Starting phenix.real_space_refine on Sat Mar 7 01:58:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mk9_23887/03_2026/7mk9_23887.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mk9_23887/03_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_23887/03_2026/7mk9_23887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mk9_23887/03_2026/7mk9_23887.map" model { file = "/net/cci-nas-00/data/ceres_data/7mk9_23887/03_2026/7mk9_23887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mk9_23887/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 7.89, per 1000 atoms: 0.22 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: 3.47 Conformation dependent library (CDL) restraints added in 1.2 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: 4.88 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: 11.50 Time building geometry restraints manager: 4.68 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=" 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=" N ASP A 188 " pdb=" CA ASP A 188 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.41e+00 bond pdb=" N ASP B1186 " pdb=" CA ASP B1186 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.15e-02 7.56e+03 8.54e+00 bond pdb=" N CYS B1182 " pdb=" CA CYS B1182 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.18e-02 7.18e+03 8.53e+00 ... (remaining 36953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 49312 2.44 - 4.89: 919 4.89 - 7.33: 72 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: 21641 35.82 - 71.63: 738 71.63 - 107.45: 51 107.45 - 143.27: 3 143.27 - 179.08: 1 Dihedral angle restraints: 22434 sinusoidal: 9894 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 22431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4653 0.059 - 0.118: 903 0.118 - 0.177: 98 0.177 - 0.236: 10 0.236 - 0.295: 2 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 -2.66 -2.36 -0.30 2.00e-01 2.50e+01 2.18e+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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.050 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 45.780 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 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= 0.259 Angle : 0.882 57.086 50353 Z= 0.473 Chirality : 0.046 0.295 5666 Planarity : 0.004 0.097 6198 Dihedral : 16.824 179.082 14308 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 covalent geometry : bond 0.00507 (36958) covalent geometry : angle 0.80020 (50326) hydrogen bonds : bond 0.19418 ( 1400) hydrogen bonds : angle 7.49755 ( 3923) metal coordination : bond 0.05343 ( 29) metal coordination : angle 16.08870 ( 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 : 0.906 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: 0.2152 time to fit residues: 348.6738 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 : 1.147 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 253 ASN A 399 HIS A 447 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A 631 HIS 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 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 GLN B 786 ASN B 881 ASN ** 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 M 239 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.123728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.083090 restraints weight = 116925.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.085932 restraints weight = 53662.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.087856 restraints weight = 33128.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.089149 restraints weight = 24094.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.090005 restraints weight = 19528.184| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 36987 Z= 0.196 Angle : 0.811 25.062 50353 Z= 0.412 Chirality : 0.047 0.307 5666 Planarity : 0.005 0.066 6198 Dihedral : 16.072 174.642 5807 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.42 % Favored : 89.53 % Rotamer: Outliers : 2.06 % Allowed : 13.44 % Favored : 84.50 % 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: -1.33 (0.13), residues: 4259 helix: 0.59 (0.14), residues: 1393 sheet: -0.67 (0.20), residues: 660 loop : -1.99 (0.13), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 97 TYR 0.022 0.002 TYR B 830 PHE 0.034 0.002 PHE J 8 TRP 0.011 0.001 TRP A 954 HIS 0.011 0.001 HIS A1387 Details of bonding type rmsd covalent geometry : bond 0.00429 (36958) covalent geometry : angle 0.78404 (50326) hydrogen bonds : bond 0.05091 ( 1400) hydrogen bonds : angle 5.78465 ( 3923) metal coordination : bond 0.01865 ( 29) metal coordination : angle 8.92272 ( 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 715 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 638 time to evaluate : 1.190 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: 0.9247 (mppt) cc_final: 0.8756 (tttt) REVERT: A 41 MET cc_start: 0.6833 (tpt) cc_final: 0.6615 (tpt) REVERT: A 92 HIS cc_start: 0.8020 (t-90) cc_final: 0.6849 (t-90) REVERT: A 117 GLU cc_start: 0.9707 (tt0) cc_final: 0.9411 (tm-30) REVERT: A 122 MET cc_start: 0.9345 (tmm) cc_final: 0.9014 (ppp) REVERT: A 225 ASN cc_start: 0.8902 (t0) cc_final: 0.8516 (t0) REVERT: A 293 GLU cc_start: 0.9029 (tp30) cc_final: 0.8688 (tm-30) REVERT: A 304 MET cc_start: 0.8982 (tpt) cc_final: 0.8703 (tpt) REVERT: A 437 MET cc_start: 0.7388 (mtt) cc_final: 0.7122 (ptp) REVERT: A 445 ASN cc_start: 0.9041 (t0) cc_final: 0.8435 (t0) REVERT: A 450 LEU cc_start: 0.9195 (mm) cc_final: 0.8740 (tp) REVERT: A 456 MET cc_start: 0.8789 (mpp) cc_final: 0.7769 (mpp) REVERT: A 487 MET cc_start: 0.7143 (mmm) cc_final: 0.6321 (mmm) REVERT: A 500 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: A 505 CYS cc_start: 0.9170 (m) cc_final: 0.8817 (m) REVERT: A 521 MET cc_start: 0.8784 (mmm) cc_final: 0.7999 (mmm) REVERT: A 557 ASP cc_start: 0.9157 (t70) cc_final: 0.8933 (t0) REVERT: A 662 PHE cc_start: 0.8470 (t80) cc_final: 0.7870 (t80) REVERT: A 696 GLU cc_start: 0.9170 (tt0) cc_final: 0.8922 (tp30) REVERT: A 741 ASN cc_start: 0.8407 (t0) cc_final: 0.7804 (t0) REVERT: A 761 MET cc_start: 0.9062 (mtm) cc_final: 0.8477 (mmp) REVERT: A 767 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: A 786 HIS cc_start: 0.8571 (m-70) cc_final: 0.7646 (m-70) REVERT: A 818 MET cc_start: 0.9346 (tpp) cc_final: 0.9133 (tpp) REVERT: A 846 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8388 (mt-10) REVERT: A 847 ASP cc_start: 0.8029 (p0) cc_final: 0.7598 (p0) REVERT: A 874 ASP cc_start: 0.7225 (p0) cc_final: 0.6770 (m-30) REVERT: A 1063 MET cc_start: 0.8488 (mmp) cc_final: 0.8273 (mmm) REVERT: A 1120 LEU cc_start: 0.9591 (mt) cc_final: 0.9157 (tp) REVERT: A 1139 GLU cc_start: 0.9159 (tt0) cc_final: 0.8928 (tp30) REVERT: A 1277 GLU cc_start: 0.9512 (pm20) cc_final: 0.9201 (pm20) REVERT: A 1285 MET cc_start: 0.8573 (mmm) cc_final: 0.8351 (mmm) REVERT: A 1315 GLU cc_start: 0.9003 (mp0) cc_final: 0.8741 (mp0) REVERT: A 1317 MET cc_start: 0.9299 (mmm) cc_final: 0.8812 (mmm) REVERT: A 1364 ASN cc_start: 0.8414 (t0) cc_final: 0.7969 (t0) REVERT: A 1419 ASP cc_start: 0.8207 (t0) cc_final: 0.7753 (t0) REVERT: A 1427 ASN cc_start: 0.8434 (m-40) cc_final: 0.8113 (t0) REVERT: B 70 ILE cc_start: 0.8081 (mm) cc_final: 0.7847 (mm) REVERT: B 173 MET cc_start: 0.5955 (tpt) cc_final: 0.5579 (tpt) REVERT: B 239 GLU cc_start: 0.8279 (tt0) cc_final: 0.7633 (tm-30) REVERT: B 296 GLU cc_start: 0.9426 (mm-30) cc_final: 0.9042 (mp0) REVERT: B 361 LEU cc_start: 0.9044 (tp) cc_final: 0.8495 (tt) REVERT: B 381 MET cc_start: 0.9385 (OUTLIER) cc_final: 0.9065 (tpt) REVERT: B 404 LYS cc_start: 0.9153 (mttt) cc_final: 0.8817 (mttt) REVERT: B 576 ASP cc_start: 0.9324 (p0) cc_final: 0.8931 (t70) REVERT: B 597 MET cc_start: 0.9589 (tpt) cc_final: 0.9038 (tpp) REVERT: B 610 ASN cc_start: 0.8550 (t0) cc_final: 0.8297 (t0) REVERT: B 629 ASP cc_start: 0.7692 (t0) cc_final: 0.7358 (t0) REVERT: B 705 MET cc_start: 0.7428 (mmm) cc_final: 0.6616 (mmm) REVERT: B 767 ASN cc_start: 0.8130 (m110) cc_final: 0.7751 (m110) REVERT: B 792 MET cc_start: 0.8515 (mmm) cc_final: 0.8163 (mmm) REVERT: B 809 MET cc_start: 0.8265 (pmm) cc_final: 0.7735 (pmm) REVERT: B 834 ASN cc_start: 0.8262 (p0) cc_final: 0.7500 (p0) REVERT: B 860 MET cc_start: 0.8430 (ppp) cc_final: 0.7907 (ppp) REVERT: B 963 PHE cc_start: 0.8592 (t80) cc_final: 0.8036 (t80) REVERT: B 967 ARG cc_start: 0.8601 (ttp-170) cc_final: 0.7807 (ttp-110) REVERT: B 999 MET cc_start: 0.9110 (tpp) cc_final: 0.8205 (mmt) REVERT: B 1069 PHE cc_start: 0.9028 (m-10) cc_final: 0.8351 (m-10) REVERT: B 1082 MET cc_start: 0.9076 (tpt) cc_final: 0.8828 (tpt) REVERT: B 1094 ARG cc_start: 0.8435 (ttt-90) cc_final: 0.7995 (ttt-90) REVERT: B 1095 LEU cc_start: 0.9139 (mm) cc_final: 0.8372 (mm) REVERT: B 1122 ARG cc_start: 0.8388 (tmm-80) cc_final: 0.7991 (ttt180) REVERT: B 1133 MET cc_start: 0.9028 (mtp) cc_final: 0.8700 (mtm) REVERT: B 1168 LEU cc_start: 0.8925 (mm) cc_final: 0.8563 (mm) REVERT: C 16 ASP cc_start: 0.9088 (p0) cc_final: 0.8363 (p0) REVERT: C 46 ILE cc_start: 0.9209 (mt) cc_final: 0.8653 (tp) REVERT: C 52 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8582 (tm-30) REVERT: C 69 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9440 (mm) REVERT: C 157 CYS cc_start: 0.9306 (m) cc_final: 0.8975 (m) REVERT: C 165 LYS cc_start: 0.9015 (tttt) cc_final: 0.8724 (tttt) REVERT: C 169 LYS cc_start: 0.9428 (mtpt) cc_final: 0.9228 (ptpp) REVERT: C 233 GLU cc_start: 0.8973 (tt0) cc_final: 0.7955 (tt0) REVERT: E 7 ARG cc_start: 0.9055 (ptm-80) cc_final: 0.8667 (ttp80) REVERT: E 58 MET cc_start: 0.9410 (ttp) cc_final: 0.8948 (tmm) REVERT: E 121 MET cc_start: 0.9304 (ppp) cc_final: 0.9012 (ppp) REVERT: E 194 GLU cc_start: 0.8114 (mp0) cc_final: 0.7768 (mp0) REVERT: E 208 TYR cc_start: 0.7389 (t80) cc_final: 0.6800 (t80) REVERT: E 211 TYR cc_start: 0.8740 (m-80) cc_final: 0.8451 (m-80) REVERT: F 81 THR cc_start: 0.9018 (m) cc_final: 0.8313 (p) REVERT: F 103 MET cc_start: 0.9060 (tmm) cc_final: 0.8813 (tmm) REVERT: F 124 GLU cc_start: 0.9171 (tm-30) cc_final: 0.8772 (tm-30) REVERT: F 140 ASP cc_start: 0.9144 (t0) cc_final: 0.8511 (p0) REVERT: G 21 ARG cc_start: 0.7911 (ttp80) cc_final: 0.7634 (ttp80) REVERT: H 1 MET cc_start: 0.0939 (pmm) cc_final: -0.0587 (tpt) REVERT: H 10 PHE cc_start: 0.8531 (m-80) cc_final: 0.7410 (m-80) REVERT: H 97 MET cc_start: 0.8112 (ppp) cc_final: 0.7677 (ppp) REVERT: H 123 MET cc_start: 0.9107 (ppp) cc_final: 0.8779 (ppp) REVERT: I 13 MET cc_start: 0.7917 (tpt) cc_final: 0.7678 (tpt) REVERT: I 65 ASP cc_start: 0.9307 (t70) cc_final: 0.8820 (t70) REVERT: I 68 LEU cc_start: 0.9480 (mp) cc_final: 0.9145 (mp) REVERT: J 6 ARG cc_start: 0.8029 (mmm-85) cc_final: 0.7761 (mmm-85) REVERT: J 16 ASP cc_start: 0.9015 (p0) cc_final: 0.8785 (p0) REVERT: K 38 GLU cc_start: 0.9133 (mp0) cc_final: 0.8840 (mp0) REVERT: K 53 ASP cc_start: 0.8271 (t0) cc_final: 0.7618 (t70) REVERT: K 92 ASN cc_start: 0.9364 (m110) cc_final: 0.9017 (m-40) REVERT: Q 28 ARG cc_start: 0.5908 (tpt-90) cc_final: 0.5686 (ttt180) REVERT: Q 365 TYR cc_start: 0.7895 (t80) cc_final: 0.6964 (t80) REVERT: Q 401 TYR cc_start: 0.7636 (p90) cc_final: 0.7370 (p90) REVERT: M 81 TRP cc_start: 0.8636 (m-10) cc_final: 0.8409 (m100) REVERT: M 132 GLU cc_start: 0.8245 (mt-10) cc_final: 0.8010 (mm-30) REVERT: M 137 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8822 (pm20) outliers start: 77 outliers final: 54 residues processed: 684 average time/residue: 0.1964 time to fit residues: 226.7206 Evaluate side-chains 599 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 540 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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 507 VAL Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 767 GLN 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 863 VAL 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 30 SER 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 314 LEU Chi-restraints excluded: chain B residue 317 CYS 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 539 LEU Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 1066 SER 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 1202 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 118 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 G residue 168 LEU 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 L residue 53 HIS Chi-restraints excluded: chain Q residue 119 LEU 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: 8.9990 chunk 285 optimal weight: 10.0000 chunk 247 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 210 optimal weight: 8.9990 chunk 203 optimal weight: 8.9990 chunk 349 optimal weight: 20.0000 chunk 384 optimal weight: 9.9990 chunk 291 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 GLN A 439 ASN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** D 179 GLN ** 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 ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.131892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.090010 restraints weight = 116407.