Starting phenix.real_space_refine on Sun Aug 9 06:44:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xgk_66852/08_2026/9xgk_66852.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xgk_66852/08_2026/9xgk_66852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xgk_66852/08_2026/9xgk_66852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xgk_66852/08_2026/9xgk_66852.map" model { file = "/net/cci-nas-00/data/ceres_data/9xgk_66852/08_2026/9xgk_66852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xgk_66852/08_2026/9xgk_66852.cif" } resolution = 2.53 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 63 5.49 5 Mg 1 5.21 5 S 197 5.16 5 C 20300 2.51 5 N 5680 2.21 5 O 6206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32455 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 11291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1427, 11291 Classifications: {'peptide': 1427} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 68, 'TRANS': 1356} Chain breaks: 4 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 9062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1134, 9062 Classifications: {'peptide': 1134} Link IDs: {'PTRANS': 53, 'TRANS': 1080} Chain breaks: 2 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1005 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1711 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1334 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} 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: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'NMCIS': 1, 'NMTRANS': 1, 'PCIS': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'SAR:plan-1': 1, 'MVA:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "M" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 56 Unusual residues: {'PXZ': 1} Classifications: {'peptide': 5, 'undetermined': 1} Modifications used: {'PEPT-D': 1} Link IDs: {'NMCIS': 1, 'NMTRANS': 1, 'PCIS': 1, 'TRANS': 1, None: 1} Not linked: pdbres="PXZ M 6 " pdbres="THR M 7 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'PXZ:plan-1': 1, 'PXZ:plan-2': 1, 'SAR:plan-1': 1, 'MVA:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 414 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain breaks: 1 Chain: "P" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 234 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna3p': 10} Chain: "T" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 650 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 110.189 84.170 83.284 1.00107.85 S ATOM 486 SG CYS A 74 109.781 87.205 81.187 1.00 83.78 S ATOM 533 SG CYS A 81 106.639 85.217 82.260 1.00 67.54 S ATOM 768 SG CYS A 111 102.591 68.192 38.616 1.00101.43 S ATOM 796 SG CYS A 114 105.139 70.564 37.098 1.00 65.64 S ATOM 1142 SG CYS A 184 105.963 66.598 36.950 1.00104.34 S ATOM 19923 SG CYS B1119 108.406 93.077 65.687 1.00 82.30 S ATOM 19945 SG CYS B1122 107.094 89.470 64.741 1.00 61.75 S ATOM 20060 SG CYS B1137 109.862 90.148 67.214 1.00 80.57 S ATOM 20081 SG CYS B1140 110.257 90.470 63.353 1.00 80.56 S ATOM 21047 SG CYS C 88 72.257 102.691 136.703 1.00111.23 S ATOM 21060 SG CYS C 90 74.396 99.714 135.946 1.00 75.74 S ATOM 21095 SG CYS C 94 72.437 99.591 139.068 1.00116.78 S ATOM 21117 SG CYS C 97 70.561 99.391 135.797 1.00112.59 S ATOM 28353 SG CYS I 17 55.636 24.587 45.657 1.00172.74 S ATOM 28377 SG CYS I 20 59.044 25.189 47.210 1.00180.83 S ATOM 28538 SG CYS I 39 57.351 28.078 45.389 1.00184.54 S ATOM 28563 SG CYS I 42 58.690 25.196 43.450 1.00164.38 S ATOM 28915 SG CYS I 86 21.624 39.656 69.928 1.00 80.42 S ATOM 28939 SG CYS I 89 20.025 37.350 72.513 1.00 97.57 S ATOM 29143 SG CYS I 114 23.040 39.147 73.415 1.00 98.76 S ATOM 29178 SG CYS I 119 23.480 36.305 71.094 1.00101.40 S ATOM 29288 SG CYS J 7 48.406 82.148 120.982 1.00102.07 S ATOM 29312 SG CYS J 10 47.248 85.585 122.345 1.00 95.08 S ATOM 29576 SG CYS J 44 45.127 83.988 119.706 1.00 68.21 S ATOM 29582 SG CYS J 45 45.400 82.654 123.271 1.00 73.58 S ATOM 30728 SG CYS L 19 83.000 55.512 125.332 1.00 98.72 S ATOM 30747 SG CYS L 22 82.468 54.087 128.825 1.00 84.75 S ATOM 30864 SG CYS L 36 85.869 55.547 127.793 1.00114.81 S ATOM 30890 SG CYS L 39 84.701 52.229 126.510 1.00115.88 S Time building chain proxies: 7.06, per 1000 atoms: 0.22 Number of scatterers: 32455 At special positions: 0 Unit cell: (169.26, 151.59, 156.24, 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 197 16.00 P 63 15.00 Mg 1 11.99 O 6206 8.00 N 5680 7.00 C 20300 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=5, symmetry=0 Links applied TRANS " DVA M 2 " - " THR M 1 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " Number of angles added : 39 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DVA M 2 " pdb=" CB DVA M 8 " Number of C-beta restraints generated: 7342 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 49 sheets defined 38.0% alpha, 16.6% beta 24 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 