: 0.8495 (mp0) REVERT: G 42 PHE cc_start: 0.8656 (m-80) cc_final: 0.8454 (m-80) REVERT: G 44 TYR cc_start: 0.8361 (t80) cc_final: 0.7910 (t80) REVERT: G 55 ASP cc_start: 0.7876 (m-30) cc_final: 0.7636 (m-30) REVERT: H 1 MET cc_start: 0.0921 (pmm) cc_final: -0.0576 (tpt) REVERT: H 10 PHE cc_start: 0.8814 (m-80) cc_final: 0.7796 (m-10) REVERT: H 97 MET cc_start: 0.7280 (ppp) cc_final: 0.6948 (ppp) REVERT: H 102 TYR cc_start: 0.8635 (p90) cc_final: 0.8230 (p90) REVERT: H 116 TYR cc_start: 0.7772 (m-80) cc_final: 0.7538 (m-80) REVERT: H 123 MET cc_start: 0.9248 (ppp) cc_final: 0.9038 (ppp) REVERT: H 133 ASN cc_start: 0.9055 (t0) cc_final: 0.8833 (t0) REVERT: I 65 ASP cc_start: 0.9471 (t70) cc_final: 0.9105 (t70) REVERT: I 68 LEU cc_start: 0.9378 (mp) cc_final: 0.9019 (mp) REVERT: J 13 VAL cc_start: 0.9448 (m) cc_final: 0.9199 (m) REVERT: K 18 LYS cc_start: 0.8324 (mmmm) cc_final: 0.8068 (mtmt) REVERT: K 37 LYS cc_start: 0.8630 (mmtt) cc_final: 0.8386 (mmmt) REVERT: K 38 GLU cc_start: 0.9403 (mp0) cc_final: 0.9082 (mp0) REVERT: K 53 ASP cc_start: 0.8339 (t0) cc_final: 0.7852 (t70) REVERT: K 91 CYS cc_start: 0.9498 (m) cc_final: 0.9256 (m) REVERT: K 92 ASN cc_start: 0.9385 (m110) cc_final: 0.9030 (m-40) REVERT: K 106 GLU cc_start: 0.8638 (mp0) cc_final: 0.8374 (mp0) REVERT: Q 393 TYR cc_start: 0.7403 (m-80) cc_final: 0.6946 (m-10) REVERT: M 129 VAL cc_start: 0.7556 (t) cc_final: 0.5907 (t) outliers start: 7 outliers final: 0 residues processed: 999 average time/residue: 0.2112 time to fit residues: 342.7252 Evaluate side-chains 607 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 606 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1183 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 20.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 ASN A 399 HIS A 447 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A 654 ASN A 742 ASN ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** A1390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1427 ASN B 538 ASN B 776 GLN B 881 ASN ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN E 143 ASN ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 GLN ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 239 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.124283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.083650 restraints weight = 116940.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.086509 restraints weight = 53591.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.088458 restraints weight = 33043.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.089770 restraints weight = 23994.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.090627 restraints weight = 19427.786| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 36987 Z= 0.208 Angle : 0.841 28.083 50353 Z= 0.427 Chirality : 0.048 0.328 5666 Planarity : 0.005 0.070 6198 Dihedral : 15.902 178.536 5771 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.38 % Favored : 89.55 % Rotamer: Outliers : 1.93 % Allowed : 13.63 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 1.08 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.13), residues: 4259 helix: 0.54 (0.14), residues: 1390 sheet: -0.74 (0.20), residues: 664 loop : -2.03 (0.13), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG Q 28 TYR 0.025 0.002 TYR B 830 PHE 0.042 0.002 PHE J 8 TRP 0.012 0.002 TRP A 954 HIS 0.010 0.001 HIS A1387 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.21 (36958) covalent geometry : angle 0.80675 / 0.42 (50326) hydrogen bonds : bond 0.05871 / 6.45 ( 1400) hydrogen bonds : angle 6.05844 / 6.61 ( 3923) metal coordination : bond 0.02431 / 1.38 ( 29) metal coordination : angle 10.35349 / 16.29 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 635 time to evaluate : 1.071 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: A 34 LYS cc_start: 0.9210 (mppt) cc_final: 0.8727 (tttt) REVERT: A 92 HIS cc_start: 0.8119 (t-90) cc_final: 0.6863 (t70) REVERT: A 95 PHE cc_start: 0.9533 (m-80) cc_final: 0.8816 (m-80) REVERT: A 117 GLU cc_start: 0.9680 (tt0) cc_final: 0.9467 (tm-30) REVERT: A 122 MET cc_start: 0.9309 (tmm) cc_final: 0.8942 (ppp) REVERT: A 225 ASN cc_start: 0.8903 (t0) cc_final: 0.8539 (t0) REVERT: A 437 MET cc_start: 0.7157 (mtt) cc_final: 0.6906 (ptp) REVERT: A 445 ASN cc_start: 0.9114 (t0) cc_final: 0.8444 (t0) REVERT: A 450 LEU cc_start: 0.9203 (mm) cc_final: 0.8773 (tp) REVERT: A 487 MET cc_start: 0.7020 (mmm) cc_final: 0.6267 (mmm) REVERT: A 500 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: A 505 CYS cc_start: 0.9200 (m) cc_final: 0.8857 (m) REVERT: A 521 MET cc_start: 0.8791 (mmm) cc_final: 0.8021 (mmm) REVERT: A 535 THR cc_start: 0.8435 (m) cc_final: 0.8169 (t) REVERT: A 557 ASP cc_start: 0.9157 (t70) cc_final: 0.8936 (t0) REVERT: A 662 PHE cc_start: 0.8438 (t80) cc_final: 0.8151 (t80) REVERT: A 696 GLU cc_start: 0.9160 (tt0) cc_final: 0.8924 (tp30) REVERT: A 741 ASN cc_start: 0.8505 (t0) cc_final: 0.7888 (t0) REVERT: A 761 MET cc_start: 0.9007 (mtm) cc_final: 0.8428 (mmp) REVERT: A 767 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: A 786 HIS cc_start: 0.8558 (m-70) cc_final: 0.7575 (m-70) REVERT: A 846 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8376 (mt-10) REVERT: A 847 ASP cc_start: 0.8100 (p0) cc_final: 0.7661 (p0) REVERT: A 874 ASP cc_start: 0.7265 (p0) cc_final: 0.6822 (m-30) REVERT: A 1063 MET cc_start: 0.8474 (mmp) cc_final: 0.8252 (mmm) REVERT: A 1120 LEU cc_start: 0.9592 (mt) cc_final: 0.9166 (tp) REVERT: A 1277 GLU cc_start: 0.9475 (pm20) cc_final: 0.9204 (pm20) REVERT: A 1285 MET cc_start: 0.8619 (mmm) cc_final: 0.8415 (mmm) REVERT: A 1309 ASP cc_start: 0.8942 (t70) cc_final: 0.8233 (p0) REVERT: A 1364 ASN cc_start: 0.8304 (t0) cc_final: 0.7910 (t0) REVERT: A 1419 ASP cc_start: 0.8313 (t0) cc_final: 0.7744 (t0) REVERT: A 1426 GLU cc_start: 0.8369 (mp0) cc_final: 0.8162 (mp0) REVERT: A 1427 ASN cc_start: 0.8335 (m-40) cc_final: 0.8019 (t0) REVERT: B 173 MET cc_start: 0.5883 (tpt) cc_final: 0.5512 (tpt) REVERT: B 239 GLU cc_start: 0.8183 (tt0) cc_final: 0.7500 (tm-30) REVERT: B 296 GLU cc_start: 0.9391 (mm-30) cc_final: 0.9038 (mp0) REVERT: B 361 LEU cc_start: 0.9028 (tp) cc_final: 0.8555 (tt) REVERT: B 396 ASP cc_start: 0.7778 (m-30) cc_final: 0.7438 (m-30) REVERT: B 404 LYS cc_start: 0.9158 (mttt) cc_final: 0.8756 (mptt) REVERT: B 576 ASP cc_start: 0.9291 (p0) cc_final: 0.8943 (t70) REVERT: B 597 MET cc_start: 0.9617 (tpt) cc_final: 0.9224 (tpp) REVERT: B 629 ASP cc_start: 0.7570 (t0) cc_final: 0.7189 (t0) REVERT: B 705 MET cc_start: 0.7392 (mmm) cc_final: 0.6510 (mmm) REVERT: B 767 ASN cc_start: 0.8157 (m110) cc_final: 0.7817 (m110) REVERT: B 809 MET cc_start: 0.8115 (pmm) cc_final: 0.7676 (pmm) REVERT: B 834 ASN cc_start: 0.8391 (p0) cc_final: 0.7649 (p0) REVERT: B 860 MET cc_start: 0.8475 (ppp) cc_final: 0.7995 (ppp) REVERT: B 963 PHE cc_start: 0.8602 (t80) cc_final: 0.8143 (t80) REVERT: B 967 ARG cc_start: 0.8587 (ttp-170) cc_final: 0.7822 (ttp-110) REVERT: B 999 MET cc_start: 0.9082 (tpp) cc_final: 0.8297 (mmt) REVERT: B 1069 PHE cc_start: 0.8985 (m-10) cc_final: 0.8502 (m-10) REVERT: B 1074 ASN cc_start: 0.8967 (t0) cc_final: 0.8745 (t0) REVERT: B 1082 MET cc_start: 0.9053 (tpt) cc_final: 0.8703 (tpt) REVERT: B 1094 ARG cc_start: 0.8341 (ttt-90) cc_final: 0.7913 (ttt-90) REVERT: B 1095 LEU cc_start: 0.9123 (mm) cc_final: 0.8316 (mm) REVERT: B 1122 ARG cc_start: 0.8355 (tmm-80) cc_final: 0.7720 (ttt90) REVERT: B 1133 MET cc_start: 0.9062 (mtp) cc_final: 0.8728 (mtm) REVERT: B 1168 LEU cc_start: 0.8846 (mm) cc_final: 0.8547 (mm) REVERT: C 16 ASP cc_start: 0.9098 (p0) cc_final: 0.8542 (p0) REVERT: C 46 ILE cc_start: 0.9209 (mt) cc_final: 0.8452 (tp) REVERT: C 52 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8657 (tm-30) REVERT: C 58 LEU cc_start: 0.8933 (tp) cc_final: 0.8697 (tt) REVERT: C 157 CYS cc_start: 0.9247 (m) cc_final: 0.8933 (m) REVERT: C 165 LYS cc_start: 0.8998 (tttt) cc_final: 0.8692 (tttt) REVERT: C 169 LYS cc_start: 0.9344 (mtpt) cc_final: 0.8750 (ptpt) REVERT: C 233 GLU cc_start: 0.8981 (tt0) cc_final: 0.8269 (tt0) REVERT: D 35 LEU cc_start: 0.8658 (mt) cc_final: 0.8437 (pt) REVERT: E 7 ARG cc_start: 0.9049 (ptm-80) cc_final: 0.8667 (ttp80) REVERT: E 22 MET cc_start: 0.9378 (tmm) cc_final: 0.9112 (ttt) REVERT: E 58 MET cc_start: 0.9444 (ttp) cc_final: 0.9152 (ppp) REVERT: E 75 MET cc_start: 0.7622 (mpp) cc_final: 0.7355 (mpp) REVERT: E 121 MET cc_start: 0.9293 (ppp) cc_final: 0.9045 (ppp) REVERT: E 140 LEU cc_start: 0.9576 (tp) cc_final: 0.9344 (tp) REVERT: E 194 GLU cc_start: 0.7980 (mp0) cc_final: 0.7676 (mp0) REVERT: F 81 THR cc_start: 0.9062 (m) cc_final: 0.8402 (p) REVERT: F 124 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8726 (tm-30) REVERT: H 1 MET cc_start: 0.1082 (pmm) cc_final: -0.0594 (tpt) REVERT: H 10 PHE cc_start: 0.8640 (m-80) cc_final: 0.7480 (m-80) REVERT: H 97 MET cc_start: 0.7959 (ppp) cc_final: 0.7684 (ppp) REVERT: H 106 GLU cc_start: 0.8134 (mp0) cc_final: 0.7933 (mp0) REVERT: H 118 PHE cc_start: 0.9078 (m-80) cc_final: 0.8726 (m-80) REVERT: H 123 MET cc_start: 0.9125 (ppp) cc_final: 0.8802 (ppp) REVERT: H 133 ASN cc_start: 0.9185 (t0) cc_final: 0.8956 (t0) REVERT: I 65 ASP cc_start: 0.9324 (t70) cc_final: 0.8752 (t70) REVERT: I 68 LEU cc_start: 0.9474 (mp) cc_final: 0.9006 (mp) REVERT: J 16 ASP cc_start: 0.8929 (p0) cc_final: 0.7549 (t0) REVERT: K 38 GLU cc_start: 0.9192 (mp0) cc_final: 0.8893 (mp0) REVERT: K 53 ASP cc_start: 0.8236 (t0) cc_final: 0.7598 (t70) REVERT: K 92 ASN cc_start: 0.9357 (m110) cc_final: 0.9022 (m-40) REVERT: L 58 LYS cc_start: 0.8840 (tppt) cc_final: 0.8283 (tptm) REVERT: Q 365 TYR cc_start: 0.7913 (t80) cc_final: 0.6864 (t80) REVERT: Q 401 TYR cc_start: 0.7485 (p90) cc_final: 0.7210 (p90) outliers start: 72 outliers final: 53 residues processed: 676 average time/residue: 0.1859 time to fit residues: 211.8858 Evaluate side-chains 606 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 551 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 757 ASN Chi-restraints excluded: chain A residue 767 GLN Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1356 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 236 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 325 optimal weight: 1.9990 chunk 285 optimal weight: 0.2980 chunk 247 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 51 optimal weight: 20.0000 chunk 210 optimal weight: 4.9990 chunk 203 optimal weight: 0.4980 chunk 349 optimal weight: 20.0000 chunk 384 optimal weight: 9.9990 chunk 291 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 HIS A 654 ASN ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1390 ASN ** B 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.126637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.085707 restraints weight = 116134.