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.092829 restraints weight = 51959.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.094742 restraints weight = 31536.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.096036 restraints weight = 22665.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.096878 restraints weight = 18226.248| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 36987 Z= 0.156 Angle : 0.740 21.041 50353 Z= 0.376 Chirality : 0.045 0.206 5666 Planarity : 0.005 0.064 6198 Dihedral : 15.996 169.154 5803 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.56 % Favored : 90.40 % Rotamer: Outliers : 3.11 % Allowed : 15.72 % Favored : 81.18 % 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: -1.26 (0.13), residues: 4259 helix: 0.65 (0.14), residues: 1399 sheet: -0.63 (0.20), residues: 660 loop : -1.96 (0.13), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 72 TYR 0.020 0.002 TYR F 88 PHE 0.031 0.002 PHE J 8 TRP 0.011 0.001 TRP A 185 HIS 0.010 0.001 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00340 (36958) covalent geometry : angle 0.71988 (50326) hydrogen bonds : bond 0.04389 ( 1400) hydrogen bonds : angle 5.36991 ( 3923) metal coordination : bond 0.02000 ( 29) metal coordination : angle 7.49771 ( 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 727 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 611 time to evaluate : 1.102 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: 0.9205 (mppt) cc_final: 0.8671 (tttp) REVERT: A 41 MET cc_start: 0.7004 (tpt) cc_final: 0.6664 (tpt) REVERT: A 74 MET cc_start: 0.8488 (ttt) cc_final: 0.8218 (mtt) REVERT: A 92 HIS cc_start: 0.7963 (t-90) cc_final: 0.5991 (t-90) REVERT: A 95 PHE cc_start: 0.9584 (m-80) cc_final: 0.8294 (m-80) REVERT: A 117 GLU cc_start: 0.9706 (tt0) cc_final: 0.9454 (tm-30) REVERT: A 122 MET cc_start: 0.9328 (tmm) cc_final: 0.9050 (ppp) REVERT: A 225 ASN cc_start: 0.8979 (t0) cc_final: 0.8636 (t0) REVERT: A 234 MET cc_start: 0.9453 (ttm) cc_final: 0.8883 (tpp) REVERT: A 293 GLU cc_start: 0.9012 (tp30) cc_final: 0.8707 (tm-30) REVERT: A 445 ASN cc_start: 0.8965 (t0) cc_final: 0.8420 (t0) REVERT: A 450 LEU cc_start: 0.9181 (mm) cc_final: 0.8677 (tp) REVERT: A 456 MET cc_start: 0.9015 (mpp) cc_final: 0.7842 (mpp) REVERT: A 487 MET cc_start: 0.7583 (mmm) cc_final: 0.6963 (mmm) REVERT: A 500 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: A 505 CYS cc_start: 0.9194 (m) cc_final: 0.8805 (m) REVERT: A 521 MET cc_start: 0.8798 (mmm) cc_final: 0.8079 (mmm) REVERT: A 557 ASP cc_start: 0.9090 (t70) cc_final: 0.8854 (t0) REVERT: A 605 MET cc_start: 0.8946 (ttm) cc_final: 0.8533 (mtt) REVERT: A 662 PHE cc_start: 0.7950 (t80) cc_final: 0.7622 (t80) REVERT: A 696 GLU cc_start: 0.9178 (tt0) cc_final: 0.8916 (tp30) REVERT: A 741 ASN cc_start: 0.8218 (t0) cc_final: 0.7639 (t0) REVERT: A 748 MET cc_start: 0.8482 (ppp) cc_final: 0.8115 (ppp) REVERT: A 761 MET cc_start: 0.9087 (mtm) cc_final: 0.8444 (mmp) REVERT: A 786 HIS cc_start: 0.8544 (m-70) cc_final: 0.7596 (m-70) REVERT: A 846 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8319 (mt-10) REVERT: A 847 ASP cc_start: 0.8009 (p0) cc_final: 0.7481 (p0) REVERT: A 1079 MET cc_start: 0.7027 (mtp) cc_final: 0.6786 (mtp) REVERT: A 1120 LEU cc_start: 0.9608 (mt) cc_final: 0.9165 (tp) REVERT: A 1277 GLU cc_start: 0.9546 (pm20) cc_final: 0.9256 (pm20) REVERT: A 1315 GLU cc_start: 0.8995 (mp0) cc_final: 0.8701 (mp0) REVERT: A 1317 MET cc_start: 0.9294 (mmm) cc_final: 0.8892 (mmm) REVERT: A 1364 ASN cc_start: 0.8527 (t0) cc_final: 0.8070 (t0) REVERT: A 1419 ASP cc_start: 0.8253 (t0) cc_final: 0.7774 (t0) REVERT: A 1427 ASN cc_start: 0.8588 (m-40) cc_final: 0.8282 (t0) REVERT: A 1433 MET cc_start: 0.9274 (ppp) cc_final: 0.8845 (ppp) REVERT: B 70 ILE cc_start: 0.8083 (mm) cc_final: 0.7875 (mm) REVERT: B 239 GLU cc_start: 0.8402 (tt0) cc_final: 0.7664 (tm-30) REVERT: B 296 GLU cc_start: 0.9450 (mm-30) cc_final: 0.8972 (mp0) REVERT: B 313 MET cc_start: 0.9730 (mmm) cc_final: 0.9484 (tpp) REVERT: B 361 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8679 (tp) REVERT: B 404 LYS cc_start: 0.9156 (mttt) cc_final: 0.8776 (mttt) REVERT: B 481 GLN cc_start: 0.8324 (mt0) cc_final: 0.8092 (mt0) REVERT: B 521 LEU cc_start: 0.9514 (mp) cc_final: 0.9264 (mm) REVERT: B 576 ASP cc_start: 0.9329 (p0) cc_final: 0.8910 (t70) REVERT: B 610 ASN cc_start: 0.8505 (t0) cc_final: 0.8217 (t0) REVERT: B 629 ASP cc_start: 0.7836 (t0) cc_final: 0.7434 (t0) REVERT: B 705 MET cc_start: 0.7514 (mmm) cc_final: 0.6725 (mmm) REVERT: B 809 MET cc_start: 0.8173 (pmm) cc_final: 0.7559 (pmm) REVERT: B 834 ASN cc_start: 0.8194 (p0) cc_final: 0.7456 (p0) REVERT: B 860 MET cc_start: 0.8272 (ppp) cc_final: 0.7817 (ppp) REVERT: B 963 PHE cc_start: 0.8597 (t80) cc_final: 0.7976 (t80) REVERT: B 1013 ASN cc_start: 0.8938 (t0) cc_final: 0.8536 (t0) REVERT: B 1074 ASN cc_start: 0.8945 (t0) cc_final: 0.8725 (t0) REVERT: B 1082 MET cc_start: 0.9009 (tpt) cc_final: 0.8792 (tpt) REVERT: B 1095 LEU cc_start: 0.9151 (mm) cc_final: 0.8769 (mm) REVERT: B 1100 ASP cc_start: 0.8445 (p0) cc_final: 0.8208 (t0) REVERT: B 1133 MET cc_start: 0.8942 (mtp) cc_final: 0.8542 (mtm) REVERT: B 1139 ILE cc_start: 0.9710 (mm) cc_final: 0.9481 (mt) REVERT: B 1168 LEU cc_start: 0.8999 (mm) cc_final: 0.8667 (mm) REVERT: B 1208 MET cc_start: 0.9016 (ptt) cc_final: 0.8372 (ptp) REVERT: C 19 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8523 (t70) REVERT: C 37 MET cc_start: 0.9384 (tpp) cc_final: 0.9152 (tpp) REVERT: C 46 ILE cc_start: 0.9204 (mt) cc_final: 0.8414 (tp) REVERT: C 52 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8546 (tm-30) REVERT: C 157 CYS cc_start: 0.9279 (m) cc_final: 0.8947 (m) REVERT: C 165 LYS cc_start: 0.9058 (tttt) cc_final: 0.8744 (tttm) REVERT: C 169 LYS cc_start: 0.9474 (mtpt) cc_final: 0.8882 (ptpt) REVERT: C 233 GLU cc_start: 0.8999 (tt0) cc_final: 0.8747 (tt0) REVERT: D 35 LEU cc_start: 0.8316 (mt) cc_final: 0.7996 (pt) REVERT: D 131 GLU cc_start: 0.5847 (OUTLIER) cc_final: 0.5382 (pt0) REVERT: E 7 ARG cc_start: 0.9058 (ptm-80) cc_final: 0.8674 (ttp80) REVERT: E 58 MET cc_start: 0.9374 (ttp) cc_final: 0.8817 (tmm) REVERT: E 121 MET cc_start: 0.9239 (ppp) cc_final: 0.8920 (ppp) REVERT: E 194 GLU cc_start: 0.8250 (mp0) cc_final: 0.7921 (mp0) REVERT: F 81 THR cc_start: 0.9111 (m) cc_final: 0.8488 (p) REVERT: F 124 GLU cc_start: 0.9257 (tm-30) cc_final: 0.8824 (tm-30) REVERT: G 37 SER cc_start: 0.8862 (p) cc_final: 0.8588 (p) REVERT: G 44 TYR cc_start: 0.7937 (t80) cc_final: 0.7590 (t80) REVERT: H 1 MET cc_start: 0.1227 (pmm) cc_final: -0.0407 (tpt) REVERT: H 10 PHE cc_start: 0.8404 (m-80) cc_final: 0.7270 (m-80) REVERT: H 97 MET cc_start: 0.8282 (ppp) cc_final: 0.7874 (ppp) REVERT: H 123 MET cc_start: 0.9160 (ppp) cc_final: 0.8841 (ppp) REVERT: H 133 ASN cc_start: 0.8893 (t0) cc_final: 0.8601 (m110) REVERT: I 68 LEU cc_start: 0.9528 (mp) cc_final: 0.9270 (mp) REVERT: K 38 GLU cc_start: 0.9070 (mp0) cc_final: 0.8520 (mp0) REVERT: K 53 ASP cc_start: 0.8338 (t0) cc_final: 0.7960 (t70) REVERT: K 92 ASN cc_start: 0.9352 (m110) cc_final: 0.8983 (m-40) REVERT: L 50 ASP cc_start: 0.7905 (p0) cc_final: 0.7663 (p0) REVERT: Q 31 PHE cc_start: 0.5831 (t80) cc_final: 0.5615 (t80) REVERT: Q 401 TYR cc_start: 0.7991 (p90) cc_final: 0.7715 (p90) REVERT: M 72 ARG cc_start: 0.8458 (ttp80) cc_final: 0.7919 (ttp80) REVERT: M 81 TRP cc_start: 0.8699 (m-10) cc_final: 0.8426 (m100) outliers start: 116 outliers final: 69 residues processed: 675 average time/residue: 0.1984 time to fit residues: 226.2815 Evaluate side-chains 608 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 535 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 262 LEU 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 737 LEU Chi-restraints excluded: chain A residue 783 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 1105 LEU Chi-restraints excluded: chain A residue 1111 MET 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 30 SER Chi-restraints excluded: chain B residue 45 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 289 LEU Chi-restraints excluded: chain B residue 361 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 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 854 LEU 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 1147 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 19 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 28 GLN 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 86 THR Chi-restraints excluded: chain F residue 94 LEU 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 G residue 168 LEU 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 24 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 345 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 105 optimal weight: 0.0470 chunk 349 optimal weight: 50.0000 chunk 152 optimal weight: 9.9990 chunk 237 optimal weight: 40.0000 chunk 247 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 409 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 427 optimal weight: 50.0000 chunk 418 optimal weight: 0.4980 chunk 249 optimal weight: 0.1980 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 451 HIS A 510 GLN A 654 ASN A 802 ASN A1070 GLN ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1390 ASN ** B 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 179 GLN E 136 ASN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.125166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.085160 restraints weight = 114843.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.088010 restraints weight = 52098.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.089950 restraints weight = 31918.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.091253 restraints weight = 23046.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.092028 restraints weight = 18546.900| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3240 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= 0.137 Angle : 0.733 15.976 50353 Z= 0.368 Chirality : 0.045 0.350 5666 Planarity : 0.004 0.067 6198 Dihedral : 15.897 170.150 5803 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.49 % Favored : 90.47 % Rotamer: Outliers : 2.73 % Allowed : 17.94 % Favored : 79.33 % 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: -1.14 (0.13), residues: 4259 helix: 0.76 (0.14), residues: 1401 sheet: -0.56 (0.20), residues: 655 loop : -1.90 (0.13), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 148 TYR 0.018 0.001 TYR D 147 PHE 0.031 0.002 PHE B1158 TRP 0.012 0.001 TRP A 185 HIS 0.008 0.001 HIS B 363 Details of bonding type rmsd covalent geometry : bond 0.00301 (36958) covalent geometry : angle 0.71906 (50326) hydrogen bonds : bond 0.03951 ( 1400) hydrogen bonds : angle 5.08481 ( 3923) metal coordination : bond 0.01627 ( 29) metal coordination : angle 6.12268 ( 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 703 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 601 time to evaluate : 1.349 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: A 34 LYS cc_start: 0.9212 (mppt) cc_final: 0.8674 (tttp) REVERT: A 74 MET cc_start: 0.8389 (ttt) cc_final: 0.8145 (mtt) REVERT: A 92 HIS cc_start: 0.7949 (t-90) cc_final: 0.6108 (t-90) REVERT: A 95 PHE cc_start: 0.9540 (m-80) cc_final: 0.8240 (m-80) REVERT: A 117 GLU cc_start: 0.9718 (tt0) cc_final: 0.9497 (tm-30) REVERT: A 122 MET cc_start: 0.9320 (tmm) cc_final: 0.8923 (ppp) REVERT: A 225 ASN cc_start: 0.8953 (t0) cc_final: 0.8583 (t0) REVERT: A 234 MET cc_start: 0.9453 (ttm) cc_final: 0.8865 (tpp) REVERT: A 293 GLU cc_start: 0.8975 (tp30) cc_final: 0.8733 (tm-30) REVERT: A 433 GLU cc_start: 0.7946 (tp30) cc_final: 0.7702 (tp30) REVERT: A 445 ASN cc_start: 0.8927 (t0) cc_final: 0.8714 (t0) REVERT: A 450 LEU cc_start: 0.9146 (mm) cc_final: 0.8606 (tp) REVERT: A 456 MET cc_start: 0.8989 (mpp) cc_final: 0.7692 (mpp) REVERT: A 478 TYR cc_start: 0.8443 (m-80) cc_final: 0.7382 (m-80) REVERT: A 500 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7726 (tm-30) REVERT: A 505 CYS cc_start: 0.9142 (m) cc_final: 0.8760 (m) REVERT: A 521 MET cc_start: 0.8684 (mmm) cc_final: 0.8037 (mmm) REVERT: A 557 ASP cc_start: 0.9085 (t70) cc_final: 0.8828 (t0) REVERT: A 605 MET cc_start: 0.8895 (ttm) cc_final: 0.8409 (mtt) REVERT: A 696 GLU cc_start: 0.9190 (tt0) cc_final: 0.8971 (tp30) REVERT: A 701 LEU cc_start: 0.9020 (pt) cc_final: 0.8126 (pt) REVERT: A 741 ASN cc_start: 0.8131 (t0) cc_final: 0.7486 (t0) REVERT: A 748 MET cc_start: 0.8523 (ppp) cc_final: 0.8095 (ppp) REVERT: A 761 MET cc_start: 0.9064 (mtm) cc_final: 0.8453 (mmp) REVERT: A 786 HIS cc_start: 0.8612 (m-70) cc_final: 0.7908 (m-70) REVERT: A 846 GLU cc_start: 0.8606 (mt-10) cc_final: 0.7974 (mp0) REVERT: A 847 ASP cc_start: 0.7974 (p0) cc_final: 0.7453 (p0) REVERT: A 1079 MET cc_start: 0.6981 (mtp) cc_final: 0.6776 (mtp) REVERT: A 1120 LEU cc_start: 0.9603 (mt) cc_final: 0.9142 (tp) REVERT: A 1209 MET cc_start: 0.9011 (ppp) cc_final: 0.8804 (ppp) REVERT: A 1277 GLU cc_start: 0.9565 (pm20) cc_final: 0.9248 (pm20) REVERT: A 1315 GLU cc_start: 0.8987 (mp0) cc_final: 0.8661 (mp0) REVERT: A 1317 MET cc_start: 0.9306 (mmm) cc_final: 0.8924 (mmm) REVERT: A 1364 ASN cc_start: 0.8430 (t0) cc_final: 0.7927 (t0) REVERT: A 1421 CYS cc_start: 0.8106 (t) cc_final: 0.7632 (m) REVERT: A 1427 ASN cc_start: 0.8478 (m-40) cc_final: 0.8040 (t0) REVERT: A 1433 MET cc_start: 0.9327 (ppp) cc_final: 0.8906 (tmm) REVERT: B 101 MET cc_start: 0.8196 (tpp) cc_final: 0.7978 (tpp) REVERT: B 109 THR cc_start: 0.6499 (OUTLIER) cc_final: 0.5881 (p) REVERT: B 239 GLU cc_start: 0.8286 (tt0) cc_final: 0.7590 (tm-30) REVERT: B 296 GLU cc_start: 0.9454 (mm-30) cc_final: 0.8963 (mp0) REVERT: B 361 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8403 (tp) REVERT: B 404 LYS cc_start: 0.9127 (mttt) cc_final: 0.8738 (mttt) REVERT: B 481 GLN cc_start: 0.8357 (mt0) cc_final: 0.8119 (mt0) REVERT: B 542 MET cc_start: 0.8587 (mpp) cc_final: 0.8353 (mpp) REVERT: B 576 ASP cc_start: 0.9310 (p0) cc_final: 0.8847 (t70) REVERT: B 610 ASN cc_start: 0.8448 (t0) cc_final: 0.8136 (t0) REVERT: B 618 ASP cc_start: 0.8358 (t0) cc_final: 0.8057 (t0) REVERT: B 629 ASP cc_start: 0.7986 (t0) cc_final: 0.7582 (t0) REVERT: B 703 ILE cc_start: 0.9499 (mm) cc_final: 0.9259 (mm) REVERT: B 705 MET cc_start: 0.7504 (mmm) cc_final: 0.6712 (mmm) REVERT: B 790 ASP cc_start: 0.8009 (t70) cc_final: 0.7771 (t70) REVERT: B 834 ASN cc_start: 0.8139 (p0) cc_final: 0.7354 (p0) REVERT: B 841 MET cc_start: 0.8642 (mtp) cc_final: 0.8386 (mtp) REVERT: B 860 MET cc_start: 0.8340 (ppp) cc_final: 0.7920 (ppp) REVERT: B 963 PHE cc_start: 0.8440 (t80) cc_final: 0.7820 (t80) REVERT: B 992 ILE cc_start: 0.9103 (pt) cc_final: 0.8754 (pt) REVERT: B 999 MET cc_start: 0.9162 (tpp) cc_final: 0.8669 (tpp) REVERT: B 1013 ASN cc_start: 0.8859 (t0) cc_final: 0.8589 (t0) REVERT: B 1015 HIS cc_start: 0.8303 (m170) cc_final: 0.7829 (m170) REVERT: B 1094 ARG cc_start: 0.8547 (ttt-90) cc_final: 0.8213 (ttp80) REVERT: B 1095 LEU cc_start: 0.9209 (mm) cc_final: 0.8775 (mm) REVERT: B 1133 MET cc_start: 0.8899 (mtp) cc_final: 0.8447 (mtm) REVERT: B 1168 LEU cc_start: 0.9090 (mm) cc_final: 0.8747 (mm) REVERT: B 1208 MET cc_start: 0.9010 (ptt) cc_final: 0.8562 (ptp) REVERT: C 37 MET cc_start: 0.9341 (tpp) cc_final: 0.9094 (tpp) REVERT: C 46 ILE cc_start: 0.9159 (mt) cc_final: 0.8426 (tp) REVERT: C 52 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8476 (tm-30) REVERT: C 157 CYS cc_start: 0.9240 (m) cc_final: 0.8872 (m) REVERT: C 165 LYS cc_start: 0.9048 (tttt) cc_final: 0.8750 (tttm) REVERT: C 169 LYS cc_start: 0.9506 (mtpt) cc_final: 0.8986 (ptpt) REVERT: D 35 LEU cc_start: 0.8463 (mt) cc_final: 0.8166 (pt) REVERT: D 131 GLU cc_start: 0.5992 (OUTLIER) cc_final: 0.5577 (pt0) REVERT: E 7 ARG cc_start: 0.9064 (ptm-80) cc_final: 0.8691 (ttp80) REVERT: E 58 MET cc_start: 0.9389 (ttp) cc_final: 0.8855 (tmm) REVERT: E 63 ASN cc_start: 0.9619 (m-40) cc_final: 0.9285 (t0) REVERT: E 121 MET cc_start: 0.9268 (ppp) cc_final: 0.8958 (ppp) REVERT: E 194 GLU cc_start: 0.8243 (mp0) cc_final: 0.7899 (mp0) REVERT: F 81 THR cc_start: 0.8982 (m) cc_final: 0.8387 (p) REVERT: F 103 MET cc_start: 0.9213 (ttt) cc_final: 0.8563 (tmm) REVERT: F 122 MET cc_start: 0.9502 (ttm) cc_final: 0.8735 (tmm) REVERT: F 124 GLU cc_start: 0.9296 (tm-30) cc_final: 0.9065 (tm-30) REVERT: G 44 TYR cc_start: 0.7834 (t80) cc_final: 0.7335 (t80) REVERT: G 52 ASP cc_start: 0.8702 (t0) cc_final: 0.8219 (t0) REVERT: H 1 MET cc_start: 0.1193 (pmm) cc_final: -0.0366 (tpt) REVERT: H 10 PHE cc_start: 0.8394 (m-80) cc_final: 0.7282 (m-80) REVERT: H 97 MET cc_start: 0.8443 (ppp) cc_final: 0.7812 (ppp) REVERT: H 118 PHE cc_start: 0.9178 (m-80) cc_final: 0.7887 (m-10) REVERT: H 123 MET cc_start: 0.9295 (ppp) cc_final: 0.8993 (ppp) REVERT: H 133 ASN cc_start: 0.9014 (t0) cc_final: 0.8673 (m110) REVERT: I 48 LEU cc_start: 0.9377 (tp) cc_final: 0.9148 (pp) REVERT: I 65 ASP cc_start: 0.8900 (t0) cc_final: 0.8690 (t0) REVERT: I 68 LEU cc_start: 0.9465 (mp) cc_final: 0.9108 (mp) REVERT: I 87 GLN cc_start: 0.8312 (pp30) cc_final: 0.8038 (pp30) REVERT: J 6 ARG cc_start: 0.7846 (mmm-85) cc_final: 0.7369 (mmm-85) REVERT: K 38 GLU cc_start: 0.8826 (mp0) cc_final: 0.8275 (mp0) REVERT: K 53 ASP cc_start: 0.8293 (t0) cc_final: 0.7910 (t70) REVERT: K 92 ASN cc_start: 0.9366 (m110) cc_final: 0.9012 (m110) REVERT: K 106 GLU cc_start: 0.9783 (tp30) cc_final: 0.9377 (tp30) REVERT: Q 401 TYR cc_start: 0.8002 (p90) cc_final: 0.7711 (p90) outliers start: 102 outliers final: 65 residues processed: 662 average time/residue: 0.1905 time to fit residues: 213.7672 Evaluate side-chains 616 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 547 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 262 LEU 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 501 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 645 LEU 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 859 SER 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 1105 LEU Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1356 ILE Chi-restraints excluded: chain A residue 1384 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 109 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 361 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 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 1034 VAL Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1175 LEU 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 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 125 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain J residue 1 MET 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 K residue 21 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 214 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 38 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 30.0000 chunk 249 optimal weight: 0.0570 chunk 408 optimal weight: 8.9990 chunk 363 optimal weight: 9.9990 chunk 258 optimal weight: 0.9990 chunk 402 optimal weight: 50.0000 chunk 85 optimal weight: 6.9990 chunk 227 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 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 = 0.4230 r_free = 0.4230 target = 0.130060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.086358 restraints weight = 116885.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.089282 restraints weight = 53474.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.091254 restraints weight = 32925.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.092587 restraints weight = 23866.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.093458 restraints weight = 19308.715| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 36987 Z= 0.169 Angle : 0.734 17.277 50353 Z= 0.371 Chirality : 0.045 0.247 5666 Planarity : 0.005 0.062 6198 Dihedral : 15.853 166.889 5803 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.65 % Favored : 90.30 % Rotamer: Outliers : 3.29 % Allowed : 19.65 % Favored : 77.05 % 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: -1.11 (0.13), residues: 4259 helix: 0.81 (0.14), residues: 1399 sheet: -0.53 (0.20), residues: 644 loop : -1.89 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 434 TYR 0.031 0.001 TYR Q 373 PHE 0.030 0.002 PHE Q 101 TRP 0.018 0.002 TRP M 81 HIS 0.007 0.001 HIS A1387 Details of bonding type rmsd covalent geometry : bond 0.00373 (36958) covalent geometry : angle 0.71983 (50326) hydrogen bonds : bond 0.03981 ( 1400) hydrogen bonds : angle 5.02261 ( 3923) metal coordination : bond 0.01518 ( 29) metal coordination : angle 6.16717 ( 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 671 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 548 time to evaluate : 1.271 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 22 PHE cc_start: 0.8538 (m-10) cc_final: 0.8086 (m-10) REVERT: A 34 LYS cc_start: 0.9157 (mppt) cc_final: 0.8633 (tttp) REVERT: A 74 MET cc_start: 0.8483 (ttt) cc_final: 0.8263 (ttt) REVERT: A 92 HIS cc_start: 0.7971 (t-90) cc_final: 0.6128 (t-90) REVERT: A 95 PHE cc_start: 0.9534 (m-80) cc_final: 0.8300 (m-80) REVERT: A 117 GLU cc_start: 0.9720 (tt0) cc_final: 0.9490 (tm-30) REVERT: A 122 MET cc_start: 0.9288 (tmm) cc_final: 0.8908 (ppp) REVERT: A 225 ASN cc_start: 0.9021 (t0) cc_final: 0.8622 (t0) REVERT: A 234 MET cc_start: 0.9455 (ttm) cc_final: 0.8854 (tpt) REVERT: A 293 GLU cc_start: 0.9078 (tp30) cc_final: 0.8722 (tm-30) REVERT: A 445 ASN cc_start: 0.8819 (t0) cc_final: 0.8586 (t0) REVERT: A 450 LEU cc_start: 0.9127 (mm) cc_final: 0.8583 (tp) REVERT: A 456 MET cc_start: 0.9068 (mpp) cc_final: 0.8581 (mpp) REVERT: A 478 TYR cc_start: 0.8780 (m-80) cc_final: 0.8547 (m-80) REVERT: A 500 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: A 504 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7467 (mm) REVERT: A 505 CYS cc_start: 0.9226 (m) cc_final: 0.8682 (m) REVERT: A 521 MET cc_start: 0.8816 (mmm) cc_final: 0.8210 (mmm) REVERT: A 557 ASP cc_start: 0.9030 (t70) cc_final: 0.8787 (t0) REVERT: A 605 MET cc_start: 0.8927 (ttm) cc_final: 0.8479 (mtt) REVERT: A 662 PHE cc_start: 0.8213 (t80) cc_final: 0.7946 (t80) REVERT: A 696 GLU cc_start: 0.9209 (tt0) cc_final: 0.8915 (tp30) REVERT: A 701 LEU cc_start: 0.9083 (pt) cc_final: 0.8197 (pt) REVERT: A 741 ASN cc_start: 0.8272 (t0) cc_final: 0.7945 (t0) REVERT: A 748 MET cc_start: 0.8575 (ppp) cc_final: 0.8090 (ppp) REVERT: A 761 MET cc_start: 0.9106 (mtm) cc_final: 0.8561 (mmm) REVERT: A 767 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: A 786 HIS cc_start: 0.8652 (m-70) cc_final: 0.7890 (m-70) REVERT: A 846 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8236 (mt-10) REVERT: A 847 ASP cc_start: 0.7989 (p0) cc_final: 0.7412 (p0) REVERT: A 874 ASP cc_start: 0.8203 (m-30) cc_final: 0.7540 (p0) REVERT: A 1120 LEU cc_start: 0.9637 (mt) cc_final: 0.9304 (tp) REVERT: A 1227 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8579 (mm) REVERT: A 1277 GLU cc_start: 0.9599 (pm20) cc_final: 0.9288 (pm20) REVERT: A 1315 GLU cc_start: 0.8977 (mp0) cc_final: 0.8675 (mp0) REVERT: A 1364 ASN cc_start: 0.8784 (t0) cc_final: 0.8404 (t0) REVERT: A 1421 CYS cc_start: 0.8381 (t) cc_final: 0.7863 (m) REVERT: A 1427 ASN cc_start: 0.8634 (m-40) cc_final: 0.8196 (t0) REVERT: A 1433 MET cc_start: 0.9258 (ppp) cc_final: 0.8923 (tmm) REVERT: B 239 GLU cc_start: 0.8383 (tt0) cc_final: 0.7619 (tm-30) REVERT: B 258 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8940 (tp) REVERT: B 296 GLU cc_start: 0.9518 (mm-30) cc_final: 0.9029 (mp0) REVERT: B 361 LEU cc_start: 0.8987 (tp) cc_final: 0.8333 (tt) REVERT: B 404 LYS cc_start: 0.9183 (mttt) cc_final: 0.8738 (mttt) REVERT: B 481 GLN cc_start: 0.8478 (mt0) cc_final: 0.8172 (mt0) REVERT: B 521 LEU cc_start: 0.9705 (mm) cc_final: 0.9141 (tp) REVERT: B 563 MET cc_start: 0.8387 (mtt) cc_final: 0.8121 (mtt) REVERT: B 576 ASP cc_start: 0.9326 (p0) cc_final: 0.8863 (t70) REVERT: B 610 ASN cc_start: 0.8542 (t0) cc_final: 0.8232 (t0) REVERT: B 618 ASP cc_start: 0.8435 (t0) cc_final: 0.8145 (t0) REVERT: B 629 ASP cc_start: 0.8086 (t0) cc_final: 0.7685 (t0) REVERT: B 687 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8305 (tm-30) REVERT: B 696 GLU cc_start: 0.9280 (tp30) cc_final: 0.9072 (tp30) REVERT: B 790 ASP cc_start: 0.8125 (t70) cc_final: 0.7689 (t70) REVERT: B 809 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7860 (pmm) REVERT: B 834 ASN cc_start: 0.8196 (p0) cc_final: 0.7433 (p0) REVERT: B 841 MET cc_start: 0.8830 (mtp) cc_final: 0.8584 (mtp) REVERT: B 860 MET cc_start: 0.8354 (ppp) cc_final: 0.8023 (ppp) REVERT: B 963 PHE cc_start: 0.8424 (t80) cc_final: 0.7838 (t80) REVERT: B 992 ILE cc_start: 0.9123 (pt) cc_final: 0.8830 (pt) REVERT: B 994 TYR cc_start: 0.7866 (m-10) cc_final: 0.7485 (m-10) REVERT: B 999 MET cc_start: 0.9126 (tpp) cc_final: 0.8662 (tpp) REVERT: B 1015 HIS cc_start: 0.8359 (m170) cc_final: 0.8123 (m170) REVERT: B 1095 LEU cc_start: 0.9236 (mm) cc_final: 0.8910 (mm) REVERT: B 1133 MET cc_start: 0.8881 (mtp) cc_final: 0.8364 (mtm) REVERT: B 1169 MET cc_start: 0.8988 (mmt) cc_final: 0.8738 (mmm) REVERT: B 1205 GLN cc_start: 0.9303 (OUTLIER) cc_final: 0.8674 (mp10) REVERT: B 1208 MET cc_start: 0.9032 (ptt) cc_final: 0.8463 (ptp) REVERT: C 16 ASP cc_start: 0.8795 (p0) cc_final: 0.7982 (p0) REVERT: C 37 MET cc_start: 0.9286 (tpp) cc_final: 0.8982 (tpp) REVERT: C 46 ILE cc_start: 0.9217 (mt) cc_final: 0.8485 (tp) REVERT: C 52 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8472 (tm-30) REVERT: C 58 LEU cc_start: 0.8777 (tp) cc_final: 0.8510 (tp) REVERT: C 157 CYS cc_start: 0.9203 (m) cc_final: 0.8855 (m) REVERT: C 165 LYS cc_start: 0.9107 (tttt) cc_final: 0.8770 (tttm) REVERT: C 169 LYS cc_start: 0.9503 (mtpt) cc_final: 0.8923 (ptpt) REVERT: C 233 GLU cc_start: 0.8774 (tt0) cc_final: 0.8464 (tt0) REVERT: D 35 LEU cc_start: 0.8427 (mt) cc_final: 0.8163 (pt) REVERT: D 131 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.5567 (pt0) REVERT: E 7 ARG cc_start: 0.9084 (ptm-80) cc_final: 0.8697 (ttp80) REVERT: E 58 MET cc_start: 0.9394 (ttp) cc_final: 0.8850 (tmm) REVERT: E 121 MET cc_start: 0.9290 (ppp) cc_final: 0.8940 (ppp) REVERT: E 194 GLU cc_start: 0.8279 (mp0) cc_final: 0.7868 (mp0) REVERT: F 81 THR cc_start: 0.9094 (m) cc_final: 0.8517 (p) REVERT: F 89 GLU cc_start: 0.7843 (pm20) cc_final: 0.7378 (pm20) REVERT: F 119 ARG cc_start: 0.9103 (tpp80) cc_final: 0.8897 (tpp80) REVERT: F 122 MET cc_start: 0.9519 (ttm) cc_final: 0.8748 (tmm) REVERT: F 124 GLU cc_start: 0.9337 (tm-30) cc_final: 0.9043 (tm-30) REVERT: F 127 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8174 (tm-30) REVERT: G 44 TYR cc_start: 0.7789 (t80) cc_final: 0.7315 (t80) REVERT: H 1 MET cc_start: 0.1546 (pmm) cc_final: -0.0004 (tpt) REVERT: H 10 PHE cc_start: 0.8316 (m-80) cc_final: 0.7279 (m-80) REVERT: H 97 MET cc_start: 0.8367 (ppp) cc_final: 0.7907 (ppp) REVERT: H 118 PHE cc_start: 0.9259 (m-80) cc_final: 0.8076 (m-10) REVERT: H 123 MET cc_start: 0.9357 (ppp) cc_final: 0.9032 (ppp) REVERT: H 133 ASN cc_start: 0.9045 (t0) cc_final: 0.8686 (m110) REVERT: I 65 ASP cc_start: 0.9087 (t0) cc_final: 0.8611 (t0) REVERT: I 68 LEU cc_start: 0.9478 (mp) cc_final: 0.9016 (mp) REVERT: I 72 ASP cc_start: 0.9081 (p0) cc_final: 0.8683 (m-30) REVERT: I 87 GLN cc_start: 0.8418 (pp30) cc_final: 0.8162 (pp30) REVERT: J 39 LEU cc_start: 0.9305 (tp) cc_final: 0.8978 (tt) REVERT: K 53 ASP cc_start: 0.8414 (t0) cc_final: 0.8042 (t70) REVERT: K 92 ASN cc_start: 0.9370 (m110) cc_final: 0.9009 (m110) REVERT: K 106 GLU cc_start: 0.9782 (tp30) cc_final: 0.9370 (tp30) REVERT: Q 114 MET cc_start: 0.9270 (mmm) cc_final: 0.8748 (ptm) REVERT: Q 401 TYR cc_start: 0.8107 (p90) cc_final: 0.7840 (p90) outliers start: 123 outliers final: 81 residues processed: 625 average time/residue: 0.1945 time to fit residues: 207.1131 Evaluate side-chains 612 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 523 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 262 LEU 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 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 619 LYS Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 737 LEU 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 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 1358 SER Chi-restraints excluded: chain A residue 1384 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 63 ILE 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 314 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 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 737 THR Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1147 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1162 ILE 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 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 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 125 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain H residue 130 ARG 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 63 VAL Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain M residue 68 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 311 optimal weight: 0.0770 chunk 331 optimal weight: 6.9990 chunk 423 optimal weight: 8.9990 chunk 394 optimal weight: 10.0000 chunk 338 optimal weight: 20.0000 chunk 346 optimal weight: 30.0000 chunk 141 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 340 optimal weight: 20.0000 chunk 165 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 654 ASN ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 GLN G 71 ASN ** H 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 ASN ** M 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.128564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.087448 restraints weight = 117294.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.090287 restraints weight = 53619.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.092199 restraints weight = 32919.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.093504 restraints weight = 23832.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.094359 restraints weight = 19208.914| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 36987 Z= 0.166 Angle : 0.740 16.107 50353 Z= 0.372 Chirality : 0.045 0.227 5666 Planarity : 0.005 0.062 6198 Dihedral : 15.780 163.793 5803 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.81 % Favored : 90.14 % Rotamer: Outliers : 3.19 % Allowed : 21.02 % Favored : 75.80 % 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: -1.10 (0.13), residues: 4259 helix: 0.80 (0.14), residues: 1407 sheet: -0.51 (0.20), residues: 643 loop : -1.88 (0.13), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 58 TYR 0.044 0.002 TYR Q 373 PHE 0.016 0.002 PHE E 72 TRP 0.031 0.002 TRP M 81 HIS 0.006 0.001 HIS A1387 Details of bonding type rmsd covalent geometry : bond 0.00363 (36958) covalent geometry : angle 0.72831 (50326) hydrogen bonds : bond 0.03890 ( 1400) hydrogen bonds : angle 4.94610 ( 3923) metal coordination : bond 0.01520 ( 29) metal coordination : angle 5.68651 ( 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 662 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 543 time to evaluate : 1.379 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 22 PHE cc_start: 0.8558 (m-10) cc_final: 0.8056 (m-10) REVERT: A 34 LYS cc_start: 0.9115 (mppt) cc_final: 0.8665 (tttm) REVERT: A 74 MET cc_start: 0.8502 (ttt) cc_final: 0.8243 (ttt) REVERT: A 95 PHE cc_start: 0.9535 (m-80) cc_final: 0.9290 (m-80) REVERT: A 117 GLU cc_start: 0.9718 (tt0) cc_final: 0.9485 (tm-30) REVERT: A 122 MET cc_start: 0.9298 (tmm) cc_final: 0.8889 (ppp) REVERT: A 225 ASN cc_start: 0.9044 (t0) cc_final: 0.8666 (t0) REVERT: A 450 LEU cc_start: 0.9105 (mm) cc_final: 0.8504 (tp) REVERT: A 456 MET cc_start: 0.9046 (mpp) cc_final: 0.8559 (mpp) REVERT: A 478 TYR cc_start: 0.8812 (m-80) cc_final: 0.8521 (m-80) REVERT: A 500 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.7724 (tm-30) REVERT: A 504 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7431 (mm) REVERT: A 505 CYS cc_start: 0.9111 (m) cc_final: 0.8786 (m) REVERT: A 521 MET cc_start: 0.8800 (mmm) cc_final: 0.8232 (mmm) REVERT: A 557 ASP cc_start: 0.9049 (t70) cc_final: 0.8810 (t0) REVERT: A 605 MET cc_start: 0.8947 (ttm) cc_final: 0.8511 (mtt) REVERT: A 654 ASN cc_start: 0.9487 (OUTLIER) cc_final: 0.9200 (t0) REVERT: A 662 PHE cc_start: 0.8221 (t80) cc_final: 0.7853 (t80) REVERT: A 696 GLU cc_start: 0.9201 (tt0) cc_final: 0.8894 (tp30) REVERT: A 701 LEU cc_start: 0.9132 (pt) cc_final: 0.8287 (pt) REVERT: A 741 ASN cc_start: 0.8146 (t0) cc_final: 0.7798 (t0) REVERT: A 748 MET cc_start: 0.8459 (ppp) cc_final: 0.8140 (ppp) REVERT: A 761 MET cc_start: 0.9095 (mtm) cc_final: 0.8545 (mmm) REVERT: A 767 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: A 786 HIS cc_start: 0.8661 (m-70) cc_final: 0.7883 (m-70) REVERT: A 846 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8238 (mt-10) REVERT: A 847 ASP cc_start: 0.8013 (p0) cc_final: 0.7393 (p0) REVERT: A 894 GLU cc_start: 0.9183 (pp20) cc_final: 0.8937 (pp20) REVERT: A 1120 LEU cc_start: 0.9627 (mt) cc_final: 0.9292 (tp) REVERT: A 1277 GLU cc_start: 0.9604 (pm20) cc_final: 0.9294 (pm20) REVERT: A 1315 GLU cc_start: 0.8900 (mp0) cc_final: 0.8550 (mp0) REVERT: A 1317 MET cc_start: 0.9357 (mmm) cc_final: 0.8859 (mmm) REVERT: A 1364 ASN cc_start: 0.8921 (t0) cc_final: 0.8509 (t0) REVERT: A 1375 MET cc_start: 0.8919 (tmm) cc_final: 0.8327 (tmm) REVERT: A 1400 CYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8616 (p) REVERT: A 1427 ASN cc_start: 0.8630 (m-40) cc_final: 0.8427 (t0) REVERT: A 1433 MET cc_start: 0.9252 (ppp) cc_final: 0.8868 (tmm) REVERT: A 1444 MET cc_start: 0.8457 (mtt) cc_final: 0.8042 (mtm) REVERT: B 239 GLU cc_start: 0.8380 (tt0) cc_final: 0.7581 (tm-30) REVERT: B 258 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8887 (tp) REVERT: B 296 GLU cc_start: 0.9508 (mm-30) cc_final: 0.9007 (mp0) REVERT: B 376 PHE cc_start: 0.9438 (OUTLIER) cc_final: 0.8813 (m-10) REVERT: B 404 LYS cc_start: 0.9137 (mttt) cc_final: 0.8759 (mttt) REVERT: B 481 GLN cc_start: 0.8504 (mt0) cc_final: 0.8184 (mm-40) REVERT: B 576 ASP cc_start: 0.9292 (p0) cc_final: 0.8828 (t70) REVERT: B 610 ASN cc_start: 0.8548 (t0) cc_final: 0.8246 (t0) REVERT: B 618 ASP cc_start: 0.8304 (t0) cc_final: 0.8030 (t0) REVERT: B 629 ASP cc_start: 0.8205 (t0) cc_final: 0.7785 (t0) REVERT: B 684 LEU cc_start: 0.9628 (tp) cc_final: 0.9401 (tt) REVERT: B 687 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8331 (tm-30) REVERT: B 696 GLU cc_start: 0.9247 (tp30) cc_final: 0.8996 (tp30) REVERT: B 705 MET cc_start: 0.8376 (mmm) cc_final: 0.7575 (mmm) REVERT: B 790 ASP cc_start: 0.8186 (t70) cc_final: 0.7675 (t70) REVERT: B 809 MET cc_start: 0.8190 (pmm) cc_final: 0.7672 (pmm) REVERT: B 834 ASN cc_start: 0.8109 (p0) cc_final: 0.7349 (p0) REVERT: B 841 MET cc_start: 0.8794 (mtp) cc_final: 0.8558 (mtp) REVERT: B 860 MET cc_start: 0.8421 (ppp) cc_final: 0.8133 (ppp) REVERT: B 963 PHE cc_start: 0.8249 (t80) cc_final: 0.7654 (t80) REVERT: B 992 ILE cc_start: 0.9130 (pt) cc_final: 0.8742 (pt) REVERT: B 994 TYR cc_start: 0.7782 (m-10) cc_final: 0.7469 (m-80) REVERT: B 999 MET cc_start: 0.9152 (tpp) cc_final: 0.8659 (tpp) REVERT: B 1015 HIS cc_start: 0.8408 (m170) cc_final: 0.8183 (m170) REVERT: B 1169 MET cc_start: 0.9017 (mmt) cc_final: 0.8706 (mmm) REVERT: B 1201 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8836 (ttpp) REVERT: B 1208 MET cc_start: 0.9006 (ptt) cc_final: 0.8480 (ptp) REVERT: C 16 ASP cc_start: 0.8883 (p0) cc_final: 0.8061 (p0) REVERT: C 37 MET cc_start: 0.9291 (tpp) cc_final: 0.8980 (tpp) REVERT: C 46 ILE cc_start: 0.9211 (mt) cc_final: 0.8281 (tp) REVERT: C 52 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8458 (tm-30) REVERT: C 67 LEU cc_start: 0.9627 (mm) cc_final: 0.9315 (tp) REVERT: C 69 LEU cc_start: 0.9667 (OUTLIER) cc_final: 0.9461 (mm) REVERT: C 157 CYS cc_start: 0.9247 (m) cc_final: 0.8520 (m) REVERT: C 165 LYS cc_start: 0.9093 (tttt) cc_final: 0.8773 (tttm) REVERT: C 169 LYS cc_start: 0.9505 (mtpt) cc_final: 0.8907 (ptpt) REVERT: C 192 TRP cc_start: 0.8850 (t60) cc_final: 0.8175 (t60) REVERT: C 233 GLU cc_start: 0.8858 (tt0) cc_final: 0.8487 (tt0) REVERT: D 35 LEU cc_start: 0.8454 (mt) cc_final: 0.8191 (pt) REVERT: D 131 GLU cc_start: 0.6097 (OUTLIER) cc_final: 0.5711 (pt0) REVERT: E 7 ARG cc_start: 0.9085 (ptm-80) cc_final: 0.8686 (ttp80) REVERT: E 58 MET cc_start: 0.9418 (ttp) cc_final: 0.8969 (tmm) REVERT: E 63 ASN cc_start: 0.9632 (m-40) cc_final: 0.9316 (t0) REVERT: E 121 MET cc_start: 0.9349 (ppp) cc_final: 0.9048 (ppp) REVERT: E 194 GLU cc_start: 0.8293 (mp0) cc_final: 0.7891 (mp0) REVERT: F 81 THR cc_start: 0.9033 (m) cc_final: 0.8493 (p) REVERT: F 124 GLU cc_start: 0.9379 (tm-30) cc_final: 0.9061 (tm-30) REVERT: F 127 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8179 (tm-30) REVERT: G 44 TYR cc_start: 0.7847 (t80) cc_final: 0.7296 (t80) REVERT: H 1 MET cc_start: 0.1855 (pmm) cc_final: 0.0191 (tpt) REVERT: H 10 PHE cc_start: 0.8263 (m-80) cc_final: 0.7234 (m-80) REVERT: H 97 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8018 (ppp) REVERT: H 118 PHE cc_start: 0.9230 (m-80) cc_final: 0.8062 (m-10) REVERT: H 123 MET cc_start: 0.9390 (ppp) cc_final: 0.9020 (ppp) REVERT: I 48 LEU cc_start: 0.9343 (tt) cc_final: 0.9074 (pp) REVERT: I 65 ASP cc_start: 0.8948 (t0) cc_final: 0.8549 (t0) REVERT: I 68 LEU cc_start: 0.9470 (mp) cc_final: 0.9072 (mp) REVERT: I 87 GLN cc_start: 0.8367 (pp30) cc_final: 0.8162 (pp30) REVERT: J 39 LEU cc_start: 0.9333 (tp) cc_final: 0.9015 (tt) REVERT: K 53 ASP cc_start: 0.8497 (t0) cc_final: 0.8145 (t70) REVERT: K 92 ASN cc_start: 0.9378 (m110) cc_final: 0.9021 (m110) REVERT: K 106 GLU cc_start: 0.9777 (tp30) cc_final: 0.9384 (tp30) REVERT: Q 352 MET cc_start: 0.7384 (tmm) cc_final: 0.7133 (tmm) REVERT: Q 401 TYR cc_start: 0.8128 (p90) cc_final: 0.7873 (p90) outliers start: 119 outliers final: 85 residues processed: 618 average time/residue: 0.1900 time to fit residues: 200.4844 Evaluate side-chains 611 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 515 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 262 LEU 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 645 LEU 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 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 1062 GLU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1356 ILE Chi-restraints excluded: chain A residue 1358 SER 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 30 SER Chi-restraints excluded: chain B residue 63 ILE 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 314 LEU Chi-restraints excluded: chain B residue 376 PHE Chi-restraints excluded: chain B residue 378 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 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 690 VAL Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1162 ILE 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 69 LEU 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 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 125 LEU Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 130 ARG 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 63 VAL Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 128 VAL 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: 6.9990 chunk 266 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 369 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 274 optimal weight: 20.0000 chunk 405 optimal weight: 0.7980 chunk 357 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 383 optimal weight: 10.0000 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 GLN ** 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 = 0.4096 r_free = 0.4096 target = 0.121961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.083277 restraints weight = 122968.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.086072 restraints weight = 55819.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.087975 restraints weight = 34226.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.089259 restraints weight = 24767.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.090099 restraints weight = 20001.853| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 36987 Z= 0.222 Angle : 0.776 16.770 50353 Z= 0.394 Chirality : 0.046 0.258 5666 Planarity : 0.005 0.065 6198 Dihedral : 15.803 160.032 5803 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.10 % Favored : 89.83 % Rotamer: Outliers : 3.59 % Allowed : 21.50 % Favored : 74.91 % 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: -1.19 (0.13), residues: 4259 helix: 0.69 (0.14), residues: 1411 sheet: -0.48 (0.21), residues: 625 loop : -1.94 (0.13), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 30 TYR 0.025 0.002 TYR B 833 PHE 0.022 0.002 PHE B 360 TRP 0.019 0.002 TRP A 656 HIS 0.007 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00482 (36958) covalent geometry : angle 0.76371 (50326) hydrogen bonds : bond 0.04249 ( 1400) hydrogen bonds : angle 5.09993 ( 3923) metal coordination : bond 0.01550 ( 29) metal coordination : angle 5.92119 ( 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 636 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 502 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.8628 (m-10) cc_final: 0.8214 (m-80) REVERT: A 34 LYS cc_start: 0.9073 (mppt) cc_final: 0.8641 (tttm) REVERT: A 74 MET cc_start: 0.8599 (ttt) cc_final: 0.8318 (ttt) REVERT: A 95 PHE cc_start: 0.9525 (m-80) cc_final: 0.9196 (m-80) REVERT: A 117 GLU cc_start: 0.9726 (tt0) cc_final: 0.9498 (tm-30) REVERT: A 122 MET cc_start: 0.9264 (tmm) cc_final: 0.8916 (ppp) REVERT: A 225 ASN cc_start: 0.9162 (t0) cc_final: 0.8812 (t0) REVERT: A 299 HIS cc_start: 0.9092 (OUTLIER) cc_final: 0.8649 (t-90) REVERT: A 450 LEU cc_start: 0.9074 (mm) cc_final: 0.8510 (tp) REVERT: A 456 MET cc_start: 0.9164 (mpp) cc_final: 0.8531 (mpp) REVERT: A 478 TYR cc_start: 0.8969 (m-80) cc_final: 0.8397 (m-80) REVERT: A 487 MET cc_start: 0.7687 (mmm) cc_final: 0.7341 (mmm) REVERT: A 500 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: A 504 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7601 (mm) REVERT: A 505 CYS cc_start: 0.9068 (m) cc_final: 0.8802 (m) REVERT: A 521 MET cc_start: 0.8897 (mmm) cc_final: 0.8382 (mmm) REVERT: A 547 LEU cc_start: 0.9049 (mt) cc_final: 0.8645 (mt) REVERT: A 557 ASP cc_start: 0.9033 (t70) cc_final: 0.8799 (t0) REVERT: A 605 MET cc_start: 0.9048 (ttm) cc_final: 0.8601 (mtt) REVERT: A 662 PHE cc_start: 0.8395 (t80) cc_final: 0.7912 (t80) REVERT: A 696 GLU cc_start: 0.9204 (tt0) cc_final: 0.8823 (tp30) REVERT: A 701 LEU cc_start: 0.9176 (pt) cc_final: 0.8342 (pt) REVERT: A 741 ASN cc_start: 0.8266 (t0) cc_final: 0.8021 (t0) REVERT: A 748 MET cc_start: 0.8580 (ppp) cc_final: 0.8109 (ppp) REVERT: A 761 MET cc_start: 0.9101 (mtm) cc_final: 0.8606 (mmm) REVERT: A 767 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: A 786 HIS cc_start: 0.8710 (m-70) cc_final: 0.7870 (m-70) REVERT: A 818 MET cc_start: 0.9280 (tpp) cc_final: 0.8678 (mmt) REVERT: A 846 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8272 (mt-10) REVERT: A 847 ASP cc_start: 0.8144 (p0) cc_final: 0.7620 (p0) REVERT: A 894 GLU cc_start: 0.9180 (pp20) cc_final: 0.8870 (pp20) REVERT: A 956 LEU cc_start: 0.8780 (mt) cc_final: 0.8531 (tt) REVERT: A 1120 LEU cc_start: 0.9633 (mt) cc_final: 0.9306 (tp) REVERT: A 1277 GLU cc_start: 0.9616 (pm20) cc_final: 0.9277 (pm20) REVERT: A 1315 GLU cc_start: 0.8869 (mp0) cc_final: 0.8564 (mp0) REVERT: A 1317 MET cc_start: 0.9356 (mmm) cc_final: 0.8920 (mmm) REVERT: A 1364 ASN cc_start: 0.9072 (t0) cc_final: 0.8627 (t0) REVERT: A 1375 MET cc_start: 0.9002 (tmm) cc_final: 0.8467 (tmm) REVERT: A 1400 CYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8870 (p) REVERT: A 1421 CYS cc_start: 0.8568 (t) cc_final: 0.7994 (m) REVERT: A 1427 ASN cc_start: 0.8574 (m-40) cc_final: 0.8123 (t0) REVERT: B 239 GLU cc_start: 0.8456 (tt0) cc_final: 0.7536 (tm-30) REVERT: B 276 ILE cc_start: 0.8772 (mm) cc_final: 0.8499 (mp) REVERT: B 296 GLU cc_start: 0.9520 (mm-30) cc_final: 0.9259 (mm-30) REVERT: B 376 PHE cc_start: 0.9491 (OUTLIER) cc_final: 0.8869 (m-10) REVERT: B 404 LYS cc_start: 0.9168 (mttt) cc_final: 0.8788 (mttt) REVERT: B 444 MET cc_start: 0.7440 (ppp) cc_final: 0.7221 (ppp) REVERT: B 481 GLN cc_start: 0.8541 (mt0) cc_final: 0.8197 (mm-40) REVERT: B 597 MET cc_start: 0.9527 (ttt) cc_final: 0.8848 (tmm) REVERT: B 610 ASN cc_start: 0.8651 (t0) cc_final: 0.8357 (t0) REVERT: B 618 ASP cc_start: 0.8386 (t0) cc_final: 0.8084 (t0) REVERT: B 629 ASP cc_start: 0.8184 (t0) cc_final: 0.7779 (t0) REVERT: B 696 GLU cc_start: 0.9311 (tp30) cc_final: 0.9047 (tp30) REVERT: B 705 MET cc_start: 0.8700 (mmm) cc_final: 0.7833 (mmm) REVERT: B 809 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7795 (pmm) REVERT: B 812 LEU cc_start: 0.9078 (mp) cc_final: 0.8710 (mp) REVERT: B 834 ASN cc_start: 0.8083 (p0) cc_final: 0.7355 (p0) REVERT: B 841 MET cc_start: 0.8823 (mtp) cc_final: 0.8573 (mtp) REVERT: B 860 MET cc_start: 0.8433 (ppp) cc_final: 0.8171 (ppp) REVERT: B 963 PHE cc_start: 0.8197 (t80) cc_final: 0.7643 (t80) REVERT: B 992 ILE cc_start: 0.9180 (pt) cc_final: 0.8925 (pt) REVERT: B 994 TYR cc_start: 0.7964 (m-10) cc_final: 0.7276 (m-80) REVERT: B 999 MET cc_start: 0.9138 (tpp) cc_final: 0.8246 (mmt) REVERT: B 1015 HIS cc_start: 0.8410 (m170) cc_final: 0.8204 (m170) REVERT: B 1062 HIS cc_start: 0.8907 (OUTLIER) cc_final: 0.8597 (t-90) REVERT: B 1169 MET cc_start: 0.9065 (mmt) cc_final: 0.8784 (mmm) REVERT: B 1201 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8865 (ttpp) REVERT: B 1208 MET cc_start: 0.9036 (ptt) cc_final: 0.8515 (ptp) REVERT: C 16 ASP cc_start: 0.8931 (p0) cc_final: 0.8666 (p0) REVERT: C 37 MET cc_start: 0.9222 (tpp) cc_final: 0.8908 (tpt) REVERT: C 46 ILE cc_start: 0.9245 (mt) cc_final: 0.8429 (tt) REVERT: C 52 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8470 (tm-30) REVERT: C 69 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9435 (mm) REVERT: C 157 CYS cc_start: 0.9248 (m) cc_final: 0.8848 (m) REVERT: C 165 LYS cc_start: 0.9151 (tttt) cc_final: 0.8854 (tttt) REVERT: C 169 LYS cc_start: 0.9478 (mtpt) cc_final: 0.8975 (ptpt) REVERT: C 192 TRP cc_start: 0.8970 (t60) cc_final: 0.8323 (t60) REVERT: D 35 LEU cc_start: 0.8403 (mt) cc_final: 0.8133 (pt) REVERT: D 131 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5686 (pt0) REVERT: E 7 ARG cc_start: 0.9112 (ptm-80) cc_final: 0.8702 (ttp80) REVERT: E 58 MET cc_start: 0.9414 (ttp) cc_final: 0.9008 (tmm) REVERT: E 121 MET cc_start: 0.9391 (ppp) cc_final: 0.9168 (ppp) REVERT: E 194 GLU cc_start: 0.8315 (mp0) cc_final: 0.7909 (mp0) REVERT: F 81 THR cc_start: 0.9054 (m) cc_final: 0.8594 (p) REVERT: F 82 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8865 (p) REVERT: F 124 GLU cc_start: 0.9374 (tm-30) cc_final: 0.9011 (tm-30) REVERT: F 127 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8220 (tm-30) REVERT: G 44 TYR cc_start: 