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.088632 restraints weight = 53100.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.090639 restraints weight = 32692.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.091995 restraints weight = 23683.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.092847 restraints weight = 19147.704| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 36987 Z= 0.148 Angle : 0.771 20.182 50353 Z= 0.391 Chirality : 0.047 0.348 5666 Planarity : 0.005 0.065 6198 Dihedral : 15.789 174.484 5767 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.60 % Favored : 90.35 % Rotamer: Outliers : 2.44 % Allowed : 15.72 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 1.08 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.13), residues: 4259 helix: 0.56 (0.14), residues: 1397 sheet: -0.67 (0.20), residues: 642 loop : -1.98 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 72 TYR 0.023 0.002 TYR B 811 PHE 0.030 0.002 PHE B1158 TRP 0.011 0.001 TRP A 185 HIS 0.011 0.001 HIS B1015 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (36958) covalent geometry : angle 0.75328 / 0.39 (50326) hydrogen bonds : bond 0.04671 / 5.11 ( 1400) hydrogen bonds : angle 5.56708 / 6.08 ( 3923) metal coordination : bond 0.01682 / 0.98 ( 29) metal coordination : angle 7.08719 / 10.53 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 652 time to evaluate : 1.418 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: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.9210 (mppt) cc_final: 0.8706 (tttp) REVERT: A 41 MET cc_start: 0.7097 (tpt) cc_final: 0.6680 (tpt) REVERT: A 92 HIS cc_start: 0.7811 (t-90) cc_final: 0.6854 (t-90) REVERT: A 117 GLU cc_start: 0.9705 (tt0) cc_final: 0.9454 (tm-30) REVERT: A 122 MET cc_start: 0.9350 (tmm) cc_final: 0.9008 (ppp) REVERT: A 225 ASN cc_start: 0.8872 (t0) cc_final: 0.8492 (t0) REVERT: A 247 ARG cc_start: 0.8586 (ptt90) cc_final: 0.8075 (ptt-90) REVERT: A 259 GLU cc_start: 0.5808 (tp30) cc_final: 0.5398 (tp30) REVERT: A 293 GLU cc_start: 0.8994 (tp30) cc_final: 0.8709 (tm-30) REVERT: A 341 MET cc_start: 0.8781 (mmt) cc_final: 0.8453 (mmt) REVERT: A 445 ASN cc_start: 0.8938 (t0) cc_final: 0.8180 (t0) REVERT: A 450 LEU cc_start: 0.9180 (mm) cc_final: 0.8764 (tp) REVERT: A 456 MET cc_start: 0.9005 (mpp) cc_final: 0.8757 (mpp) REVERT: A 487 MET cc_start: 0.7140 (mmm) cc_final: 0.6516 (mmm) REVERT: A 500 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: A 505 CYS cc_start: 0.9136 (m) cc_final: 0.8755 (m) REVERT: A 521 MET cc_start: 0.8608 (mmm) cc_final: 0.7808 (mmm) REVERT: A 535 THR cc_start: 0.8343 (m) cc_final: 0.8139 (t) REVERT: A 551 TYR cc_start: 0.7849 (t80) cc_final: 0.7509 (t80) REVERT: A 557 ASP cc_start: 0.9078 (t70) cc_final: 0.8842 (t0) REVERT: A 605 MET cc_start: 0.8838 (ttm) cc_final: 0.8604 (ttm) REVERT: A 662 PHE cc_start: 0.8225 (t80) cc_final: 0.7543 (t80) REVERT: A 696 GLU cc_start: 0.9154 (tt0) cc_final: 0.8939 (tp30) REVERT: A 741 ASN cc_start: 0.8261 (t0) cc_final: 0.7608 (t0) REVERT: A 748 MET cc_start: 0.8350 (ppp) cc_final: 0.8022 (ppp) REVERT: A 761 MET cc_start: 0.9045 (mtm) cc_final: 0.8401 (mmp) REVERT: A 786 HIS cc_start: 0.8542 (m-70) cc_final: 0.7557 (m-70) REVERT: A 846 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8012 (mp0) REVERT: A 847 ASP cc_start: 0.8112 (p0) cc_final: 0.7655 (p0) REVERT: A 852 TYR cc_start: 0.8595 (m-10) cc_final: 0.8036 (m-10) REVERT: A 874 ASP cc_start: 0.7007 (p0) cc_final: 0.6794 (m-30) REVERT: A 1120 LEU cc_start: 0.9592 (mt) cc_final: 0.9168 (tp) REVERT: A 1277 GLU cc_start: 0.9556 (pm20) cc_final: 0.9293 (pm20) REVERT: A 1364 ASN cc_start: 0.8183 (t0) cc_final: 0.7711 (t0) REVERT: A 1419 ASP cc_start: 0.8195 (t0) cc_final: 0.7814 (t0) REVERT: A 1427 ASN cc_start: 0.8348 (m-40) cc_final: 0.8140 (t0) REVERT: A 1433 MET cc_start: 0.9264 (ppp) cc_final: 0.8874 (ppp) REVERT: B 70 ILE cc_start: 0.8074 (mm) cc_final: 0.7861 (mm) REVERT: B 173 MET cc_start: 0.5730 (tpt) cc_final: 0.5443 (tpt) REVERT: B 239 GLU cc_start: 0.8234 (tt0) cc_final: 0.7586 (tm-30) REVERT: B 296 GLU cc_start: 0.9410 (mm-30) cc_final: 0.8939 (mp0) REVERT: B 313 MET cc_start: 0.9741 (mmm) cc_final: 0.9485 (tpp) REVERT: B 404 LYS cc_start: 0.9130 (mttt) cc_final: 0.8772 (mttt) REVERT: B 521 LEU cc_start: 0.9504 (mp) cc_final: 0.9258 (mm) REVERT: B 576 ASP cc_start: 0.9340 (p0) cc_final: 0.8953 (t70) REVERT: B 610 ASN cc_start: 0.8458 (t0) cc_final: 0.8138 (t0) REVERT: B 629 ASP cc_start: 0.7680 (t0) cc_final: 0.7258 (t0) REVERT: B 697 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: B 705 MET cc_start: 0.7347 (mmm) cc_final: 0.6572 (mmm) REVERT: B 809 MET cc_start: 0.7963 (pmm) cc_final: 0.7447 (pmm) REVERT: B 834 ASN cc_start: 0.8224 (p0) cc_final: 0.7434 (p0) REVERT: B 860 MET cc_start: 0.8395 (ppp) cc_final: 0.7927 (ppp) REVERT: B 963 PHE cc_start: 0.8555 (t80) cc_final: 0.7934 (t80) REVERT: B 967 ARG cc_start: 0.8572 (ttp-170) cc_final: 0.7880 (ttp-110) REVERT: B 999 MET cc_start: 0.9068 (tpp) cc_final: 0.8115 (mmm) REVERT: B 1013 ASN cc_start: 0.8850 (t0) cc_final: 0.8603 (t0) REVERT: B 1069 PHE cc_start: 0.8912 (m-10) cc_final: 0.8385 (m-10) REVERT: B 1082 MET cc_start: 0.9060 (tpt) cc_final: 0.8829 (tpt) REVERT: B 1095 LEU cc_start: 0.9102 (mm) cc_final: 0.8513 (mm) REVERT: B 1122 ARG cc_start: 0.8189 (tmm-80) cc_final: 0.7897 (ttt90) REVERT: B 1133 MET cc_start: 0.8963 (mtp) cc_final: 0.8612 (mtm) REVERT: B 1139 ILE cc_start: 0.9676 (mm) cc_final: 0.9434 (mt) REVERT: B 1168 LEU cc_start: 0.8864 (mm) cc_final: 0.8479 (mm) REVERT: B 1186 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7946 (p0) REVERT: C 16 ASP cc_start: 0.9038 (p0) cc_final: 0.8494 (p0) REVERT: C 19 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8522 (t70) REVERT: C 37 MET cc_start: 0.9329 (tpp) cc_final: 0.8971 (tpp) REVERT: C 46 ILE cc_start: 0.9172 (mt) cc_final: 0.8386 (tp) REVERT: C 52 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8572 (tm-30) REVERT: C 157 CYS cc_start: 0.9267 (m) cc_final: 0.8878 (m) REVERT: C 165 LYS cc_start: 0.8951 (tttt) cc_final: 0.8704 (tttt) REVERT: C 169 LYS cc_start: 0.9440 (mtpt) cc_final: 0.8870 (ptpt) REVERT: C 233 GLU cc_start: 0.8973 (tt0) cc_final: 0.8322 (tt0) REVERT: D 35 LEU cc_start: 0.8651 (mt) cc_final: 0.8414 (pt) REVERT: D 131 GLU cc_start: 0.6067 (OUTLIER) cc_final: 0.5541 (pt0) REVERT: E 7 ARG cc_start: 0.9026 (ptm-80) cc_final: 0.8640 (ttp80) REVERT: E 22 MET cc_start: 0.9378 (tmm) cc_final: 0.8980 (ttt) REVERT: E 58 MET cc_start: 0.9383 (ttp) cc_final: 0.8899 (tmm) REVERT: E 74 ASP cc_start: 0.9457 (p0) cc_final: 0.9239 (p0) REVERT: E 75 MET cc_start: 0.7625 (mpp) cc_final: 0.7332 (pmm) REVERT: E 121 MET cc_start: 0.9276 (ppp) cc_final: 0.9003 (ppp) REVERT: E 140 LEU cc_start: 0.9585 (tp) cc_final: 0.9327 (tp) REVERT: E 194 GLU cc_start: 0.8196 (mp0) cc_final: 0.7817 (mp0) REVERT: E 208 TYR cc_start: 0.7047 (t80) cc_final: 0.6532 (t80) REVERT: F 81 THR cc_start: 0.9031 (m) cc_final: 0.8381 (p) REVERT: F 89 GLU cc_start: 0.7718 (pm20) cc_final: 0.7455 (mp0) REVERT: F 103 MET cc_start: 0.9119 (tmm) cc_final: 0.8378 (tmm) REVERT: F 124 GLU cc_start: 0.9288 (tm-30) cc_final: 0.8812 (tm-30) REVERT: F 140 ASP cc_start: 0.9118 (t0) cc_final: 0.8473 (p0) REVERT: F 149 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7919 (tm-30) REVERT: G 44 TYR cc_start: 0.7941 (t80) cc_final: 0.7469 (t80) REVERT: H 1 MET cc_start: 0.1020 (pmm) cc_final: -0.0546 (tpt) REVERT: H 10 PHE cc_start: 0.8504 (m-80) cc_final: 0.7238 (m-80) REVERT: H 118 PHE cc_start: 0.9099 (m-80) cc_final: 0.8612 (m-10) REVERT: H 123 MET cc_start: 0.9105 (ppp) cc_final: 0.8757 (ppp) REVERT: H 133 ASN cc_start: 0.9192 (t0) cc_final: 0.8980 (t0) REVERT: I 68 LEU cc_start: 0.9524 (mp) cc_final: 0.9294 (mt) REVERT: J 6 ARG cc_start: 0.7950 (mmm-85) cc_final: 0.7610 (mmm-85) REVERT: J 60 PHE cc_start: 0.8867 (m-10) cc_final: 0.8576 (m-80) REVERT: K 38 GLU cc_start: 0.9071 (mp0) cc_final: 0.8819 (mp0) REVERT: K 53 ASP cc_start: 0.8199 (t0) cc_final: 0.7578 (t70) REVERT: K 92 ASN cc_start: 0.9338 (m110) cc_final: 0.9006 (m110) REVERT: Q 401 TYR cc_start: 0.7721 (p90) cc_final: 0.7444 (p90) REVERT: M 72 ARG cc_start: 0.8659 (ttp80) cc_final: 0.8185 (ttp80) REVERT: M 81 TRP cc_start: 0.8435 (m100) cc_final: 0.8094 (m-90) REVERT: M 199 ASP cc_start: 0.7362 (m-30) cc_final: 0.7127 (m-30) outliers start: 91 outliers final: 55 residues processed: 704 average time/residue: 0.1919 time to fit residues: 226.4657 Evaluate side-chains 610 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 550 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1356 ILE Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 214 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 105 optimal weight: 7.9990 chunk 349 optimal weight: 50.0000 chunk 152 optimal weight: 5.9990 chunk 237 optimal weight: 0.6980 chunk 247 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 409 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 427 optimal weight: 50.0000 chunk 418 optimal weight: 50.0000 chunk 249 optimal weight: 0.9980 overall best weight: 5.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN H 131 ASN ** H 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** 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 = 0.4130 r_free = 0.4130 target = 0.125819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.085549 restraints weight = 119903.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.088275 restraints weight = 54910.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.090117 restraints weight = 33862.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.091342 restraints weight = 24613.