0.7917 (t80) cc_final: 0.7385 (t80) REVERT: H 1 MET cc_start: 0.2064 (pmm) cc_final: 0.0655 (tpt) REVERT: H 10 PHE cc_start: 0.8244 (m-80) cc_final: 0.7303 (m-80) REVERT: H 97 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8062 (ppp) REVERT: H 118 PHE cc_start: 0.9208 (m-80) cc_final: 0.8014 (m-10) REVERT: H 123 MET cc_start: 0.9423 (ppp) cc_final: 0.9072 (ppp) REVERT: I 13 MET cc_start: 0.8303 (tpt) cc_final: 0.8044 (tpp) REVERT: I 48 LEU cc_start: 0.9334 (tt) cc_final: 0.9076 (pp) REVERT: I 65 ASP cc_start: 0.8988 (t0) cc_final: 0.8557 (t0) REVERT: I 68 LEU cc_start: 0.9510 (mp) cc_final: 0.9098 (mp) REVERT: I 72 ASP cc_start: 0.9039 (p0) cc_final: 0.8642 (m-30) REVERT: I 87 GLN cc_start: 0.8406 (pp30) cc_final: 0.8179 (pp30) REVERT: K 92 ASN cc_start: 0.9381 (m110) cc_final: 0.9022 (m110) REVERT: K 106 GLU cc_start: 0.9776 (tp30) cc_final: 0.9379 (tp30) REVERT: Q 352 MET cc_start: 0.7470 (tmm) cc_final: 0.7216 (tmm) REVERT: Q 401 TYR cc_start: 0.8187 (p90) cc_final: 0.7955 (p90) REVERT: M 137 GLU cc_start: 0.9408 (OUTLIER) cc_final: 0.9084 (pm20) outliers start: 134 outliers final: 94 residues processed: 586 average time/residue: 0.1874 time to fit residues: 188.0321 Evaluate side-chains 589 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 481 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASP 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 444 PHE Chi-restraints excluded: chain A residue 485 ASP 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 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 979 SER 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 1332 PHE 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 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 30 SER Chi-restraints excluded: chain B residue 63 ILE 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 298 LEU Chi-restraints excluded: chain B residue 376 PHE Chi-restraints excluded: chain B residue 388 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 461 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 697 GLU 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 1034 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1062 HIS Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1147 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1162 ILE 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 69 LEU Chi-restraints excluded: chain C residue 115 SER 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 D residue 138 ASN 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 94 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain I residue 28 GLU 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 56 VAL 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 L residue 56 LEU Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain M residue 68 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: 8.9990 chunk 348 optimal weight: 5.9990 chunk 312 optimal weight: 4.9990 chunk 363 optimal weight: 0.9990 chunk 155 optimal weight: 20.0000 chunk 355 optimal weight: 0.7980 chunk 366 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 401 optimal weight: 7.9990 chunk 268 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN ** 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** F 104 ASN H 35 GLN ** H 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 GLN ** M 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.128961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.086587 restraints weight = 116722.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.089443 restraints weight = 53062.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.091363 restraints weight = 32510.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.092660 restraints weight = 23477.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.093539 restraints weight = 18930.864| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4112 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= 0.156 Angle : 0.752 17.008 50353 Z= 0.377 Chirality : 0.045 0.294 5666 Planarity : 0.005 0.064 6198 Dihedral : 15.723 157.873 5803 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.70 % Favored : 90.26 % Rotamer: Outliers : 3.13 % Allowed : 22.76 % Favored : 74.11 % 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: -1.10 (0.13), residues: 4259 helix: 0.77 (0.14), residues: 1410 sheet: -0.40 (0.21), residues: 625 loop : -1.90 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 969 TYR 0.020 0.001 TYR M 133 PHE 0.020 0.001 PHE B 360 TRP 0.040 0.002 TRP M 81 HIS 0.006 0.001 HIS B1015 Details of bonding type rmsd covalent geometry : bond 0.00346 (36958) covalent geometry : angle 0.74220 (50326) hydrogen bonds : bond 0.03879 ( 1400) hydrogen bonds : angle 4.92319 ( 3923) metal coordination : bond 0.01508 ( 29) metal coordination : angle 5.30558 ( 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 638 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 521 time to evaluate : 1.263 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 22 PHE cc_start: 0.8544 (m-10) cc_final: 0.8057 (m-10) REVERT: A 34 LYS cc_start: 0.9070 (mppt) cc_final: 0.8620 (tttm) REVERT: A 62 ASP cc_start: 0.8992 (p0) cc_final: 0.8776 (t0) REVERT: A 74 MET cc_start: 0.8577 (ttt) cc_final: 0.8259 (ttt) REVERT: A 95 PHE cc_start: 0.9532 (m-80) cc_final: 0.9034 (m-80) REVERT: A 117 GLU cc_start: 0.9722 (tt0) cc_final: 0.9496 (tm-30) REVERT: A 122 MET cc_start: 0.9280 (tmm) cc_final: 0.8919 (ppp) REVERT: A 225 ASN cc_start: 0.9219 (t0) cc_final: 0.8912 (t0) REVERT: A 234 MET cc_start: 0.9351 (ttm) cc_final: 0.8855 (mmt) REVERT: A 450 LEU cc_start: 0.9065 (mm) cc_final: 0.8493 (tp) REVERT: A 456 MET cc_start: 0.9110 (mpp) cc_final: 0.8632 (mpp) REVERT: A 478 TYR cc_start: 0.8912 (m-80) cc_final: 0.8577 (m-80) REVERT: A 500 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.7784 (tm-30) REVERT: A 504 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7519 (mm) REVERT: A 505 CYS cc_start: 0.9038 (m) cc_final: 0.8779 (m) REVERT: A 521 MET cc_start: 0.8805 (mmm) cc_final: 0.8208 (mmm) REVERT: A 541 ILE cc_start: 0.9064 (tp) cc_final: 0.8649 (tt) REVERT: A 557 ASP cc_start: 0.8959 (t70) cc_final: 0.8710 (t0) REVERT: A 605 MET cc_start: 0.8979 (ttm) cc_final: 0.8528 (mtt) REVERT: A 654 ASN cc_start: 0.9530 (OUTLIER) cc_final: 0.9222 (t0) REVERT: A 662 PHE cc_start: 0.8296 (t80) cc_final: 0.7807 (t80) REVERT: A 668 ASP cc_start: 0.7949 (t70) cc_final: 0.7747 (t0) REVERT: A 696 GLU cc_start: 0.9203 (tt0) cc_final: 0.8826 (tp30) REVERT: A 701 LEU cc_start: 0.9172 (pt) cc_final: 0.8332 (pt) REVERT: A 741 ASN cc_start: 0.8257 (t0) cc_final: 0.7827 (t0) REVERT: A 748 MET cc_start: 0.8483 (ppp) cc_final: 0.8090 (ppp) REVERT: A 761 MET cc_start: 0.9069 (mtm) cc_final: 0.8631 (mmm) REVERT: A 767 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: A 786 HIS cc_start: 0.8685 (m-70) cc_final: 0.7841 (m-70) REVERT: A 825 ILE cc_start: 0.9561 (pt) cc_final: 0.9297 (mm) REVERT: A 846 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8374 (mt-10) REVERT: A 847 ASP cc_start: 0.8094 (p0) cc_final: 0.7658 (p0) REVERT: A 848 ILE cc_start: 0.9478 (mm) cc_final: 0.9172 (mp) REVERT: A 874 ASP cc_start: 0.8054 (m-30) cc_final: 0.7318 (p0) REVERT: A 894 GLU cc_start: 0.9131 (pp20) cc_final: 0.8780 (pp20) REVERT: A 956 LEU cc_start: 0.8693 (mt) cc_final: 0.8456 (tt) REVERT: A 1120 LEU cc_start: 0.9649 (mt) cc_final: 0.9193 (tp) REVERT: A 1277 GLU cc_start: 0.9620 (pm20) cc_final: 0.9302 (pm20) REVERT: A 1315 GLU cc_start: 0.8855 (mp0) cc_final: 0.8507 (mp0) REVERT: A 1317 MET cc_start: 0.9317 (mmm) cc_final: 0.8873 (mmm) REVERT: A 1364 ASN cc_start: 0.9027 (t0) cc_final: 0.8527 (t0) REVERT: A 1375 MET cc_start: 0.8997 (tmm) cc_final: 0.8464 (tmm) REVERT: A 1400 CYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8622 (p) REVERT: A 1433 MET cc_start: 0.9162 (ppp) cc_final: 0.8760 (ppp) REVERT: B 239 GLU cc_start: 0.8453 (tt0) cc_final: 0.7530 (tm-30) REVERT: B 276 ILE cc_start: 0.8724 (mm) cc_final: 0.8429 (mp) REVERT: B 296 GLU cc_start: 0.9494 (mm-30) cc_final: 0.9203 (mm-30) REVERT: B 376 PHE cc_start: 0.9477 (OUTLIER) cc_final: 0.8820 (m-10) REVERT: B 404 LYS cc_start: 0.9160 (mttt) cc_final: 0.8764 (mttt) REVERT: B 481 GLN cc_start: 0.8580 (mt0) cc_final: 0.8187 (mm-40) REVERT: B 486 TYR cc_start: 0.7982 (m-80) cc_final: 0.7546 (m-10) REVERT: B 521 LEU cc_start: 0.9557 (mp) cc_final: 0.9263 (mm) REVERT: B 552 MET cc_start: 0.9083 (mmm) cc_final: 0.8824 (mmp) REVERT: B 610 ASN cc_start: 0.8633 (t0) cc_final: 0.8333 (t0) REVERT: B 618 ASP cc_start: 0.8369 (t0) cc_final: 0.8088 (t0) REVERT: B 625 LYS cc_start: 0.8960 (mmmm) cc_final: 0.8745 (mmmm) REVERT: B 629 ASP cc_start: 0.8323 (t0) cc_final: 0.7980 (t0) REVERT: B 705 MET cc_start: 0.8523 (mmm) cc_final: 0.7562 (mmm) REVERT: B 809 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7836 (pmm) REVERT: B 812 LEU cc_start: 0.9125 (mp) cc_final: 0.8759 (mp) REVERT: B 834 ASN cc_start: 0.8176 (p0) cc_final: 0.7470 (p0) REVERT: B 841 MET cc_start: 0.8785 (mtp) cc_final: 0.8531 (mtp) REVERT: B 860 MET cc_start: 0.8393 (ppp) cc_final: 0.8148 (ppp) REVERT: B 963 PHE cc_start: 0.8063 (t80) cc_final: 0.7559 (t80) REVERT: B 992 ILE cc_start: 0.9132 (pt) cc_final: 0.8751 (pt) REVERT: B 994 TYR cc_start: 0.8081 (m-10) cc_final: 0.7817 (m-80) REVERT: B 999 MET cc_start: 0.9094 (tpp) cc_final: 0.8622 (tpp) REVERT: B 1062 HIS cc_start: 0.8801 (OUTLIER) cc_final: 0.8527 (t-90) REVERT: B 1153 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8706 (mm-30) REVERT: B 1169 MET cc_start: 0.9045 (mmt) cc_final: 0.8764 (mmm) REVERT: B 1201 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8800 (ttpp) REVERT: B 1208 MET cc_start: 0.8991 (ptt) cc_final: 0.8534 (ptp) REVERT: B 1210 MET cc_start: 0.8949 (mtp) cc_final: 0.8727 (ttm) REVERT: C 16 ASP cc_start: 0.8997 (p0) cc_final: 0.8727 (p0) REVERT: C 37 MET cc_start: 0.9255 (tpp) cc_final: 0.8946 (tpt) REVERT: C 46 ILE cc_start: 0.9213 (mt) cc_final: 0.8683 (mt) REVERT: C 52 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8391 (tm-30) REVERT: C 69 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9482 (mm) REVERT: C 169 LYS cc_start: 0.9488 (mtpt) cc_final: 0.8987 (ptpt) REVERT: C 192 TRP cc_start: 0.8814 (t60) cc_final: 0.8130 (t60) REVERT: D 131 GLU cc_start: 0.5984 (OUTLIER) cc_final: 0.5594 (pt0) REVERT: E 7 ARG cc_start: 0.9073 (ptm-80) cc_final: 0.8615 (ttp80) REVERT: E 58 MET cc_start: 0.9395 (ttp) cc_final: 0.9005 (tmm) REVERT: E 63 ASN cc_start: 0.9644 (m-40) cc_final: 0.9332 (t0) REVERT: E 121 MET cc_start: 0.9397 (ppp) cc_final: 0.9149 (ppp) REVERT: E 194 GLU cc_start: 0.8342 (mp0) cc_final: 0.7958 (mp0) REVERT: F 81 THR cc_start: 0.9056 (m) cc_final: 0.8596 (p) REVERT: F 89 GLU cc_start: 0.7852 (pm20) cc_final: 0.7523 (pm20) REVERT: F 104 ASN cc_start: 0.9445 (OUTLIER) cc_final: 0.9244 (t0) REVERT: F 124 GLU cc_start: 0.9365 (tm-30) cc_final: 0.9050 (tm-30) REVERT: F 127 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8181 (tm-30) REVERT: G 44 TYR cc_start: 0.7874 (t80) cc_final: 0.7308 (t80) REVERT: H 1 MET cc_start: 0.2411 (pmm) cc_final: 0.0981 (tpt) REVERT: H 10 PHE cc_start: 0.8251 (m-80) cc_final: 0.7227 (m-80) REVERT: H 97 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8141 (ppp) REVERT: H 118 PHE cc_start: 0.9188 (m-80) cc_final: 0.7954 (m-10) REVERT: H 123 MET cc_start: 0.9423 (ppp) cc_final: 0.9058 (ppp) REVERT: I 48 LEU cc_start: 0.9354 (tt) cc_final: 0.9092 (pp) REVERT: I 65 ASP cc_start: 0.8952 (t0) cc_final: 0.8582 (t0) REVERT: I 68 LEU cc_start: 0.9493 (mp) cc_final: 0.9125 (mp) REVERT: I 72 ASP cc_start: 0.9119 (p0) cc_final: 0.8734 (m-30) REVERT: I 87 GLN cc_start: 0.8410 (pp30) cc_final: 0.8199 (pp30) REVERT: J 52 THR cc_start: 0.9001 (t) cc_final: 0.8560 (t) REVERT: K 92 ASN cc_start: 0.9374 (m110) cc_final: 0.9001 (m110) REVERT: K 106 GLU cc_start: 0.9764 (tp30) cc_final: 0.9317 (tp30) REVERT: Q 352 MET cc_start: 0.7475 (tmm) cc_final: 0.7134 (tmm) REVERT: Q 401 TYR cc_start: 0.8216 (p90) cc_final: 0.7988 (p90) REVERT: M 137 GLU cc_start: 0.9423 (OUTLIER) cc_final: 0.9087 (pm20) outliers start: 117 outliers final: 88 residues processed: 587 average time/residue: 0.1890 time to fit residues: 189.1686 Evaluate side-chains 600 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 498 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 341 MET 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 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 979 SER Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1356 ILE Chi-restraints excluded: chain A residue 1358 SER 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 30 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 ILE 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 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 570 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 729 ILE 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 1037 LEU Chi-restraints excluded: chain B residue 1062 HIS Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1162 ILE 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 69 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 260 LEU 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 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 104 ASN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 33 SER 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 K residue 63 VAL Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain M residue 68 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: 7.9990 chunk 401 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 393 optimal weight: 5.9990 chunk 368 optimal weight: 7.9990 chunk 310 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 227 optimal weight: 0.9990 chunk 291 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 HIS ** 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** K 112 GLN ** M 138 GLN ** 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 = 0.4214 r_free = 0.4214 target = 0.129753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.087716 restraints weight = 116611.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.090593 restraints weight = 53227.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.092541 restraints weight = 32648.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.093878 restraints weight = 23553.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.094733 restraints weight = 18939.073| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4271 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= 0.136 Angle : 0.761 16.689 50353 Z= 0.377 Chirality : 0.045 0.241 5666 Planarity : 0.004 0.063 6198 Dihedral : 15.635 158.454 5803 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.53 % Favored : 90.42 % Rotamer: Outliers : 3.00 % Allowed : 23.40 % Favored : 73.60 % 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: -1.03 (0.13), residues: 4259 helix: 0.86 (0.14), residues: 1406 sheet: -0.44 (0.21), residues: 649 loop : -1.87 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 119 TYR 0.017 0.001 TYR H 20 PHE 0.023 0.001 PHE E 72 TRP 0.021 0.001 TRP A 552 HIS 0.006 0.001 HIS B1015 Details of bonding type rmsd covalent geometry : bond 0.00302 (36958) covalent geometry : angle 0.75283 (50326) hydrogen bonds : bond 0.03639 ( 1400) hydrogen bonds : angle 4.78707 ( 3923) metal coordination : bond 0.01455 ( 29) metal coordination : angle 4.94688 ( 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 640 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 528 time to evaluate : 1.455 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 22 PHE cc_start: 0.8469 (m-10) cc_final: 0.7975 (m-10) REVERT: A 34 LYS cc_start: 0.9061 (mppt) cc_final: 0.8621 (tttm) REVERT: A 41 MET cc_start: 0.7489 (tpt) cc_final: 0.6478 (tpt) REVERT: A 62 ASP cc_start: 0.8993 (p0) cc_final: 0.8732 (t0) REVERT: A 74 MET cc_start: 0.8586 (ttt) cc_final: 0.8167 (ttm) REVERT: A 95 PHE cc_start: 0.9525 (m-80) cc_final: 0.9313 (m-80) REVERT: A 117 GLU cc_start: 0.9722 (tt0) cc_final: 0.9501 (tm-30) REVERT: A 122 MET cc_start: 0.9275 (tmm) cc_final: 0.8919 (ppp) REVERT: A 225 ASN cc_start: 0.9210 (t0) cc_final: 0.8902 (t0) REVERT: A 234 MET cc_start: 0.9408 (ttm) cc_final: 0.9165 (ttm) REVERT: A 450 LEU cc_start: 0.9089 (mm) cc_final: 0.8515 (tp) REVERT: A 453 MET cc_start: 0.9300 (mmp) cc_final: 0.8992 (mmm) REVERT: A 456 MET cc_start: 0.9056 (mpp) cc_final: 0.8534 (mpp) REVERT: A 500 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: A 521 MET cc_start: 0.8767 (mmm) cc_final: 0.8190 (mmm) REVERT: A 541 ILE cc_start: 0.9095 (tp) cc_final: 0.8689 (tt) REVERT: A 557 ASP cc_start: 0.8942 (t70) cc_final: 0.8688 (t0) REVERT: A 605 MET cc_start: 0.8959 (ttm) cc_final: 0.8640 (mtt) REVERT: A 654 ASN cc_start: 0.9431 (OUTLIER) cc_final: 0.9150 (t0) REVERT: A 696 GLU cc_start: 0.9210 (tt0) cc_final: 0.8869 (tp30) REVERT: A 701 LEU cc_start: 0.9121 (pt) cc_final: 0.8275 (pt) REVERT: A 741 ASN cc_start: 0.8055 (t0) cc_final: 0.7625 (t0) REVERT: A 748 MET cc_start: 0.8449 (ppp) cc_final: 0.8067 (ppp) REVERT: A 761 MET cc_start: 0.9065 (mtm) cc_final: 0.8616 (mmm) REVERT: A 767 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: A 786 HIS cc_start: 0.8698 (m-70) cc_final: 0.8441 (m-70) REVERT: A 847 ASP cc_start: 0.8014 (p0) cc_final: 0.7511 (p0) REVERT: A 848 ILE cc_start: 0.9453 (mm) cc_final: 0.9143 (mp) REVERT: A 894 GLU cc_start: 0.9150 (pp20) cc_final: 0.8844 (pp20) REVERT: A 956 LEU cc_start: 0.8705 (mt) cc_final: 0.8408 (tt) REVERT: A 1111 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8508 (tpp) REVERT: A 1120 LEU cc_start: 0.9634 (mt) cc_final: 0.9176 (tp) REVERT: A 1277 GLU cc_start: 0.9614 (pm20) cc_final: 0.9282 (pm20) REVERT: A 1315 GLU cc_start: 0.8853 (mp0) cc_final: 0.8481 (mp0) REVERT: A 1317 MET cc_start: 0.9296 (mmm) cc_final: 0.8810 (mmm) REVERT: A 1364 ASN cc_start: 0.8970 (t0) cc_final: 0.8440 (t0) REVERT: A 1375 MET cc_start: 0.8960 (tmm) cc_final: 0.8489 (tmm) REVERT: A 1400 CYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8604 (p) REVERT: A 1433 MET cc_start: 0.9163 (ppp) cc_final: 0.8686 (tmm) REVERT: A 1444 MET cc_start: 0.8602 (mtt) cc_final: 0.7935 (mtm) REVERT: B 101 MET cc_start: 0.8029 (tpp) cc_final: 0.7672 (tmm) REVERT: B 239 GLU cc_start: 0.8399 (tt0) cc_final: 0.7541 (tm-30) REVERT: B 276 ILE cc_start: 0.8657 (mm) cc_final: 0.8367 (mp) REVERT: B 296 GLU cc_start: 0.9482 (mm-30) cc_final: 0.9197 (mm-30) REVERT: B 376 PHE cc_start: 0.9443 (OUTLIER) cc_final: 0.8735 (m-10) REVERT: B 404 LYS cc_start: 0.9130 (mttt) cc_final: 0.8747 (mttt) REVERT: B 444 MET cc_start: 0.7636 (ppp) cc_final: 0.7239 (ppp) REVERT: B 445 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7597 (mmmt) REVERT: B 481 GLN cc_start: 0.8548 (mt0) cc_final: 0.8121 (mm-40) REVERT: B 521 LEU cc_start: 0.9559 (mp) cc_final: 0.9262 (mm) REVERT: B 618 ASP cc_start: 0.8570 (t0) cc_final: 0.8315 (t0) REVERT: B 625 LYS cc_start: 0.8943 (mmmm) cc_final: 0.8729 (mmmm) REVERT: B 629 ASP cc_start: 0.8364 (t0) cc_final: 0.8062 (t0) REVERT: B 639 ILE cc_start: 0.8836 (pt) cc_final: 0.8604 (pt) REVERT: B 705 MET cc_start: 0.8451 (mmm) cc_final: 0.8245 (mmm) REVERT: B 809 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7792 (pmm) REVERT: B 812 LEU cc_start: 0.9121 (mp) cc_final: 0.8728 (mp) REVERT: B 834 ASN cc_start: 0.8064 (p0) cc_final: 0.7318 (p0) REVERT: B 860 MET cc_start: 0.8379 (ppp) cc_final: 0.8165 (ppp) REVERT: B 963 PHE cc_start: 0.7894 (t80) cc_final: 0.7430 (t80) REVERT: B 992 ILE cc_start: 0.9218 (pt) cc_final: 0.8806 (pt) REVERT: B 994 TYR cc_start: 0.8053 (m-10) cc_final: 0.7390 (m-80) REVERT: B 999 MET cc_start: 0.9110 (tpp) cc_final: 0.8118 (mmt) REVERT: B 1168 LEU cc_start: 0.9399 (mm) cc_final: 0.9113 (mm) REVERT: B 1169 MET cc_start: 0.9105 (mmt) cc_final: 0.8745 (mmm) REVERT: B 1201 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8759 (ttpp) REVERT: B 1208 MET cc_start: 0.8995 (ptt) cc_final: 0.8496 (ptp) REVERT: C 16 ASP cc_start: 0.8988 (p0) cc_final: 0.8706 (p0) REVERT: C 37 MET cc_start: 0.9294 (tpp) cc_final: 0.9005 (tpt) REVERT: C 46 ILE cc_start: 0.9057 (mt) cc_final: 0.8635 (mt) REVERT: C 52 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8377 (tm-30) REVERT: C 169 LYS cc_start: 0.9496 (mtpt) cc_final: 0.9040 (ptpt) REVERT: C 192 TRP cc_start: 0.8677 (t60) cc_final: 0.7972 (t60) REVERT: D 131 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5650 (pt0) REVERT: E 7 ARG cc_start: 0.9054 (ptm-80) cc_final: 0.8616 (ttp80) REVERT: E 58 MET cc_start: 0.9428 (ttp) cc_final: 0.9099 (tmm) REVERT: E 63 ASN cc_start: 0.9648 (m-40) cc_final: 0.9323 (t0) REVERT: E 121 MET cc_start: 0.9406 (ppp) cc_final: 0.9162 (ppp) REVERT: E 194 GLU cc_start: 0.8309 (mp0) cc_final: 0.7901 (mp0) REVERT: F 81 THR cc_start: 0.9060 (m) cc_final: 0.8595 (p) REVERT: F 89 GLU cc_start: 0.7839 (pm20) cc_final: 0.7468 (pm20) REVERT: F 124 GLU cc_start: 0.9368 (tm-30) cc_final: 0.9064 (tm-30) REVERT: F 127 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8165 (tm-30) REVERT: G 44 TYR cc_start: 0.7866 (t80) cc_final: 0.7304 (t80) REVERT: H 1 MET cc_start: 0.2346 (pmm) cc_final: 0.0917 (tpt) REVERT: H 10 PHE cc_start: 0.8222 (m-80) cc_final: 0.7182 (m-80) REVERT: H 97 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8259 (ppp) REVERT: H 118 PHE cc_start: 0.9130 (m-80) cc_final: 0.7891 (m-10) REVERT: H 123 MET cc_start: 0.9414 (ppp) cc_final: 0.9036 (ppp) REVERT: H 130 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7416 (pmt-80) REVERT: I 15 TYR cc_start: 0.7458 (m-10) cc_final: 0.7182 (m-10) REVERT: I 48 LEU cc_start: 0.9371 (tt) cc_final: 0.9142 (pp) REVERT: I 65 ASP cc_start: 0.8870 (t0) cc_final: 0.8490 (t0) REVERT: I 68 LEU cc_start: 0.9448 (mp) cc_final: 0.9078 (mp) REVERT: I 72 ASP cc_start: 0.9119 (p0) cc_final: 0.8741 (m-30) REVERT: I 87 GLN cc_start: 0.8325 (pp30) cc_final: 0.8105 (pp30) REVERT: K 92 ASN cc_start: 0.9413 (m110) cc_final: 0.9074 (m110) REVERT: K 106 GLU cc_start: 0.9747 (tp30) cc_final: 0.9320 (tp30) REVERT: Q 352 MET cc_start: 0.7375 (tmm) cc_final: 0.6975 (tmm) REVERT: Q 401 TYR cc_start: 0.8179 (p90) cc_final: 0.7655 (p90) REVERT: M 133 TYR cc_start: 0.8981 (m-10) cc_final: 0.8399 (m-80) REVERT: M 137 GLU cc_start: 0.9435 (OUTLIER) cc_final: 0.9078 (pm20) outliers start: 112 outliers final: 79 residues processed: 592 average time/residue: 0.1899 time to fit residues: 192.6378 Evaluate side-chains 594 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 502 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 341 MET 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 507 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 657 LEU 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 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 1338 VAL Chi-restraints excluded: chain A residue 1356 ILE Chi-restraints excluded: chain A residue 1358 SER 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 30 SER Chi-restraints excluded: chain B residue 63 ILE 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 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 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 585 VAL Chi-restraints excluded: chain B residue 651 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 1037 LEU Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1092 TYR Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1162 ILE 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 C residue 260 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 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 125 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain I residue 33 SER 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 K residue 21 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain M residue 68 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 233 optimal weight: 6.9990 chunk 250 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 235 optimal weight: 0.0770 chunk 356 optimal weight: 20.0000 chunk 168 optimal weight: 4.9990 chunk 338 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 363 optimal weight: 7.