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.092142 restraints weight = 19999.515| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (25 function evaluations) r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 36987 Z= 0.206 Angle : 0.771 21.399 50353 Z= 0.395 Chirality : 0.046 0.244 5666 Planarity : 0.005 0.065 6198 Dihedral : 15.743 172.899 5767 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.21 % Favored : 89.74 % Rotamer: Outliers : 3.61 % Allowed : 17.35 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 1.08 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.13), residues: 4259 helix: 0.58 (0.14), residues: 1399 sheet: -0.69 (0.20), residues: 632 loop : -2.01 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 434 TYR 0.018 0.002 TYR B 833 PHE 0.026 0.002 PHE B 360 TRP 0.012 0.002 TRP A 556 HIS 0.011 0.001 HIS B1015 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.21 (36958) covalent geometry : angle 0.75251 / 0.39 (50326) hydrogen bonds : bond 0.04651 / 5.04 ( 1400) hydrogen bonds : angle 5.48765 / 6.04 ( 3923) metal coordination : bond 0.01614 / 0.96 ( 29) metal coordination : angle 7.22237 / 10.14 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 544 time to evaluate : 1.517 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 34 LYS cc_start: 0.9214 (mppt) cc_final: 0.8713 (tttt) REVERT: A 95 PHE cc_start: 0.9563 (m-80) cc_final: 0.9310 (m-80) REVERT: A 117 GLU cc_start: 0.9706 (tt0) cc_final: 0.9436 (tm-30) REVERT: A 122 MET cc_start: 0.9337 (tmm) cc_final: 0.9053 (ppp) REVERT: A 225 ASN cc_start: 0.8919 (t0) cc_final: 0.8559 (t0) REVERT: A 293 GLU cc_start: 0.9079 (tp30) cc_final: 0.8716 (tm-30) REVERT: A 299 HIS cc_start: 0.9005 (OUTLIER) cc_final: 0.8397 (t-90) REVERT: A 437 MET cc_start: 0.7371 (mtt) cc_final: 0.7125 (ptp) REVERT: A 450 LEU cc_start: 0.9149 (mm) cc_final: 0.8677 (tp) REVERT: A 456 MET cc_start: 0.9098 (mpp) cc_final: 0.8572 (mpp) REVERT: A 500 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: A 505 CYS cc_start: 0.9176 (m) cc_final: 0.8792 (m) REVERT: A 521 MET cc_start: 0.8879 (mmm) cc_final: 0.8115 (mmm) REVERT: A 535 THR cc_start: 0.8626 (m) cc_final: 0.8148 (t) REVERT: A 557 ASP cc_start: 0.9087 (t70) cc_final: 0.8861 (t0) REVERT: A 654 ASN cc_start: 0.9482 (OUTLIER) cc_final: 0.9228 (t0) REVERT: A 696 GLU cc_start: 0.9180 (tt0) cc_final: 0.8931 (tp30) REVERT: A 741 ASN cc_start: 0.8279 (t0) cc_final: 0.7613 (t0) REVERT: A 748 MET cc_start: 0.8542 (ppp) cc_final: 0.8161 (ppp) REVERT: A 761 MET cc_start: 0.9068 (mtm) cc_final: 0.8463 (mmp) REVERT: A 767 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7637 (tt0) REVERT: A 786 HIS cc_start: 0.8616 (m-70) cc_final: 0.7845 (m-70) REVERT: A 846 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8286 (mt-10) REVERT: A 847 ASP cc_start: 0.8076 (p0) cc_final: 0.7519 (p0) REVERT: A 1079 MET cc_start: 0.7102 (mtp) cc_final: 0.6878 (mtp) REVERT: A 1120 LEU cc_start: 0.9610 (mt) cc_final: 0.9290 (tp) REVERT: A 1317 MET cc_start: 0.9337 (mmm) cc_final: 0.9065 (mmm) REVERT: A 1331 SER cc_start: 0.8347 (m) cc_final: 0.8135 (p) REVERT: A 1364 ASN cc_start: 0.8550 (t0) cc_final: 0.8127 (t0) REVERT: A 1427 ASN cc_start: 0.8646 (m-40) cc_final: 0.8347 (t0) REVERT: B 70 ILE cc_start: 0.8128 (mm) cc_final: 0.7915 (mm) REVERT: B 173 MET cc_start: 0.6131 (tpt) cc_final: 0.5806 (tpt) REVERT: B 239 GLU cc_start: 0.8308 (tt0) cc_final: 0.7687 (tm-30) REVERT: B 296 GLU cc_start: 0.9479 (mm-30) cc_final: 0.8991 (mp0) REVERT: B 313 MET cc_start: 0.9718 (mmm) cc_final: 0.9508 (tpp) REVERT: B 319 GLU cc_start: 0.9447 (tp30) cc_final: 0.9156 (mm-30) REVERT: B 381 MET cc_start: 0.9462 (OUTLIER) cc_final: 0.9185 (tpt) REVERT: B 394 ASP cc_start: 0.8735 (p0) cc_final: 0.8461 (p0) REVERT: B 404 LYS cc_start: 0.9150 (mttt) cc_final: 0.8764 (mttt) REVERT: B 481 GLN cc_start: 0.8413 (mt0) cc_final: 0.8152 (mt0) REVERT: B 576 ASP cc_start: 0.9333 (p0) cc_final: 0.8956 (t70) REVERT: B 610 ASN cc_start: 0.8559 (t0) cc_final: 0.8275 (t0) REVERT: B 629 ASP cc_start: 0.7889 (t0) cc_final: 0.7450 (t0) REVERT: B 705 MET cc_start: 0.7588 (mmm) cc_final: 0.6762 (mmm) REVERT: B 809 MET cc_start: 0.8229 (pmm) cc_final: 0.7920 (pmm) REVERT: B 834 ASN cc_start: 0.8109 (p0) cc_final: 0.7391 (p0) REVERT: B 847 ASP cc_start: 0.8959 (OUTLIER) cc_final: 0.8745 (t0) REVERT: B 860 MET cc_start: 0.8382 (ppp) cc_final: 0.7964 (ppp) REVERT: B 963 PHE cc_start: 0.8572 (t80) cc_final: 0.7981 (t80) REVERT: B 1015 HIS cc_start: 0.8341 (m170) cc_final: 0.7652 (m170) REVERT: B 1082 MET cc_start: 0.9049 (tpt) cc_final: 0.8824 (tpt) REVERT: B 1095 LEU cc_start: 0.9232 (mm) cc_final: 0.8841 (mm) REVERT: B 1133 MET cc_start: 0.8939 (mtp) cc_final: 0.8439 (mtm) REVERT: B 1205 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8286 (mp10) REVERT: C 16 ASP cc_start: 0.9044 (p0) cc_final: 0.8666 (p0) REVERT: C 37 MET cc_start: 0.9315 (tpp) cc_final: 0.9095 (tpp) REVERT: C 46 ILE cc_start: 0.9171 (mt) cc_final: 0.8410 (tp) REVERT: C 52 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8608 (tm-30) REVERT: C 157 CYS cc_start: 0.9246 (m) cc_final: 0.8895 (m) REVERT: C 165 LYS cc_start: 0.9083 (tttt) cc_final: 0.8740 (tttt) REVERT: C 169 LYS cc_start: 0.9463 (mtpt) cc_final: 0.8990 (ptpt) REVERT: D 35 LEU cc_start: 0.8648 (mt) cc_final: 0.8399 (pt) REVERT: E 7 ARG cc_start: 0.9097 (ptm-80) cc_final: 0.8685 (ttp80) REVERT: E 58 MET cc_start: 0.9412 (ttp) cc_final: 0.8853 (tmm) REVERT: E 74 ASP cc_start: 0.9452 (p0) cc_final: 0.9219 (p0) REVERT: E 75 MET cc_start: 0.7784 (mpp) cc_final: 0.7509 (mpp) REVERT: E 121 MET cc_start: 0.9270 (ppp) cc_final: 0.8951 (ppp) REVERT: E 194 GLU cc_start: 0.8324 (mp0) cc_final: 0.8015 (mp0) REVERT: E 208 TYR cc_start: 0.7424 (t80) cc_final: 0.6930 (t80) REVERT: F 81 THR cc_start: 0.9007 (m) cc_final: 0.8388 (p) REVERT: F 103 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8299 (tmm) REVERT: F 122 MET cc_start: 0.9511 (ttm) cc_final: 0.8756 (tmm) REVERT: F 124 GLU cc_start: 0.9345 (tm-30) cc_final: 0.9044 (tm-30) REVERT: F 149 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7844 (tm-30) REVERT: H 1 MET cc_start: 0.1218 (pmm) cc_final: -0.0416 (tpt) REVERT: H 10 PHE cc_start: 0.8421 (m-80) cc_final: 0.7312 (m-80) REVERT: H 118 PHE cc_start: 0.9194 (m-80) cc_final: 0.8702 (m-10) REVERT: H 123 MET cc_start: 0.9179 (ppp) cc_final: 0.8607 (ppp) REVERT: I 65 ASP cc_start: 0.8938 (t0) cc_final: 0.8725 (t0) REVERT: I 68 LEU cc_start: 0.9434 (mp) cc_final: 0.9072 (mp) REVERT: J 16 ASP cc_start: 0.9075 (p0) cc_final: 0.8720 (p0) REVERT: K 38 GLU cc_start: 0.9070 (mp0) cc_final: 0.8470 (mp0) REVERT: K 53 ASP cc_start: 0.8332 (t0) cc_final: 0.7982 (t70) REVERT: K 92 ASN cc_start: 0.9347 (m110) cc_final: 0.9014 (m110) REVERT: Q 31 PHE cc_start: 0.5749 (t80) cc_final: 0.5532 (t80) REVERT: Q 114 MET cc_start: 0.9090 (mmm) cc_final: 0.8695 (mmp) REVERT: Q 401 TYR cc_start: 0.7966 (p90) cc_final: 0.7694 (p90) REVERT: M 81 TRP cc_start: 0.8362 (m100) cc_final: 0.8155 (m-90) REVERT: M 95 ILE cc_start: 0.9605 (pt) cc_final: 0.9343 (mm) REVERT: M 137 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8706 (pm20) outliers start: 135 outliers final: 84 residues processed: 627 average time/residue: 0.2109 time to fit residues: 223.6939 Evaluate side-chains 601 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 508 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 757 ASN Chi-restraints excluded: chain A residue 767 GLN Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1356 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1372 VAL Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain B residue 847 ASP Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1147 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1205 GLN Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain Q residue 342 LEU Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 236 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 38 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 249 optimal weight: 1.9990 chunk 408 optimal weight: 30.0000 chunk 363 optimal weight: 9.9990 chunk 258 optimal weight: 9.9990 chunk 402 optimal weight: 40.0000 chunk 85 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS A 439 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A 654 ASN ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.121848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.082429 restraints weight = 123182.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.085155 restraints weight = 55356.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.086989 restraints weight = 33856.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.088219 restraints weight = 24540.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.089008 restraints weight = 19898.959| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 36987 Z= 0.254 Angle : 0.801 21.812 50353 Z= 0.410 Chirality : 0.047 0.339 5666 Planarity : 0.005 0.065 6198 Dihedral : 15.777 171.876 5767 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.52 % Favored : 89.43 % Rotamer: Outliers : 3.91 % Allowed : 18.98 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 1.08 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.13), residues: 4259 helix: 0.50 (0.14), residues: 1406 sheet: -0.69 (0.21), residues: 631 loop : -2.08 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 146 TYR 0.048 0.002 TYR Q 373 PHE 0.032 0.002 PHE B 360 TRP 0.015 0.002 TRP A 556 HIS 0.008 0.002 HIS A1387 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.25 (36958) covalent geometry : angle 0.78235 / 0.41 (50326) hydrogen bonds : bond 0.04706 / 5.09 ( 1400) hydrogen bonds : angle 5.50802 / 6.12 ( 3923) metal coordination : bond 0.01576 / 1.04 ( 29) metal coordination : angle 7.41715 / 9.94 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 515 time to evaluate : 1.214 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 34 LYS cc_start: 0.9197 (mppt) cc_final: 0.8707 (tttt) REVERT: A 40 THR cc_start: 0.6954 (OUTLIER) cc_final: 0.6715 (p) REVERT: A 41 MET cc_start: 0.7038 (tpt) cc_final: 0.6283 (tpp) REVERT: A 95 PHE cc_start: 0.9372 (m-80) cc_final: 0.9097 (m-80) REVERT: A 117 GLU cc_start: 0.9724 (tt0) cc_final: 0.9498 (tm-30) REVERT: A 122 MET cc_start: 0.9295 (tmm) cc_final: 0.8892 (ppp) REVERT: A 225 ASN cc_start: 0.8992 (t0) cc_final: 0.8610 (t0) REVERT: A 234 MET cc_start: 0.9277 (ttt) cc_final: 0.8875 (ttt) REVERT: A 299 HIS cc_start: 0.9079 (OUTLIER) cc_final: 0.8486 (t-90) REVERT: A 391 LEU cc_start: 0.9369 (mt) cc_final: 0.9168 (tt) REVERT: A 450 LEU cc_start: 0.9149 (mm) cc_final: 0.8635 (tp) REVERT: A 456 MET cc_start: 0.9047 (mpp) cc_final: 0.8443 (mpp) REVERT: A 500 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: A 504 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7531 (mm) REVERT: A 505 CYS cc_start: 0.9190 (m) cc_final: 0.8718 (m) REVERT: A 521 MET cc_start: 0.8895 (mmm) cc_final: 0.8310 (mmm) REVERT: A 535 THR cc_start: 0.8656 (m) cc_final: 0.8149 (t) REVERT: A 557 ASP cc_start: 0.9039 (t70) cc_final: 0.8823 (t0) REVERT: A 696 GLU cc_start: 0.9215 (tt0) cc_final: 0.8895 (tp30) REVERT: A 701 LEU cc_start: 0.9064 (pt) cc_final: 0.8162 (pt) REVERT: A 748 MET cc_start: 0.8603 (ppp) cc_final: 0.8199 (ppp) REVERT: A 761 MET cc_start: 0.9100 (mtm) cc_final: 0.8561 (mmm) REVERT: A 767 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: A 786 HIS cc_start: 0.8696 (m-70) cc_final: 0.7993 (m-70) REVERT: A 818 MET cc_start: 0.9348 (tpp) cc_final: 0.8781 (mmt) REVERT: A 846 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8314 (mt-10) REVERT: A 847 ASP cc_start: 0.8144 (p0) cc_final: 0.7639 (p0) REVERT: A 1120 LEU cc_start: 0.9634 (mt) cc_final: 0.9311 (tp) REVERT: A 1400 CYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8814 (p) REVERT: A 1421 CYS cc_start: 0.8593 (t) cc_final: 0.7937 (m) REVERT: A 1427 ASN cc_start: 0.8665 (m-40) cc_final: 0.8087 (t0) REVERT: A 1433 MET cc_start: 0.9213 (ppp) cc_final: 0.8880 (tmm) REVERT: B 70 ILE cc_start: 0.8252 (mm) cc_final: 