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1390 ASN ** B 221 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** K 112 GLN ** M 138 GLN ** 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 = 0.4249 r_free = 0.4249 target = 0.131561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.088318 restraints weight = 116242.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.091224 restraints weight = 52631.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.093188 restraints weight = 32145.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.094525 restraints weight = 23170.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.095433 restraints weight = 18631.261| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 36987 Z= 0.142 Angle : 0.764 16.469 50353 Z= 0.378 Chirality : 0.045 0.247 5666 Planarity : 0.005 0.063 6198 Dihedral : 15.585 158.462 5803 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.51 % Favored : 90.44 % Rotamer: Outliers : 2.65 % Allowed : 24.15 % Favored : 73.20 % 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: -1.01 (0.13), residues: 4259 helix: 0.85 (0.14), residues: 1408 sheet: -0.40 (0.21), residues: 633 loop : -1.83 (0.13), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 84 TYR 0.017 0.001 TYR H 20 PHE 0.035 0.001 PHE K 58 TRP 0.016 0.001 TRP A 552 HIS 0.008 0.001 HIS B1015 Details of bonding type rmsd covalent geometry : bond 0.00319 (36958) covalent geometry : angle 0.75546 (50326) hydrogen bonds : bond 0.03638 ( 1400) hydrogen bonds : angle 4.77581 ( 3923) metal coordination : bond 0.01416 ( 29) metal coordination : angle 4.88782 ( 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 609 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 510 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.8456 (m-10) cc_final: 0.8002 (m-10) REVERT: A 34 LYS cc_start: 0.9049 (mppt) cc_final: 0.8631 (tttt) REVERT: A 62 ASP cc_start: 0.8971 (p0) cc_final: 0.8715 (t0) REVERT: A 74 MET cc_start: 0.8545 (ttt) cc_final: 0.8106 (ttm) REVERT: A 91 PHE cc_start: 0.9027 (m-10) cc_final: 0.8808 (m-10) REVERT: A 117 GLU cc_start: 0.9722 (tt0) cc_final: 0.9500 (tm-30) REVERT: A 122 MET cc_start: 0.9264 (tmm) cc_final: 0.8913 (ppp) REVERT: A 225 ASN cc_start: 0.9221 (t0) cc_final: 0.8913 (t0) REVERT: A 234 MET cc_start: 0.9410 (ttm) cc_final: 0.9156 (ttm) REVERT: A 450 LEU cc_start: 0.9069 (mm) cc_final: 0.8460 (tp) REVERT: A 453 MET cc_start: 0.9326 (mmp) cc_final: 0.9071 (mmm) REVERT: A 456 MET cc_start: 0.9062 (mpp) cc_final: 0.7959 (mpp) REVERT: A 487 MET cc_start: 0.7464 (mmm) cc_final: 0.7166 (mmm) REVERT: A 500 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.7942 (tm-30) REVERT: A 521 MET cc_start: 0.8735 (mmm) cc_final: 0.8159 (mmm) REVERT: A 541 ILE cc_start: 0.9157 (tp) cc_final: 0.8778 (tt) REVERT: A 557 ASP cc_start: 0.8951 (t70) cc_final: 0.8694 (t0) REVERT: A 598 LEU cc_start: 0.9600 (tp) cc_final: 0.9293 (mt) REVERT: A 605 MET cc_start: 0.9003 (ttm) cc_final: 0.8637 (mtt) REVERT: A 654 ASN cc_start: 0.9470 (OUTLIER) cc_final: 0.9144 (t0) REVERT: A 696 GLU cc_start: 0.9199 (tt0) cc_final: 0.8838 (tp30) REVERT: A 701 LEU cc_start: 0.9127 (pt) cc_final: 0.8284 (pt) REVERT: A 741 ASN cc_start: 0.7845 (t0) cc_final: 0.7530 (t0) REVERT: A 748 MET cc_start: 0.8344 (ppp) cc_final: 0.7959 (ppp) REVERT: A 761 MET cc_start: 0.9066 (mtm) cc_final: 0.8619 (mmm) REVERT: A 767 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7734 (tt0) REVERT: A 786 HIS cc_start: 0.8715 (m-70) cc_final: 0.8327 (m-70) REVERT: A 847 ASP cc_start: 0.7856 (p0) cc_final: 0.7414 (p0) REVERT: A 848 ILE cc_start: 0.9450 (mm) cc_final: 0.9161 (mp) REVERT: A 874 ASP cc_start: 0.7690 (m-30) cc_final: 0.7334 (p0) REVERT: A 894 GLU cc_start: 0.9152 (pp20) cc_final: 0.8780 (pp20) REVERT: A 956 LEU cc_start: 0.8707 (mt) cc_final: 0.8419 (tt) REVERT: A 1111 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8455 (tpp) REVERT: A 1120 LEU cc_start: 0.9634 (mt) cc_final: 0.9174 (tp) REVERT: A 1277 GLU cc_start: 0.9612 (pm20) cc_final: 0.9281 (pm20) REVERT: A 1315 GLU cc_start: 0.8854 (mp0) cc_final: 0.8505 (mp0) REVERT: A 1317 MET cc_start: 0.9368 (mmm) cc_final: 0.9161 (mmm) REVERT: A 1364 ASN cc_start: 0.8968 (t0) cc_final: 0.8439 (t0) REVERT: A 1375 MET cc_start: 0.8956 (tmm) cc_final: 0.8490 (tmm) REVERT: A 1400 CYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8636 (p) REVERT: B 239 GLU cc_start: 0.8394 (tt0) cc_final: 0.7546 (tm-30) REVERT: B 276 ILE cc_start: 0.8625 (mm) cc_final: 0.8328 (mp) REVERT: B 296 GLU cc_start: 0.9492 (mm-30) cc_final: 0.9217 (mm-30) REVERT: B 376 PHE cc_start: 0.9450 (OUTLIER) cc_final: 0.8793 (m-10) REVERT: B 445 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7699 (mmtp) REVERT: B 481 GLN cc_start: 0.8577 (mt0) cc_final: 0.8135 (mm-40) REVERT: B 521 LEU cc_start: 0.9560 (mp) cc_final: 0.9261 (mm) REVERT: B 618 ASP cc_start: 0.8572 (t0) cc_final: 0.8320 (t0) REVERT: B 625 LYS cc_start: 0.8950 (mmmm) cc_final: 0.8733 (mmmm) REVERT: B 629 ASP cc_start: 0.8354 (t0) cc_final: 0.8082 (t0) REVERT: B 639 ILE cc_start: 0.8851 (pt) cc_final: 0.8622 (pt) REVERT: B 705 MET cc_start: 0.8598 (mmm) cc_final: 0.8249 (mmm) REVERT: B 809 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7731 (pmm) REVERT: B 812 LEU cc_start: 0.9121 (mp) cc_final: 0.8722 (mp) REVERT: B 834 ASN cc_start: 0.8063 (p0) cc_final: 0.7307 (p0) REVERT: B 860 MET cc_start: 0.8389 (ppp) cc_final: 0.8183 (ppp) REVERT: B 963 PHE cc_start: 0.7869 (t80) cc_final: 0.7435 (t80) REVERT: B 992 ILE cc_start: 0.9284 (pt) cc_final: 0.8827 (pt) REVERT: B 994 TYR cc_start: 0.8081 (m-10) cc_final: 0.7804 (m-80) REVERT: B 999 MET cc_start: 0.9132 (tpp) cc_final: 0.8540 (tpp) REVERT: B 1168 LEU cc_start: 0.9393 (mm) cc_final: 0.9114 (mm) REVERT: B 1169 MET cc_start: 0.9110 (mmt) cc_final: 0.8757 (mmm) REVERT: B 1201 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8793 (ttpp) REVERT: B 1208 MET cc_start: 0.8950 (ptt) cc_final: 0.8449 (ptp) REVERT: C 16 ASP cc_start: 0.9007 (p0) cc_final: 0.8741 (p0) REVERT: C 37 MET cc_start: 0.9283 (tpp) cc_final: 0.8996 (tpt) REVERT: C 46 ILE cc_start: 0.8984 (mt) cc_final: 0.8277 (tt) REVERT: C 52 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8413 (tm-30) REVERT: C 169 LYS cc_start: 0.9477 (mtpt) cc_final: 0.8993 (ptpt) REVERT: C 192 TRP cc_start: 0.8669 (t60) cc_final: 0.7979 (t60) REVERT: D 131 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5596 (pt0) REVERT: E 7 ARG cc_start: 0.9049 (ptm-80) cc_final: 0.8608 (ttp80) REVERT: E 58 MET cc_start: 0.9438 (ttp) cc_final: 0.9115 (tmm) REVERT: E 63 ASN cc_start: 0.9650 (m-40) cc_final: 0.9326 (t0) REVERT: E 121 MET cc_start: 0.9398 (ppp) cc_final: 0.9143 (ppp) REVERT: E 194 GLU cc_start: 0.8304 (mp0) cc_final: 0.7916 (mp0) REVERT: F 81 THR cc_start: 0.9053 (m) cc_final: 0.8593 (p) REVERT: F 89 GLU cc_start: 0.7818 (pm20) cc_final: 0.7433 (pm20) REVERT: F 124 GLU cc_start: 0.9369 (tm-30) cc_final: 0.9051 (tm-30) REVERT: F 127 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8145 (tm-30) REVERT: G 44 TYR cc_start: 0.7872 (t80) cc_final: 0.7315 (t80) REVERT: H 1 MET cc_start: 0.2357 (pmm) cc_final: 0.0925 (tpt) REVERT: H 10 PHE cc_start: 0.8220 (m-80) cc_final: 0.7188 (m-80) REVERT: H 97 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8271 (ppp) REVERT: H 118 PHE cc_start: 0.9093 (m-80) cc_final: 0.7840 (m-10) REVERT: H 123 MET cc_start: 0.9414 (ppp) cc_final: 0.9036 (ppp) REVERT: H 130 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7519 (pmt-80) REVERT: I 11 ASN cc_start: 0.9200 (m-40) cc_final: 0.8864 (m-40) REVERT: I 48 LEU cc_start: 0.9371 (tt) cc_final: 0.9141 (pp) REVERT: I 65 ASP cc_start: 0.8856 (t0) cc_final: 0.8472 (t0) REVERT: I 68 LEU cc_start: 0.9438 (mp) cc_final: 0.9043 (mp) REVERT: I 72 ASP cc_start: 0.9117 (p0) cc_final: 0.8742 (m-30) REVERT: I 87 GLN cc_start: 0.8331 (pp30) cc_final: 0.8115 (pp30) REVERT: K 92 ASN cc_start: 0.9415 (m110) cc_final: 0.9074 (m110) REVERT: K 106 GLU cc_start: 0.9741 (tp30) cc_final: 0.9302 (tp30) REVERT: Q 31 PHE cc_start: 0.5074 (t80) cc_final: 0.4823 (t80) REVERT: Q 352 MET cc_start: 0.7512 (tmm) cc_final: 0.7275 (tmm) REVERT: Q 401 TYR cc_start: 0.7903 (p90) cc_final: 0.7604 (p90) REVERT: M 133 TYR cc_start: 0.9000 (m-10) cc_final: 0.8406 (m-80) REVERT: M 137 GLU cc_start: 0.9436 (OUTLIER) cc_final: 0.9078 (pm20) outliers start: 99 outliers final: 77 residues processed: 566 average time/residue: 0.1974 time to fit residues: 191.7170 Evaluate side-chains 594 residues out of total 3815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 504 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 341 MET 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 507 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 709 THR 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 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 1338 VAL Chi-restraints excluded: chain A residue 1356 ILE Chi-restraints excluded: chain A residue 1358 SER 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 30 SER Chi-restraints excluded: chain B residue 63 ILE 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 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 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 585 VAL Chi-restraints excluded: chain B residue 651 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 846 ILE Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1092 TYR Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1162 ILE 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 131 GLU 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 125 LEU Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 97 MET 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 K residue 21 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain M residue 68 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: 4.9990 chunk 188 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 278 optimal weight: 8.9990 chunk 431 optimal weight: 20.0000 chunk 361 optimal weight: 8.9990 chunk 391 optimal weight: 10.0000 chunk 415 optimal weight: 8.9990 chunk 165 optimal weight: 4.9990 chunk 351 optimal weight: 30.0000 chunk 62 optimal weight: 0.8980 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 GLN ** 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 = 0.4179 r_free = 0.4179 target = 0.127250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.085688 restraints weight = 118039.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.088442 restraints weight = 54449.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.090318 restraints weight = 33625.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.091586 restraints weight = 24402.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.092418 restraints weight = 19694.547| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 36987 Z= 0.191 Angle : 0.783 16.103 50353 Z= 0.391 Chirality : 0.045 0.247 5666 Planarity : 0.005 0.081 6198 Dihedral : 15.598 158.000 5803 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.24 % Favored : 89.72 % Rotamer: Outliers : 2.65 % Allowed : 24.15 % Favored : 73.20 % 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: -1.08 (0.13), residues: 4259 helix: 0.77 (0.14), residues: 1407 sheet: -0.40 (0.22), residues: 611 loop : -1.85 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 434 TYR 0.024 0.002 TYR B 486 PHE 0.023 0.002 PHE J 8 TRP 0.018 0.002 TRP A 552 HIS 0.007 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00421 (36958) covalent geometry : angle 0.77371 (50326) hydrogen bonds : bond 0.03951 ( 1400) hydrogen bonds : angle 4.91287 ( 3923) metal coordination : bond 0.01428 ( 29) metal coordination : angle 5.32661 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8449.12 seconds wall clock time: 145 minutes 47.88 seconds (8747.88 seconds total)