0.8043 (mm) REVERT: B 173 MET cc_start: 0.6129 (tpt) cc_final: 0.5758 (tpt) REVERT: B 239 GLU cc_start: 0.8431 (tt0) cc_final: 0.7685 (tm-30) REVERT: B 296 GLU cc_start: 0.9498 (mm-30) cc_final: 0.8996 (mp0) REVERT: B 319 GLU cc_start: 0.9416 (tp30) cc_final: 0.9082 (mm-30) REVERT: B 331 LEU cc_start: 0.8789 (mt) cc_final: 0.8584 (mp) REVERT: B 381 MET cc_start: 0.9497 (OUTLIER) cc_final: 0.9214 (tpt) REVERT: B 404 LYS cc_start: 0.9196 (mttt) cc_final: 0.8825 (mttt) REVERT: B 481 GLN cc_start: 0.8589 (mt0) cc_final: 0.8294 (mm-40) REVERT: B 576 ASP cc_start: 0.9314 (p0) cc_final: 0.8948 (t70) REVERT: B 629 ASP cc_start: 0.7946 (t0) cc_final: 0.7513 (t0) REVERT: B 696 GLU cc_start: 0.9323 (tp30) cc_final: 0.9100 (tp30) REVERT: B 705 MET cc_start: 0.7669 (mmm) cc_final: 0.6869 (mmm) REVERT: B 790 ASP cc_start: 0.8190 (t70) cc_final: 0.7862 (t70) REVERT: B 834 ASN cc_start: 0.8140 (p0) cc_final: 0.7493 (p0) REVERT: B 860 MET cc_start: 0.8362 (ppp) cc_final: 0.8017 (ppp) REVERT: B 963 PHE cc_start: 0.8561 (t80) cc_final: 0.7995 (t80) REVERT: B 967 ARG cc_start: 0.8604 (ttp-170) cc_final: 0.8020 (ttp-170) REVERT: B 1015 HIS cc_start: 0.8394 (m170) cc_final: 0.8076 (m170) REVERT: B 1082 MET cc_start: 0.9121 (tpt) cc_final: 0.8883 (tpt) REVERT: B 1095 LEU cc_start: 0.9354 (mm) cc_final: 0.9027 (mm) REVERT: B 1133 MET cc_start: 0.8885 (mtp) cc_final: 0.8369 (mtm) REVERT: B 1169 MET cc_start: 0.8868 (mmt) cc_final: 0.8661 (mmm) REVERT: B 1201 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.9004 (ttpp) REVERT: C 16 ASP cc_start: 0.9058 (p0) cc_final: 0.8694 (p0) REVERT: C 37 MET cc_start: 0.9332 (tpp) cc_final: 0.9032 (tpp) REVERT: C 46 ILE cc_start: 0.9202 (mt) cc_final: 0.8426 (tp) REVERT: C 52 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8597 (tm-30) REVERT: C 157 CYS cc_start: 0.9252 (m) cc_final: 0.8907 (m) REVERT: C 165 LYS cc_start: 0.9137 (tttt) cc_final: 0.8806 (tttt) REVERT: C 169 LYS cc_start: 0.9434 (mtpt) cc_final: 0.8953 (ptpt) REVERT: C 233 GLU cc_start: 0.8983 (tt0) cc_final: 0.8664 (tt0) REVERT: D 35 LEU cc_start: 0.8652 (mt) cc_final: 0.8395 (pt) REVERT: D 131 GLU cc_start: 0.6030 (OUTLIER) cc_final: 0.5641 (pt0) REVERT: E 7 ARG cc_start: 0.9102 (ptm-80) cc_final: 0.8680 (ttp80) REVERT: E 22 MET cc_start: 0.9274 (tmm) cc_final: 0.9057 (tmm) REVERT: E 58 MET cc_start: 0.9452 (ttp) cc_final: 0.8951 (tmm) REVERT: E 121 MET cc_start: 0.9307 (ppp) cc_final: 0.8988 (ppp) REVERT: E 194 GLU cc_start: 0.8319 (mp0) cc_final: 0.7952 (mp0) REVERT: E 208 TYR cc_start: 0.7485 (t80) cc_final: 0.6994 (t80) REVERT: F 81 THR cc_start: 0.9137 (m) cc_final: 0.8600 (p) REVERT: F 84 TYR cc_start: 0.9230 (m-10) cc_final: 0.8945 (m-10) REVERT: F 103 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8357 (tmm) REVERT: F 122 MET cc_start: 0.9528 (ttm) cc_final: 0.8765 (tmm) REVERT: F 124 GLU cc_start: 0.9370 (tm-30) cc_final: 0.9070 (tm-30) REVERT: G 44 TYR cc_start: 0.8003 (t80) cc_final: 0.7617 (t80) REVERT: H 1 MET cc_start: 0.1595 (pmm) cc_final: 0.0058 (tpt) REVERT: H 10 PHE cc_start: 0.8309 (m-80) cc_final: 0.7288 (m-80) REVERT: H 118 PHE cc_start: 0.9329 (m-80) cc_final: 0.8941 (m-10) REVERT: H 123 MET cc_start: 0.9236 (ppp) cc_final: 0.8871 (ppp) REVERT: H 133 ASN cc_start: 0.8930 (t0) cc_final: 0.8653 (m110) REVERT: I 65 ASP cc_start: 0.9009 (t0) cc_final: 0.8697 (t0) REVERT: I 68 LEU cc_start: 0.9498 (mp) cc_final: 0.9047 (mp) REVERT: I 87 GLN cc_start: 0.8499 (pp30) cc_final: 0.8253 (pp30) REVERT: J 39 LEU cc_start: 0.9365 (tp) cc_final: 0.9041 (tt) REVERT: K 53 ASP cc_start: 0.8523 (t0) cc_final: 0.8229 (t70) REVERT: K 92 ASN cc_start: 0.9348 (m110) cc_final: 0.9008 (m110) REVERT: K 106 GLU cc_start: 0.8782 (mp0) cc_final: 0.8459 (mp0) REVERT: L 50 ASP cc_start: 0.8259 (p0) cc_final: 0.7909 (p0) REVERT: Q 31 PHE cc_start: 0.5862 (t80) cc_final: 0.5599 (t80) REVERT: Q 114 MET cc_start: 0.9127 (mmm) cc_final: 0.8832 (mmm) REVERT: Q 352 MET cc_start: 0.7303 (tmm) cc_final: 0.7070 (tmm) REVERT: Q 401 TYR cc_start: 0.8083 (p90) cc_final: 0.7835 (p90) REVERT: M 137 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8793 (pm20) outliers start: 146 outliers final: 102 residues processed: 610 average time/residue: 0.2095 time to fit residues: 217.2190 Evaluate side-chains 599 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 486 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 757 ASN Chi-restraints excluded: chain A residue 767 GLN Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1356 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1372 VAL Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1191 ILE Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain B residue 1205 GLN Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain Q residue 342 LEU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 236 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 311 optimal weight: 10.0000 chunk 331 optimal weight: 4.9990 chunk 423 optimal weight: 3.9990 chunk 394 optimal weight: 9.9990 chunk 338 optimal weight: 0.6980 chunk 346 optimal weight: 0.6980 chunk 141 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 340 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 GLN ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.124669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.083378 restraints weight = 115822.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.086147 restraints weight = 52504.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.088028 restraints weight = 32228.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.089294 restraints weight = 23342.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.090139 restraints weight = 18868.048| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 36987 Z= 0.147 Angle : 0.759 17.278 50353 Z= 0.384 Chirality : 0.046 0.282 5666 Planarity : 0.005 0.063 6198 Dihedral : 15.697 171.291 5767 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.70 % Favored : 90.26 % Rotamer: Outliers : 3.00 % Allowed : 21.07 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 0.54 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.13), residues: 4259 helix: 0.69 (0.14), residues: 1402 sheet: -0.58 (0.21), residues: 610 loop : -2.00 (0.13), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG B 337 TYR 0.016 0.001 TYR D 147 PHE 0.020 0.002 PHE J 8 TRP 0.013 0.002 TRP A 185 HIS 0.006 0.001 HIS B 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (36958) covalent geometry : angle 0.74664 / 0.38 (50326) hydrogen bonds : bond 0.04225 / 4.60 ( 1400) hydrogen bonds : angle 5.18787 / 5.76 ( 3923) metal coordination : bond 0.01537 / 0.96 ( 29) metal coordination : angle 6.04948 / 8.43 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 553 time to evaluate : 1.491 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: A 34 LYS cc_start: 0.9113 (mppt) cc_final: 0.8645 (tttt) REVERT: A 95 PHE cc_start: 0.9367 (m-80) cc_final: 0.9020 (m-80) REVERT: A 117 GLU cc_start: 0.9722 (tt0) cc_final: 0.9497 (tm-30) REVERT: A 122 MET cc_start: 0.9350 (tmm) cc_final: 0.8931 (ppp) REVERT: A 225 ASN cc_start: 0.8965 (t0) cc_final: 0.8592 (t0) REVERT: A 234 MET cc_start: 0.9253 (ttt) cc_final: 0.8733 (ttt) REVERT: A 450 LEU cc_start: 0.9116 (mm) cc_final: 0.8514 (tp) REVERT: A 456 MET cc_start: 0.8992 (mpp) cc_final: 0.8441 (mpp) REVERT: A 500 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: A 504 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7392 (mm) REVERT: A 505 CYS cc_start: 0.9140 (m) cc_final: 0.8750 (m) REVERT: A 521 MET cc_start: 0.8815 (mmm) cc_final: 0.8187 (mmm) REVERT: A 557 ASP cc_start: 0.8994 (t70) cc_final: 0.8768 (t0) REVERT: A 605 MET cc_start: 0.8829 (ttm) cc_final: 0.8419 (mtt) REVERT: A 696 GLU cc_start: 0.9207 (tt0) cc_final: 0.8882 (tp30) REVERT: A 701 LEU cc_start: 0.9073 (pt) cc_final: 0.8170 (pt) REVERT: A 748 MET cc_start: 0.8551 (ppp) cc_final: 0.8082 (ppp) REVERT: A 761 MET cc_start: 0.9080 (mtm) cc_final: 0.8614 (mmt) REVERT: A 767 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: A 786 HIS cc_start: 0.8623 (m-70) cc_final: 0.7944 (m-70) REVERT: A 846 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8208 (mt-10) REVERT: A 847 ASP cc_start: 0.7966 (p0) cc_final: 0.7461 (p0) REVERT: A 874 ASP cc_start: 0.7340 (p0) cc_final: 0.6945 (m-30) REVERT: A 1079 MET cc_start: 0.7230 (mtp) cc_final: 0.6902 (mtp) REVERT: A 1120 LEU cc_start: 0.9612 (mt) cc_final: 0.9160 (tp) REVERT: A 1227 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8534 (mm) REVERT: A 1400 CYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8547 (p) REVERT: A 1421 CYS cc_start: 0.8562 (t) cc_final: 0.7900 (m) REVERT: A 1427 ASN cc_start: 0.8624 (m-40) cc_final: 0.8143 (t0) REVERT: A 1433 MET cc_start: 0.9244 (ppp) cc_final: 0.8911 (tmm) REVERT: B 70 ILE cc_start: 0.8164 (mm) cc_final: 0.7950 (mm) REVERT: B 173 MET cc_start: 0.6018 (tpt) cc_final: 0.5638 (tpt) REVERT: B 239 GLU cc_start: 0.8352 (tt0) cc_final: 0.7607 (tm-30) REVERT: B 258 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9104 (tp) REVERT: B 296 GLU cc_start: 0.9490 (mm-30) cc_final: 0.9000 (mp0) REVERT: B 319 GLU cc_start: 0.9392 (tp30) cc_final: 0.9083 (mm-30) REVERT: B 381 MET cc_start: 0.9407 (ttt) cc_final: 0.9189 (tpt) REVERT: B 404 LYS cc_start: 0.9149 (mttt) cc_final: 0.8782 (mttt) REVERT: B 481 GLN cc_start: 0.8477 (mt0) cc_final: 0.8164 (mm-40) REVERT: B 521 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9293 (mm) REVERT: B 576 ASP cc_start: 0.9350 (p0) cc_final: 0.8904 (t70) REVERT: B 629 ASP cc_start: 0.8093 (t0) cc_final: 0.7680 (t0) REVERT: B 639 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8686 (pt) REVERT: B 705 MET cc_start: 0.7539 (mmm) cc_final: 0.6749 (mmm) REVERT: B 790 ASP cc_start: 0.8141 (t70) cc_final: 0.7718 (t70) REVERT: B 809 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7765 (pmm) REVERT: B 834 ASN cc_start: 0.8126 (p0) cc_final: 0.7353 (p0) REVERT: B 847 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8695 (t0) REVERT: B 860 MET cc_start: 0.8341 (ppp) cc_final: 0.7991 (ppp) REVERT: B 963 PHE cc_start: 0.8424 (t80) cc_final: 0.7871 (t80) REVERT: B 1015 HIS cc_start: 0.8330 (m170) cc_final: 0.8090 (m170) REVERT: B 1082 MET cc_start: 0.9040 (tpt) cc_final: 0.8797 (tpt) REVERT: B 1095 LEU cc_start: 0.9364 (mm) cc_final: 0.9032 (mm) REVERT: B 1169 MET cc_start: 0.8885 (mmt) cc_final: 0.8636 (mmm) REVERT: B 1201 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8296 (ttpp) REVERT: B 1205 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8293 (mp10) REVERT: B 1208 MET cc_start: 0.8918 (ptp) cc_final: 0.8221 (ptp) REVERT: C 16 ASP cc_start: 0.9040 (p0) cc_final: 0.8674 (p0) REVERT: C 37 MET cc_start: 0.9319 (tpp) cc_final: 0.9011 (tpp) REVERT: C 46 ILE cc_start: 0.9180 (mt) cc_final: 0.8234 (tp) REVERT: C 52 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8526 (tm-30) REVERT: C 67 LEU cc_start: 0.9643 (mm) cc_final: 0.9339 (tp) REVERT: C 157 CYS cc_start: 0.9290 (m) cc_final: 0.8569 (m) REVERT: C 165 LYS cc_start: 0.9034 (tttt) cc_final: 0.8718 (tttt) REVERT: C 169 LYS cc_start: 0.9481 (mtpt) cc_final: 0.8994 (ptpt) REVERT: D 35 LEU cc_start: 0.8551 (mt) cc_final: 0.8328 (pt) REVERT: D 131 GLU cc_start: 0.5948 (OUTLIER) cc_final: 0.5578 (pt0) REVERT: E 7 ARG cc_start: 0.9096 (ptm-80) cc_final: 0.8709 (ttp80) REVERT: E 58 MET cc_start: 0.9441 (ttp) cc_final: 0.8986 (tmm) REVERT: E 121 MET cc_start: 0.9316 (ppp) cc_final: 0.9108 (ppp) REVERT: E 194 GLU cc_start: 0.8271 (mp0) cc_final: 0.7865 (mp0) REVERT: F 81 THR cc_start: 0.9062 (m) cc_final: 0.8529 (p) REVERT: F 84 TYR cc_start: 0.9095 (m-10) cc_final: 0.8876 (m-10) REVERT: F 85 MET cc_start: 0.8382 (tmm) cc_final: 0.8053 (tmm) REVERT: F 89 GLU cc_start: 0.7787 (pm20) cc_final: 0.7249 (pm20) REVERT: F 103 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8373 (tmm) REVERT: F 122 MET cc_start: 0.9517 (ttm) cc_final: 0.8764 (tmm) REVERT: F 124 GLU cc_start: 0.9393 (tm-30) cc_final: 0.9111 (tm-30) REVERT: G 44 TYR cc_start: 0.7931 (t80) cc_final: 0.7400 (t80) REVERT: H 1 MET cc_start: 0.1494 (pmm) cc_final: -0.0062 (tpt) REVERT: H 10 PHE cc_start: 0.8284 (m-80) cc_final: 0.7239 (m-80) REVERT: H 118 PHE cc_start: 0.9277 (m-80) cc_final: 0.8827 (m-10) REVERT: H 123 MET cc_start: 0.9287 (ppp) cc_final: 0.8664 (ppp) REVERT: I 65 ASP cc_start: 0.8934 (t0) cc_final: 0.8563 (t0) REVERT: I 68 LEU cc_start: 0.9472 (mp) cc_final: 0.9013 (mp) REVERT: I 87 GLN cc_start: 0.8371 (pp30) cc_final: 0.8160 (pp30) REVERT: J 39 LEU cc_start: 0.9302 (tp) cc_final: 0.8988 (tt) REVERT: K 38 GLU cc_start: 0.8971 (mp0) cc_final: 0.8439 (mp0) REVERT: K 53 ASP cc_start: 0.8405 (t0) cc_final: 0.8081 (t70) REVERT: Q 114 MET cc_start: 0.9146 (mmm) cc_final: 0.8863 (mmm) REVERT: Q 352 MET cc_start: 0.7473 (tmm) cc_final: 0.7106 (tmm) REVERT: Q 401 TYR cc_start: 0.8062 (p90) cc_final: 0.7818 (p90) REVERT: M 81 TRP cc_start: 0.8447 (m100) cc_final: 0.8118 (m100) REVERT: M 137 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8780 (pm20) outliers start: 112 outliers final: 77 residues processed: 622 average time/residue: 0.2090 time to fit residues: 221.0493 Evaluate side-chains 602 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 510 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 757 ASN Chi-restraints excluded: chain A residue 767 GLN Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1331 SER Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1356 ILE Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 847 ASP Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1205 GLN Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain Q residue 342 LEU Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 224 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 145 optimal weight: 1.9990 chunk 266 optimal weight: 0.3980 chunk 155 optimal weight: 30.0000 chunk 369 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 274 optimal weight: 8.9990 chunk 405 optimal weight: 30.0000 chunk 357 optimal weight: 20.0000 chunk 68 optimal weight: 20.0000 chunk 383 optimal weight: 0.9980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN ** B 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.128306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.087304 restraints weight = 117101.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.090189 restraints weight = 53331.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.092145 restraints weight = 32753.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.093478 restraints weight = 23720.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.094332 restraints weight = 19116.289| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 36987 Z= 0.141 Angle : 0.751 16.288 50353 Z= 0.380 Chirality : 0.046 0.256 5666 Planarity : 0.004 0.063 6198 Dihedral : 15.627 170.290 5767 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.67 % Favored : 90.28 % Rotamer: Outliers : 3.11 % Allowed : 22.14 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 0.54 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.13), residues: 4259 helix: 0.75 (0.14), residues: 1412 sheet: -0.48 (0.21), residues: 623 loop : -1.97 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 68 TYR 0.018 0.001 TYR B 833 PHE 0.024 0.002 PHE J 8 TRP 0.013 0.001 TRP A 185 HIS 0.005 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (36958) covalent geometry : angle 0.74067 / 0.38 (50326) hydrogen bonds : bond 0.04004 / 4.37 ( 1400) hydrogen bonds : angle 5.05184 / 5.62 ( 3923) metal coordination : bond 0.01499 / 0.78 ( 29) metal coordination : angle 5.41912 / 7.56 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 548 time to evaluate : 1.269 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: A 34 LYS cc_start: 0.9093 (mppt) cc_final: 0.8648 (tttm) REVERT: A 40 THR cc_start: 0.6943 (OUTLIER) cc_final: 0.6717 (p) REVERT: A 95 PHE cc_start: 0.9366 (m-80) cc_final: 0.8662 (m-80) REVERT: A 117 GLU cc_start: 0.9716 (tt0) cc_final: 0.9490 (tm-30) REVERT: A 122 MET cc_start: 0.9329 (tmm) cc_final: 0.8867 (ppp) REVERT: A 225 ASN cc_start: 0.8997 (t0) cc_final: 0.8610 (t0) REVERT: A 259 GLU cc_start: 0.6287 (tp30) cc_final: 0.6014 (tm-30) REVERT: A 433 GLU cc_start: 0.7835 (tp30) cc_final: 0.7586 (tp30) REVERT: A 450 LEU cc_start: 0.9101 (mm) cc_final: 0.8515 (tp) REVERT: A 453 MET cc_start: 0.9271 (mmp) cc_final: 0.9070 (mmm) REVERT: A 456 MET cc_start: 0.8980 (mpp) cc_final: 0.8447 (mpp) REVERT: A 500 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: A 504 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7344 (mm) REVERT: A 505 CYS cc_start: 0.9128 (m) cc_final: 0.8773 (m) REVERT: A 521 MET cc_start: 0.8779 (mmm) cc_final: 0.8189 (mmm) REVERT: A 541 ILE cc_start: 0.8882 (tp) cc_final: 0.8674 (tp) REVERT: A 557 ASP cc_start: 0.8976 (t70) cc_final: 0.8751 (t0) REVERT: A 605 MET cc_start: 0.8796 (ttm) cc_final: 0.8450 (mtt) REVERT: A 654 ASN cc_start: 0.9418 (OUTLIER) cc_final: 0.9085 (t0) REVERT: A 662 PHE cc_start: 0.8167 (t80) cc_final: 0.7413 (t80) REVERT: A 696 GLU cc_start: 0.9203 (tt0) cc_final: 0.8895 (tp30) REVERT: A 701 LEU cc_start: 0.9092 (pt) cc_final: 0.8213 (pt) REVERT: A 748 MET cc_start: 0.8497 (ppp) cc_final: 0.8082 (ppp) REVERT: A 761 MET cc_start: 0.9082 (mtm) cc_final: 0.8552 (mmm) REVERT: A 767 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: A 786 HIS cc_start: 0.8600 (m-70) cc_final: 0.7922 (m-70) REVERT: A 812 GLU cc_start: 0.9434 (mp0) cc_final: 0.8760 (mm-30) REVERT: A 846 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8182 (mt-10) REVERT: A 847 ASP cc_start: 0.7910 (p0) cc_final: 0.7304 (p0) REVERT: A 1079 MET cc_start: 0.7095 (mtp) cc_final: 0.6772 (mtp) REVERT: A 1120 LEU cc_start: 0.9621 (mt) cc_final: 0.9165 (tp) REVERT: A 1327 ILE cc_start: 0.9445 (tt) cc_final: 0.9186 (tp) REVERT: A 1375 MET cc_start: 0.8884 (tmm) cc_final: 0.8294 (tmm) REVERT: A 1400 CYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8543 (p) REVERT: A 1433 MET cc_start: 0.9236 (ppp) cc_final: 0.8940 (tmm) REVERT: B 173 MET cc_start: 0.5959 (tpt) cc_final: 0.5581 (tpt) REVERT: B 239 GLU cc_start: 0.8358 (tt0) cc_final: 0.7595 (tm-30) REVERT: B 296 GLU cc_start: 0.9491 (mm-30) cc_final: 0.8998 (mp0) REVERT: B 319 GLU cc_start: 0.9402 (tp30) cc_final: 0.9050 (mm-30) REVERT: B 376 PHE cc_start: 0.9375 (OUTLIER) cc_final: 0.8730 (m-10) REVERT: B 404 LYS cc_start: 0.9163 (mttt) cc_final: 0.8742 (mttt) REVERT: B 445 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8053 (mmtt) REVERT: B 446 LEU cc_start: 0.8580 (mt) cc_final: 0.7969 (mp) REVERT: B 481 GLN cc_start: 0.8496 (mt0) cc_final: 0.8170 (mt0) REVERT: B 521 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9281 (mm) REVERT: B 576 ASP cc_start: 0.9304 (p0) cc_final: 0.8854 (t70) REVERT: B 629 ASP cc_start: 0.8159 (t0) cc_final: 0.7779 (t0) REVERT: B 639 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8660 (pt) REVERT: B 697 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: B 705 MET cc_start: 0.7552 (mmm) cc_final: 0.6731 (mmm) REVERT: B 790 ASP cc_start: 0.8186 (t70) cc_final: 0.7717 (t70) REVERT: B 809 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7763 (pmm) REVERT: B 812 LEU cc_start: 0.9282 (mp) cc_final: 0.8906 (mp) REVERT: B 834 ASN cc_start: 0.8100 (p0) cc_final: 0.7310 (p0) REVERT: B 847 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8693 (t0) REVERT: B 860 MET cc_start: 0.8380 (ppp) cc_final: 0.8058 (ppp) REVERT: B 963 PHE cc_start: 0.8298 (t80) cc_final: 0.7771 (t80) REVERT: B 992 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8717 (pt) REVERT: B 999 MET cc_start: 0.9210 (tpp) cc_final: 0.8629 (tpp) REVERT: B 1015 HIS cc_start: 0.8408 (m170) cc_final: 0.7889 (m170) REVERT: B 1072 MET cc_start: 0.7520 (tpt) cc_final: 0.7289 (tpt) REVERT: B 1087 PHE cc_start: 0.7474 (t80) cc_final: 0.6576 (t80) REVERT: B 1095 LEU cc_start: 0.9409 (mm) cc_final: 0.9079 (mm) REVERT: B 1169 MET cc_start: 0.8905 (mmt) cc_final: 0.8640 (mmm) REVERT: B 1201 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8284 (ttpp) REVERT: B 1205 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8304 (mp10) REVERT: B 1208 MET cc_start: 0.8885 (ptp) cc_final: 0.8186 (ptp) REVERT: C 16 ASP cc_start: 0.8987 (p0) cc_final: 0.8608 (p0) REVERT: C 37 MET cc_start: 0.9314 (tpp) cc_final: 0.8983 (tpp) REVERT: C 46 ILE cc_start: 0.9196 (mt) cc_final: 0.8251 (tp) REVERT: C 52 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8439 (tm-30) REVERT: C 58 LEU cc_start: 0.8713 (tp) cc_final: 0.8442 (tp) REVERT: C 67 LEU cc_start: 0.9648 (mm) cc_final: 0.9311 (tp) REVERT: C 157 CYS cc_start: 0.9259 (m) cc_final: 0.8503 (m) REVERT: C 165 LYS cc_start: 0.9040 (tttt) cc_final: 0.8731 (tttm) REVERT: C 169 LYS cc_start: 0.9460 (mtpt) cc_final: 0.8961 (ptpt) REVERT: C 233 GLU cc_start: 0.9017 (tt0) cc_final: 0.8715 (tt0) REVERT: D 35 LEU cc_start: 0.8546 (mt) cc_final: 0.8320 (pt) REVERT: D 131 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5602 (pt0) REVERT: E 7 ARG cc_start: 0.9078 (ptm-80) cc_final: 0.8698 (ttp80) REVERT: E 58 MET cc_start: 0.9436 (ttp) cc_final: 0.8952 (tmm) REVERT: E 194 GLU cc_start: 0.8265 (mp0) cc_final: 0.7833 (mp0) REVERT: F 81 THR cc_start: 0.9072 (m) cc_final: 0.8527 (p) REVERT: F 84 TYR cc_start: 0.9109 (m-10) cc_final: 0.8904 (m-10) REVERT: F 85 MET cc_start: 0.8334 (tmm) cc_final: 0.8062 (tmm) REVERT: F 89 GLU cc_start: 0.7837 (pm20) cc_final: 0.7558 (pm20) REVERT: F 103 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8377 (tmm) REVERT: F 122 MET cc_start: 0.9513 (ttm) cc_final: 0.8746 (tmm) REVERT: F 124 GLU cc_start: 0.9370 (tm-30) cc_final: 0.9034 (tm-30) REVERT: G 44 TYR cc_start: 0.7916 (t80) cc_final: 0.7358 (t80) REVERT: G 52 ASP cc_start: 0.8788 (t0) cc_final: 0.8440 (t0) REVERT: H 1 MET cc_start: 0.1761 (pmm) cc_final: 0.0101 (tpt) REVERT: H 10 PHE cc_start: 0.8296 (m-80) cc_final: 0.7255 (m-80) REVERT: H 118 PHE cc_start: 0.9331 (m-80) cc_final: 0.8841 (m-10) REVERT: H 123 MET cc_start: 0.9298 (ppp) cc_final: 0.8661 (ppp) REVERT: I 65 ASP cc_start: 0.8945 (t0) cc_final: 0.8574 (t0) REVERT: I 68 LEU cc_start: 0.9460 (mp) cc_final: 0.8995 (mp) REVERT: J 29 GLU cc_start: 0.9030 (mp0) cc_final: 0.8807 (mp0) REVERT: J 39 LEU cc_start: 0.9320 (tp) cc_final: 0.9018 (tt) REVERT: K 53 ASP cc_start: 0.8405 (t0) cc_final: 0.8073 (t70) REVERT: Q 114 MET cc_start: 0.9166 (mmm) cc_final: 0.8898 (mmm) REVERT: Q 352 MET cc_start: 0.7521 (tmm) cc_final: 0.7158 (tmm) REVERT: Q 401 TYR cc_start: 0.8100 (p90) cc_final: 0.7843 (p90) REVERT: M 137 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8779 (pm20) outliers start: 116 outliers final: 78 residues processed: 620 average time/residue: 0.2059 time to fit residues: 217.2519 Evaluate side-chains 621 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 524 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 757 ASN Chi-restraints excluded: chain A residue 767 GLN Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1331 SER Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1356 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 376 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 847 ASP Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1028 GLU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1205 GLN Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 224 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 331 optimal weight: 0.8980 chunk 348 optimal weight: 20.0000 chunk 312 optimal weight: 0.0970 chunk 363 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 355 optimal weight: 0.0000 chunk 366 optimal weight: 0.0970 chunk 0 optimal weight: 50.0000 chunk 401 optimal weight: 40.0000 chunk 268 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN ** B 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN ** F 100 GLN ** 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 = 0.4218 r_free = 0.4218 target = 0.130165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.089578 restraints weight = 115949.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.092533 restraints weight = 52354.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.094537 restraints weight = 31847.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.095874 restraints weight = 22847.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.096734 restraints weight = 18355.425| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 36987 Z= 0.135 Angle : 0.778 16.701 50353 Z= 0.386 Chirality : 0.047 0.458 5666 Planarity : 0.004 0.062 6198 Dihedral : 15.564 170.553 5767 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.25 % Favored : 90.70 % Rotamer: Outliers : 2.81 % Allowed : 23.03 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 0.54 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.13), residues: 4259 helix: 0.76 (0.14), residues: 1413 sheet: -0.46 (0.20), residues: 652 loop : -1.93 (0.13), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 68 TYR 0.016 0.001 TYR D 147 PHE 0.022 0.001 PHE J 8 TRP 0.022 0.001 TRP M 81 HIS 0.009 0.001 HIS B1015 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (36958) covalent geometry : angle 0.76941 / 0.39 (50326) hydrogen bonds : bond 0.03808 / 4.19 ( 1400) hydrogen bonds : angle 4.92573 / 5.50 ( 3923) metal coordination : bond 0.01486 / 0.75 ( 29) metal coordination : angle 4.93909 / 7.01 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 560 time to evaluate : 1.372 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: A 40 THR cc_start: 0.6802 (OUTLIER) cc_final: 0.6590 (p) REVERT: A 41 MET cc_start: 0.7072 (tpt) cc_final: 0.6267 (tpt) REVERT: A 95 PHE cc_start: 0.9377 (m-80) cc_final: 0.8954 (m-80) REVERT: A 117 GLU cc_start: 0.9710 (tt0) cc_final: 0.9496 (tm-30) REVERT: A 122 MET cc_start: 0.9335 (tmm) cc_final: 0.8889 (ppp) REVERT: A 225 ASN cc_start: 0.8994 (t0) cc_final: 0.8605 (t0) REVERT: A 234 MET cc_start: 0.9111 (ttt) cc_final: 0.8607 (ttt) REVERT: A 259 GLU cc_start: 0.6175 (tp30) cc_final: 0.5873 (tm-30) REVERT: A 450 LEU cc_start: 0.9081 (mm) cc_final: 0.8472 (tp) REVERT: A 456 MET cc_start: 0.8945 (mpp) cc_final: 0.8380 (mpp) REVERT: A 500 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: A 504 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7226 (mm) REVERT: A 505 CYS cc_start: 0.9073 (m) cc_final: 0.8720 (m) REVERT: A 521 MET cc_start: 0.8663 (mmm) cc_final: 0.8072 (mmm) REVERT: A 557 ASP cc_start: 0.8910 (t70) cc_final: 0.8680 (t0) REVERT: A 605 MET cc_start: 0.8717 (ttm) cc_final: 0.8444 (mtt) REVERT: A 662 PHE cc_start: 0.7565 (t80) cc_final: 0.6939 (t80) REVERT: A 696 GLU cc_start: 0.9181 (tt0) cc_final: 0.8892 (tp30) REVERT: A 701 LEU cc_start: 0.9064 (pt) cc_final: 0.8211 (pt) REVERT: A 746 MET cc_start: 0.9563 (OUTLIER) cc_final: 0.9351 (mmm) REVERT: A 748 MET cc_start: 0.8505 (ppp) cc_final: 0.8000 (ppp) REVERT: A 761 MET cc_start: 0.9102 (mtm) cc_final: 0.8406 (mmp) REVERT: A 767 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: A 786 HIS cc_start: 0.8576 (m-70) cc_final: 0.7883 (m-70) REVERT: A 812 GLU cc_start: 0.9436 (mp0) cc_final: 0.8775 (mm-30) REVERT: A 846 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8321 (mt-10) REVERT: A 847 ASP cc_start: 0.7998 (p0) cc_final: 0.7409 (p0) REVERT: A 874 ASP cc_start: 0.7797 (m-30) cc_final: 0.7535 (p0) REVERT: A 894 GLU cc_start: 0.9197 (pp20) cc_final: 0.8963 (pp20) REVERT: A 956 LEU cc_start: 0.8594 (mt) cc_final: 0.8168 (tt) REVERT: A 992 ASP cc_start: 0.9486 (m-30) cc_final: 0.9201 (t70) REVERT: A 1079 MET cc_start: 0.6965 (mtp) cc_final: 0.6675 (mtp) REVERT: A 1120 LEU cc_start: 0.9615 (mt) cc_final: 0.9169 (tp) REVERT: A 1285 MET cc_start: 0.8689 (mmm) cc_final: 0.8477 (mmm) REVERT: A 1327 ILE cc_start: 0.9311 (tt) cc_final: 0.9048 (tp) REVERT: A 1375 MET cc_start: 0.8847 (tmm) cc_final: 0.8242 (tmm) REVERT: A 1400 CYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8576 (p) REVERT: A 1421 CYS cc_start: 0.8510 (t) cc_final: 0.7850 (m) REVERT: B 38 PHE cc_start: 0.9442 (OUTLIER) cc_final: 0.9233 (m-10) REVERT: B 173 MET cc_start: 0.6044 (tpt) cc_final: 0.5671 (tpt) REVERT: B 239 GLU cc_start: 0.8315 (tt0) cc_final: 0.7577 (tm-30) REVERT: B 276 ILE cc_start: 0.9083 (mm) cc_final: 0.8773 (mp) REVERT: B 296 GLU cc_start: 0.9489 (mm-30) cc_final: 0.8993 (mp0) REVERT: B 319 GLU cc_start: 0.9416 (tp30) cc_final: 0.9074 (mm-30) REVERT: B 374 LYS cc_start: 0.9063 (mmmt) cc_final: 0.8577 (mptt) REVERT: B 376 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8724 (m-10) REVERT: B 393 LYS cc_start: 0.8432 (tppt) cc_final: 0.7806 (tptp) REVERT: B 394 ASP cc_start: 0.8895 (p0) cc_final: 0.8681 (p0) REVERT: B 404 LYS cc_start: 0.9125 (mttt) cc_final: 0.8734 (mttt) REVERT: B 444 MET cc_start: 0.7176 (ppp) cc_final: 0.6830 (ppp) REVERT: B 445 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7984 (mmtt) REVERT: B 446 LEU cc_start: 0.8551 (mt) cc_final: 0.7932 (mp) REVERT: B 481 GLN cc_start: 0.8472 (mt0) cc_final: 0.8165 (mt0) REVERT: B 521 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9259 (mm) REVERT: B 542 MET cc_start: 0.8382 (mpp) cc_final: 0.7967 (mpp) REVERT: B 576 ASP cc_start: 0.9279 (p0) cc_final: 0.8810 (t70) REVERT: B 629 ASP cc_start: 0.8184 (t0) cc_final: 0.7853 (t0) REVERT: B 639 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8635 (pt) REVERT: B 697 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: B 705 MET cc_start: 0.7544 (mmm) cc_final: 0.6737 (mmm) REVERT: B 767 ASN cc_start: 0.9036 (OUTLIER) cc_final: 0.8474 (m110) REVERT: B 790 ASP cc_start: 0.8129 (t70) cc_final: 0.7648 (t70) REVERT: B 809 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7706 (pmm) REVERT: B 812 LEU cc_start: 0.9293 (mp) cc_final: 0.8928 (mp) REVERT: B 834 ASN cc_start: 0.8086 (p0) cc_final: 0.7299 (p0) REVERT: B 860 MET cc_start: 0.8349 (ppp) cc_final: 0.8010 (ppp) REVERT: B 963 PHE cc_start: 0.8192 (t80) cc_final: 0.7679 (t80) REVERT: B 992 ILE cc_start: 0.9278 (pt) cc_final: 0.8900 (pt) REVERT: B 994 TYR cc_start: 0.7725 (m-80) cc_final: 0.7357 (m-10) REVERT: B 999 MET cc_start: 0.9178 (tpp) cc_final: 0.8558 (tpp) REVERT: B 1015 HIS cc_start: 0.8195 (m170) cc_final: 0.7953 (m170) REVERT: B 1087 PHE cc_start: 0.7382 (t80) cc_final: 0.6600 (t80) REVERT: B 1095 LEU cc_start: 0.9368 (mm) cc_final: 0.9088 (mm) REVERT: B 1169 MET cc_start: 0.8883 (mmt) cc_final: 0.8506 (mmm) REVERT: B 1201 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8840 (ttpp) REVERT: B 1208 MET cc_start: 0.8835 (ptp) cc_final: 0.8592 (ptt) REVERT: C 16 ASP cc_start: 0.8968 (p0) cc_final: 0.8598 (p0) REVERT: C 37 MET cc_start: 0.9321 (tpp) cc_final: 0.8976 (tpp) REVERT: C 46 ILE cc_start: 0.9153 (mt) cc_final: 0.8198 (tp) REVERT: C 52 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8411 (tm-30) REVERT: C 67 LEU cc_start: 0.9643 (mm) cc_final: 0.9325 (tp) REVERT: C 157 CYS cc_start: 0.9313 (m) cc_final: 0.8563 (m) REVERT: C 165 LYS cc_start: 0.9013 (tttt) cc_final: 0.8763 (tttm) REVERT: C 169 LYS cc_start: 0.9478 (mtpt) cc_final: 0.8949 (ptpt) REVERT: C 192 TRP cc_start: 0.8941 (t60) cc_final: 0.8314 (t60) REVERT: C 233 GLU cc_start: 0.9010 (tt0) cc_final: 0.8724 (tt0) REVERT: D 35 LEU cc_start: 0.8553 (mt) cc_final: 0.8319 (pt) REVERT: D 131 GLU cc_start: 0.5933 (OUTLIER) cc_final: 0.5604 (pt0) REVERT: E 7 ARG cc_start: 0.9048 (ptm-80) cc_final: 0.8628 (ttp80) REVERT: E 22 MET cc_start: 0.9413 (tmm) cc_final: 0.9025 (ttt) REVERT: E 58 MET cc_start: 0.9424 (ttp) cc_final: 0.8920 (tmm) REVERT: E 63 ASN cc_start: 0.9613 (m-40) cc_final: 0.9299 (t0) REVERT: E 121 MET cc_start: 0.9276 (ppp) cc_final: 0.9039 (ppp) REVERT: E 194 GLU cc_start: 0.8258 (mp0) cc_final: 0.7839 (mp0) REVERT: F 81 THR cc_start: 0.9073 (m) cc_final: 0.8521 (p) REVERT: F 85 MET cc_start: 0.8335 (tmm) cc_final: 0.8056 (tmm) REVERT: F 89 GLU cc_start: 0.7873 (pm20) cc_final: 0.7565 (pm20) REVERT: F 103 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8365 (tmm) REVERT: F 122 MET cc_start: 0.9506 (ttm) cc_final: 0.8726 (tmm) REVERT: F 124 GLU cc_start: 0.9399 (tm-30) cc_final: 0.9072 (tm-30) REVERT: G 44 TYR cc_start: 0.7736 (t80) cc_final: 0.7194 (t80) REVERT: H 1 MET cc_start: 0.1986 (pmm) cc_final: 0.0330 (tpt) REVERT: H 10 PHE cc_start: 0.8288 (m-80) cc_final: 0.7228 (m-80) REVERT: H 97 MET cc_start: 0.7937 (ppp) cc_final: 0.7613 (ppp) REVERT: H 118 PHE cc_start: 0.9298 (m-80) cc_final: 0.8572 (m-10) REVERT: H 123 MET cc_start: 0.9304 (ppp) cc_final: 0.8627 (ppp) REVERT: H 133 ASN cc_start: 0.8724 (t0) cc_final: 0.8414 (m110) REVERT: I 36 GLU cc_start: 0.9497 (tp30) cc_final: 0.9257 (tp30) REVERT: I 65 ASP cc_start: 0.8906 (t0) cc_final: 0.8551 (t0) REVERT: I 68 LEU cc_start: 0.9446 (mp) cc_final: 0.9006 (mp) REVERT: J 6 ARG cc_start: 0.7704 (mmm-85) cc_final: 0.7340 (mmm-85) REVERT: J 39 LEU cc_start: 0.9293 (tp) cc_final: 0.8990 (tt) REVERT: K 38 GLU cc_start: 0.8806 (mp0) cc_final: 0.8278 (mp0) REVERT: Q 103 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9241 (pt) REVERT: Q 114 MET cc_start: 0.9174 (mmm) cc_final: 0.8912 (mmm) REVERT: Q 352 MET cc_start: 0.7467 (tmm) cc_final: 0.7253 (tmm) REVERT: Q 401 TYR cc_start: 0.8030 (p90) cc_final: 0.7740 (p90) REVERT: M 137 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8764 (pm20) outliers start: 105 outliers final: 67 residues processed: 620 average time/residue: 0.2039 time to fit residues: 216.3500 Evaluate side-chains 615 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 529 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 757 ASN Chi-restraints excluded: chain A residue 767 GLN Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 376 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 1028 GLU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1205 GLN Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 372 SER Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 224 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 164 optimal weight: 6.9990 chunk 401 optimal weight: 40.0000 chunk 100 optimal weight: 6.9990 chunk 393 optimal weight: 0.7980 chunk 368 optimal weight: 5.9990 chunk 310 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 291 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 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 = 0.4134 r_free = 0.4134 target = 0.124552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.085553 restraints weight = 120925.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.088468 restraints weight = 54221.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.090442 restraints weight = 33006.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.091778 restraints weight = 23733.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.092670 restraints weight = 19097.243| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 36987 Z= 0.180 Angle : 0.776 16.497 50353 Z= 0.391 Chirality : 0.046 0.387 5666 Planarity : 0.005 0.064 6198 Dihedral : 15.546 168.966 5767 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.74 % Favored : 90.21 % Rotamer: Outliers : 2.70 % Allowed : 23.64 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 0.54 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.13), residues: 4259 helix: 0.78 (0.14), residues: 1416 sheet: -0.48 (0.21), residues: 625 loop : -1.91 (0.13), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 68 TYR 0.017 0.001 TYR H 20 PHE 0.022 0.002 PHE B 360 TRP 0.013 0.002 TRP A 552 HIS 0.009 0.001 HIS B1015 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (36958) covalent geometry : angle 0.76641 / 0.39 (50326) hydrogen bonds : bond 0.03968 / 4.32 ( 1400) hydrogen bonds : angle 4.97886 / 5.56 ( 3923) metal coordination : bond 0.01237 / 0.72 ( 29) metal coordination : angle 5.22092 / 7.10 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 510 time to evaluate : 1.503 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: A 34 LYS cc_start: 0.9091 (mppt) cc_final: 0.8665 (tttm) REVERT: A 95 PHE cc_start: 0.9353 (m-80) cc_final: 0.8941 (m-80) REVERT: A 117 GLU cc_start: 0.9716 (tt0) cc_final: 0.9501 (tm-30) REVERT: A 122 MET cc_start: 0.9314 (tmm) cc_final: 0.8889 (ppp) REVERT: A 225 ASN cc_start: 0.9062 (t0) cc_final: 0.8689 (t0) REVERT: A 234 MET cc_start: 0.9144 (ttt) cc_final: 0.8673 (ttt) REVERT: A 304 MET cc_start: 0.9161 (tpp) cc_final: 0.8900 (tpp) REVERT: A 450 LEU cc_start: 0.9068 (mm) cc_final: 0.8488 (tp) REVERT: A 453 MET cc_start: 0.9129 (mmm) cc_final: 0.8875 (mmm) REVERT: A 456 MET cc_start: 0.8987 (mpp) cc_final: 0.8129 (mpp) REVERT: A 500 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.7607 (tm-30) REVERT: A 504 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7381 (mm) REVERT: A 505 CYS cc_start: 0.9081 (m) cc_final: 0.8716 (m) REVERT: A 521 MET cc_start: 0.8874 (mmm) cc_final: 0.8096 (mmp) REVERT: A 557 ASP cc_start: 0.8933 (t70) cc_final: 0.8710 (t0) REVERT: A 605 MET cc_start: 0.8799 (ttm) cc_final: 0.8479 (mtt) REVERT: A 662 PHE cc_start: 0.7807 (t80) cc_final: 0.7075 (t80) REVERT: A 696 GLU cc_start: 0.9203 (tt0) cc_final: 0.8900 (tp30) REVERT: A 701 LEU cc_start: 0.9137 (pt) cc_final: 0.8295 (pt) REVERT: A 746 MET cc_start: 0.9459 (OUTLIER) cc_final: 0.9186 (mmm) REVERT: A 748 MET cc_start: 0.8459 (ppp) cc_final: 0.8072 (ppp) REVERT: A 767 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: A 786 HIS cc_start: 0.8698 (m-70) cc_final: 0.8039 (m-70) REVERT: A 812 GLU cc_start: 0.9436 (mp0) cc_final: 0.8797 (mm-30) REVERT: A 818 MET cc_start: 0.9263 (tpp) cc_final: 0.8689 (mmt) REVERT: A 846 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8208 (mt-10) REVERT: A 847 ASP cc_start: 0.7980 (p0) cc_final: 0.7388 (p0) REVERT: A 894 GLU cc_start: 0.9172 (pp20) cc_final: 0.8940 (pp20) REVERT: A 1079 MET cc_start: 0.7077 (mtp) cc_final: 0.6777 (mtp) REVERT: A 1120 LEU cc_start: 0.9639 (mt) cc_final: 0.9307 (tp) REVERT: A 1327 ILE cc_start: 0.9410 (tt) cc_final: 0.9145 (tp) REVERT: A 1368 MET cc_start: 0.9105 (mtp) cc_final: 0.8766 (mtp) REVERT: A 1375 MET cc_start: 0.8898 (tmm) cc_final: 0.8299 (tmm) REVERT: A 1400 CYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8799 (p) REVERT: A 1444 MET cc_start: 0.8551 (tpp) cc_final: 0.8303 (tpp) REVERT: B 239 GLU cc_start: 0.8343 (tt0) cc_final: 0.7613 (tm-30) REVERT: B 273 LEU cc_start: 0.8171 (mp) cc_final: 0.7782 (tt) REVERT: B 276 ILE cc_start: 0.9107 (mm) cc_final: 0.8815 (mp) REVERT: B 296 GLU cc_start: 0.9515 (mm-30) cc_final: 0.8991 (mp0) REVERT: B 319 GLU cc_start: 0.9425 (tp30) cc_final: 0.9091 (mm-30) REVERT: B 404 LYS cc_start: 0.9153 (mttt) cc_final: 0.8766 (mttt) REVERT: B 445 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8025 (mmtt) REVERT: B 446 LEU cc_start: 0.8646 (mt) cc_final: 0.8002 (mp) REVERT: B 481 GLN cc_start: 0.8553 (mt0) cc_final: 0.8192 (mm-40) REVERT: B 542 MET cc_start: 0.8461 (mpp) cc_final: 0.8256 (mpp) REVERT: B 564 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7766 (mm-30) REVERT: B 597 MET cc_start: 0.9505 (ttt) cc_final: 0.8831 (tmm) REVERT: B 629 ASP cc_start: 0.8192 (t0) cc_final: 0.7853 (t0) REVERT: B 639 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8668 (pt) REVERT: B 790 ASP cc_start: 0.8221 (t70) cc_final: 0.7785 (t70) REVERT: B 809 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7792 (pmm) REVERT: B 812 LEU cc_start: 0.9298 (mp) cc_final: 0.8933 (mp) REVERT: B 834 ASN cc_start: 0.8099 (p0) cc_final: 0.7320 (p0) REVERT: B 860 MET cc_start: 0.8417 (ppp) cc_final: 0.8128 (ppp) REVERT: B 963 PHE cc_start: 0.8242 (t80) cc_final: 0.7772 (t80) REVERT: B 992 ILE cc_start: 0.9242 (pt) cc_final: 0.8898 (pt) REVERT: B 994 TYR cc_start: 0.7921 (m-80) cc_final: 0.7628 (m-10) REVERT: B 999 MET cc_start: 0.9146 (tpp) cc_final: 0.8569 (tpp) REVERT: B 1015 HIS cc_start: 0.8252 (m170) cc_final: 0.8015 (m170) REVERT: B 1169 MET cc_start: 0.8967 (mmt) cc_final: 0.8610 (mmm) REVERT: B 1205 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8548 (mp10) REVERT: B 1208 MET cc_start: 0.8963 (ptp) cc_final: 0.8702 (ptt) REVERT: C 16 ASP cc_start: 0.9038 (p0) cc_final: 0.8665 (p0) REVERT: C 37 MET cc_start: 0.9307 (tpp) cc_final: 0.8954 (tpp) REVERT: C 46 ILE cc_start: 0.9227 (mt) cc_final: 0.8280 (tp) REVERT: C 52 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8425 (tm-30) REVERT: C 58 LEU cc_start: 0.8615 (tp) cc_final: 0.8327 (tp) REVERT: C 67 LEU cc_start: 0.9683 (mm) cc_final: 0.9315 (tp) REVERT: C 157 CYS cc_start: 0.9217 (m) cc_final: 0.8453 (m) REVERT: C 165 LYS cc_start: 0.9107 (tttt) cc_final: 0.8791 (tttm) REVERT: C 169 LYS cc_start: 0.9446 (mtpt) cc_final: 0.9020 (ptpt) REVERT: D 35 LEU cc_start: 0.8570 (mt) cc_final: 0.8333 (pt) REVERT: D 131 GLU cc_start: 0.5941 (OUTLIER) cc_final: 0.5612 (pt0) REVERT: E 7 ARG cc_start: 0.9072 (ptm-80) cc_final: 0.8685 (ttp80) REVERT: E 58 MET cc_start: 0.9442 (ttp) cc_final: 0.8857 (ptm) REVERT: E 121 MET cc_start: 0.9279 (ppp) cc_final: 0.9023 (ppp) REVERT: E 194 GLU cc_start: 0.8278 (mp0) cc_final: 0.7840 (mp0) REVERT: F 81 THR cc_start: 0.9100 (m) cc_final: 0.8611 (p) REVERT: F 85 MET cc_start: 0.8421 (tmm) cc_final: 0.8144 (tmm) REVERT: F 88 TYR cc_start: 0.7478 (m-10) cc_final: 0.7268 (m-10) REVERT: F 103 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8275 (tmm) REVERT: F 122 MET cc_start: 0.9524 (ttm) cc_final: 0.8753 (tmm) REVERT: F 124 GLU cc_start: 0.9363 (tm-30) cc_final: 0.9019 (tm-30) REVERT: G 1 MET cc_start: 0.8839 (pmm) cc_final: 0.8620 (ptt) REVERT: G 44 TYR cc_start: 0.7850 (t80) cc_final: 0.7350 (t80) REVERT: H 1 MET cc_start: 0.2111 (pmm) cc_final: 0.0450 (tpt) REVERT: H 10 PHE cc_start: 0.8252 (m-80) cc_final: 0.7223 (m-80) REVERT: H 118 PHE cc_start: 0.9309 (m-80) cc_final: 0.8887 (m-10) REVERT: H 123 MET cc_start: 0.9337 (ppp) cc_final: 0.8970 (ppp) REVERT: I 48 LEU cc_start: 0.9587 (tp) cc_final: 0.9373 (pp) REVERT: I 65 ASP cc_start: 0.8976 (t0) cc_final: 0.8608 (t0) REVERT: I 68 LEU cc_start: 0.9440 (mp) cc_final: 0.8956 (mp) REVERT: Q 31 PHE cc_start: 0.5410 (t80) cc_final: 0.5160 (t80) REVERT: Q 114 MET cc_start: 0.9175 (mmm) cc_final: 0.8915 (mmm) REVERT: Q 352 MET cc_start: 0.7679 (tmm) cc_final: 0.7156 (tmm) REVERT: Q 401 TYR cc_start: 0.8106 (p90) cc_final: 0.7857 (p90) REVERT: M 133 TYR cc_start: 0.8991 (m-80) cc_final: 0.8745 (m-10) REVERT: M 137 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8767 (pm20) outliers start: 101 outliers final: 76 residues processed: 568 average time/residue: 0.1859 time to fit residues: 180.2760 Evaluate side-chains 586 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 498 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 767 GLN Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1092 TYR Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1205 GLN Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 18 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 224 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 233 optimal weight: 8.9990 chunk 250 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 235 optimal weight: 30.0000 chunk 356 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 338 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 363 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 HIS ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** 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 = 0.4213 r_free = 0.4213 target = 0.129375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.087021 restraints weight = 116976.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.089873 restraints weight = 52859.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.091810 restraints weight = 32298.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.093105 restraints weight = 23298.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.093974 restraints weight = 18794.122| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 36987 Z= 0.170 Angle : 0.787 16.892 50353 Z= 0.394 Chirality : 0.046 0.391 5666 Planarity : 0.005 0.073 6198 Dihedral : 15.512 167.041 5767 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.86 % Favored : 90.09 % Rotamer: Outliers : 2.54 % Allowed : 24.15 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 0.54 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.13), residues: 4259 helix: 0.74 (0.14), residues: 1417 sheet: -0.48 (0.21), residues: 616 loop : -1.93 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 434 TYR 0.020 0.002 TYR D 147 PHE 0.021 0.002 PHE J 8 TRP 0.030 0.002 TRP M 81 HIS 0.007 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (36958) covalent geometry : angle 0.77786 / 0.39 (50326) hydrogen bonds : bond 0.03950 / 4.32 ( 1400) hydrogen bonds : angle 4.97350 / 5.59 ( 3923) metal coordination : bond 0.01304 / 0.76 ( 29) metal coordination : angle 5.10540 / 6.91 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 511 time to evaluate : 0.936 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: A 34 LYS cc_start: 0.9088 (mppt) cc_final: 0.8650 (tttm) REVERT: A 95 PHE cc_start: 0.9394 (m-80) cc_final: 0.8983 (m-80) REVERT: A 117 GLU cc_start: 0.9719 (tt0) cc_final: 0.9504 (tm-30) REVERT: A 122 MET cc_start: 0.9307 (tmm) cc_final: 0.8888 (ppp) REVERT: A 225 ASN cc_start: 0.9047 (t0) cc_final: 0.8669 (t0) REVERT: A 234 MET cc_start: 0.9138 (ttt) cc_final: 0.8679 (ttt) REVERT: A 450 LEU cc_start: 0.9056 (mm) cc_final: 0.8600 (tp) REVERT: A 453 MET cc_start: 0.9129 (mmm) cc_final: 0.8713 (mmm) REVERT: A 456 MET cc_start: 0.8980 (mpp) cc_final: 0.8330 (mpp) REVERT: A 500 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: A 504 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7310 (mm) REVERT: A 505 CYS cc_start: 0.9085 (m) cc_final: 0.8745 (m) REVERT: A 521 MET cc_start: 0.8819 (mmm) cc_final: 0.8216 (mmm) REVERT: A 557 ASP cc_start: 0.8955 (t70) cc_final: 0.8732 (t0) REVERT: A 605 MET cc_start: 0.8843 (ttm) cc_final: 0.8479 (mtt) REVERT: A 662 PHE cc_start: 0.7778 (t80) cc_final: 0.7383 (t80) REVERT: A 696 GLU cc_start: 0.9206 (tt0) cc_final: 0.8888 (tp30) REVERT: A 701 LEU cc_start: 0.9128 (pt) cc_final: 0.8286 (pt) REVERT: A 746 MET cc_start: 0.9478 (OUTLIER) cc_final: 0.9220 (mmm) REVERT: A 748 MET cc_start: 0.8454 (ppp) cc_final: 0.8071 (ppp) REVERT: A 767 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7646 (tt0) REVERT: A 786 HIS cc_start: 0.8581 (m-70) cc_final: 0.7975 (m-70) REVERT: A 812 GLU cc_start: 0.9453 (mp0) cc_final: 0.8858 (mm-30) REVERT: A 818 MET cc_start: 0.9249 (tpp) cc_final: 0.8691 (mmt) REVERT: A 846 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8307 (mt-10) REVERT: A 847 ASP cc_start: 0.8007 (p0) cc_final: 0.7404 (p0) REVERT: A 874 ASP cc_start: 0.7367 (p0) cc_final: 0.6658 (m-30) REVERT: A 894 GLU cc_start: 0.9154 (pp20) cc_final: 0.8901 (pp20) REVERT: A 956 LEU cc_start: 0.8682 (mt) cc_final: 0.8234 (tt) REVERT: A 1079 MET cc_start: 0.7082 (mtp) cc_final: 0.6765 (mtp) REVERT: A 1111 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8530 (tpp) REVERT: A 1120 LEU cc_start: 0.9638 (mt) cc_final: 0.9179 (tp) REVERT: A 1327 ILE cc_start: 0.9399 (tt) cc_final: 0.9132 (tp) REVERT: A 1368 MET cc_start: 0.9118 (mtp) cc_final: 0.8863 (mtp) REVERT: A 1375 MET cc_start: 0.8918 (tmm) cc_final: 0.8395 (tmm) REVERT: A 1400 CYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8780 (p) REVERT: A 1444 MET cc_start: 0.8582 (tpp) cc_final: 0.8300 (tpp) REVERT: B 112 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8421 (mm) REVERT: B 239 GLU cc_start: 0.8340 (tt0) cc_final: 0.7583 (tm-30) REVERT: B 273 LEU cc_start: 0.8157 (mp) cc_final: 0.7754 (tt) REVERT: B 276 ILE cc_start: 0.9066 (mm) cc_final: 0.8768 (mp) REVERT: B 296 GLU cc_start: 0.9508 (mm-30) cc_final: 0.8975 (mp0) REVERT: B 319 GLU cc_start: 0.9421 (tp30) cc_final: 0.9086 (mm-30) REVERT: B 376 PHE cc_start: 0.9419 (OUTLIER) cc_final: 0.8737 (m-10) REVERT: B 404 LYS cc_start: 0.9143 (mttt) cc_final: 0.8760 (mttt) REVERT: B 444 MET cc_start: 0.7320 (ppp) cc_final: 0.6997 (ppp) REVERT: B 445 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7931 (mmtt) REVERT: B 446 LEU cc_start: 0.8632 (mt) cc_final: 0.7995 (mp) REVERT: B 481 GLN cc_start: 0.8596 (mt0) cc_final: 0.8207 (mm-40) REVERT: B 521 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9255 (mm) REVERT: B 629 ASP cc_start: 0.8196 (t0) cc_final: 0.7856 (t0) REVERT: B 639 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8563 (pt) REVERT: B 705 MET cc_start: 0.8296 (mmm) cc_final: 0.7635 (mmm) REVERT: B 790 ASP cc_start: 0.8218 (t70) cc_final: 0.7770 (t70) REVERT: B 809 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7821 (pmm) REVERT: B 812 LEU cc_start: 0.9287 (mp) cc_final: 0.8941 (mp) REVERT: B 834 ASN cc_start: 0.8070 (p0) cc_final: 0.7268 (p0) REVERT: B 860 MET cc_start: 0.8418 (ppp) cc_final: 0.8141 (ppp) REVERT: B 963 PHE cc_start: 0.8171 (t80) cc_final: 0.7642 (t80) REVERT: B 992 ILE cc_start: 0.9330 (pt) cc_final: 0.8945 (pt) REVERT: B 994 TYR cc_start: 0.7858 (m-80) cc_final: 0.7588 (m-80) REVERT: B 999 MET cc_start: 0.9147 (tpp) cc_final: 0.8523 (tpp) REVERT: B 1015 HIS cc_start: 0.8206 (m170) cc_final: 0.7806 (m170) REVERT: B 1072 MET cc_start: 0.7746 (tpt) cc_final: 0.7461 (tpt) REVERT: B 1098 MET cc_start: 0.8713 (mpp) cc_final: 0.8027 (mmp) REVERT: B 1169 MET cc_start: 0.8973 (mmt) cc_final: 0.8606 (mmm) REVERT: B 1205 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8534 (mp10) REVERT: B 1208 MET cc_start: 0.8949 (ptp) cc_final: 0.8690 (ptt) REVERT: C 16 ASP cc_start: 0.9034 (p0) cc_final: 0.8653 (p0) REVERT: C 37 MET cc_start: 0.9255 (tpp) cc_final: 0.8906 (tpp) REVERT: C 46 ILE cc_start: 0.9172 (mt) cc_final: 0.8283 (mt) REVERT: C 52 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8417 (tm-30) REVERT: C 58 LEU cc_start: 0.8555 (tp) cc_final: 0.8262 (tp) REVERT: C 67 LEU cc_start: 0.9677 (mm) cc_final: 0.9232 (tp) REVERT: C 157 CYS cc_start: 0.9256 (m) cc_final: 0.8760 (m) REVERT: C 165 LYS cc_start: 0.9080 (tttt) cc_final: 0.8793 (tttm) REVERT: C 169 LYS cc_start: 0.9440 (mtpt) cc_final: 0.9022 (ptpt) REVERT: D 131 GLU cc_start: 0.6051 (OUTLIER) cc_final: 0.5714 (pt0) REVERT: E 7 ARG cc_start: 0.9078 (ptm-80) cc_final: 0.8657 (ttp80) REVERT: E 58 MET cc_start: 0.9465 (ttp) cc_final: 0.8923 (tmm) REVERT: E 121 MET cc_start: 0.9291 (ppp) cc_final: 0.9022 (ppp) REVERT: E 194 GLU cc_start: 0.8323 (mp0) cc_final: 0.7944 (mp0) REVERT: F 81 THR cc_start: 0.9096 (m) cc_final: 0.8603 (p) REVERT: F 85 MET cc_start: 0.8313 (tmm) cc_final: 0.8046 (tmm) REVERT: F 103 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8349 (tmm) REVERT: F 122 MET cc_start: 0.9533 (ttm) cc_final: 0.8761 (tmm) REVERT: F 124 GLU cc_start: 0.9376 (tm-30) cc_final: 0.9035 (tm-30) REVERT: G 1 MET cc_start: 0.8846 (pmm) cc_final: 0.8630 (ptt) REVERT: G 44 TYR cc_start: 0.7798 (t80) cc_final: 0.7246 (t80) REVERT: H 1 MET cc_start: 0.1984 (pmm) cc_final: 0.0537 (tpt) REVERT: H 10 PHE cc_start: 0.8191 (m-80) cc_final: 0.7196 (m-80) REVERT: H 97 MET cc_start: 0.7701 (ppp) cc_final: 0.7494 (ppp) REVERT: H 118 PHE cc_start: 0.9220 (m-80) cc_final: 0.8701 (m-10) REVERT: H 123 MET cc_start: 0.9356 (ppp) cc_final: 0.8982 (ppp) REVERT: I 48 LEU cc_start: 0.9576 (tp) cc_final: 0.9370 (pp) REVERT: I 65 ASP cc_start: 0.8961 (t0) cc_final: 0.8588 (t0) REVERT: I 68 LEU cc_start: 0.9439 (mp) cc_final: 0.8960 (mp) REVERT: K 92 ASN cc_start: 0.9735 (m-40) cc_final: 0.9400 (m110) REVERT: Q 31 PHE cc_start: 0.5307 (t80) cc_final: 0.5020 (t80) REVERT: Q 114 MET cc_start: 0.9149 (mmm) cc_final: 0.8895 (mmm) REVERT: Q 352 MET cc_start: 0.7508 (tmm) cc_final: 0.7085 (tmm) REVERT: Q 401 TYR cc_start: 0.8089 (p90) cc_final: 0.7831 (p90) REVERT: M 133 TYR cc_start: 0.8985 (m-80) cc_final: 0.8763 (m-10) REVERT: M 137 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8750 (pm20) outliers start: 95 outliers final: 73 residues processed: 571 average time/residue: 0.1866 time to fit residues: 180.8147 Evaluate side-chains 584 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 495 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 767 GLN Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1389 PHE Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 1028 GLU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1205 GLN Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 18 PHE Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 224 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 90 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 278 optimal weight: 0.3980 chunk 431 optimal weight: 7.9990 chunk 361 optimal weight: 4.9990 chunk 391 optimal weight: 6.9990 chunk 415 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 351 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 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 = 0.4123 r_free = 0.4123 target = 0.123813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.084632 restraints weight = 121064.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.087502 restraints weight = 54723.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.089438 restraints weight = 33503.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.090730 restraints weight = 24248.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.091610 restraints weight = 19639.554| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36987 Z= 0.185 Angle : 0.791 16.506 50353 Z= 0.398 Chirality : 0.046 0.357 5666 Planarity : 0.005 0.078 6198 Dihedral : 15.483 165.863 5767 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.12 % Favored : 89.83 % Rotamer: Outliers : 2.81 % Allowed : 24.02 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.37 % Twisted Proline : 0.54 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.13), residues: 4259 helix: 0.74 (0.14), residues: 1416 sheet: -0.45 (0.21), residues: 608 loop : -1.95 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 434 TYR 0.018 0.002 TYR B 486 PHE 0.024 0.002 PHE B 360 TRP 0.020 0.002 TRP M 81 HIS 0.008 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (36958) covalent geometry : angle 0.78289 / 0.40 (50326) hydrogen bonds : bond 0.04025 / 4.39 ( 1400) hydrogen bonds : angle 4.99471 / 5.63 ( 3923) metal coordination : bond 0.01221 / 0.75 ( 29) metal coordination : angle 5.08406 / 6.80 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8347.62 seconds wall clock time: 144 minutes 18.22 seconds (8658.22 seconds total)