150 removed outlier: 4.156A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.501A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 301 through 319 Processing helix chain 'A' and resid 338 through 345 removed outlier: 4.743A pdb=" N GLY A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 438 removed outlier: 3.866A pdb=" N LEU A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.667A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 539 through 550 removed outlier: 3.658A pdb=" N LYS A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.835A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.643A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 662 through 684 removed outlier: 3.700A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 693 Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 773 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.682A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY A 858 " --> pdb=" O THR A 854 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 928 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.683A pdb=" N VAL A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.852A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 974 removed outlier: 4.430A pdb=" N ASP A 974 " --> pdb=" O PRO A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.563A pdb=" N LYS A 992 " --> pdb=" O TRP A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.643A pdb=" N VAL A1010 " --> pdb=" O PRO A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1049 removed outlier: 4.849A pdb=" N LEU A1040 " --> pdb=" O ASN A1036 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N PHE A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1100 Proline residue: A1098 - end of helix Processing helix chain 'A' and resid 1120 through 1130 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 3.868A pdb=" N ARG A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.676A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1199 removed outlier: 4.307A pdb=" N MET A1199 " --> pdb=" O VAL A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1225 Processing helix chain 'A' and resid 1227 through 1239 Processing helix chain 'A' and resid 1281 through 1296 removed outlier: 3.783A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET A1296 " --> pdb=" O MET A1292 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 removed outlier: 3.574A pdb=" N GLU A1349 " --> pdb=" O ARG A1345 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1367 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.891A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1421 Processing helix chain 'A' and resid 1425 through 1431 Processing helix chain 'A' and resid 1435 through 1446 Processing helix chain 'A' and resid 1453 through 1460 Processing helix chain 'A' and resid 1476 through 1482 removed outlier: 3.589A pdb=" N TYR A1482 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.539A pdb=" N ALA B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 248 through 253 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.602A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.581A pdb=" N ASP B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.773A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 496 through 500 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.859A pdb=" N TRP B 506 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 552 through 556 removed outlier: 3.764A pdb=" N ILE B 556 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 564 removed outlier: 3.804A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP B 563 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 730 removed outlier: 3.905A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 768 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.391A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.081A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.537A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1059 Processing helix chain 'B' and resid 1087 through 1097 Processing helix chain 'B' and resid 1099 through 1109 Processing helix chain 'B' and resid 1153 through 1164 Processing helix chain 'C' and resid 27 through 38 removed outlier: 3.862A pdb=" N ALA C 31 " --> pdb=" O ASP C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 116 through 120 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.569A pdb=" N TRP C 203 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.583A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 23 through 27 removed outlier: 3.782A pdb=" N GLU D 27 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.839A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.603A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.546A pdb=" N LYS E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 136 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 22 through 35 removed outlier: 3.590A pdb=" N GLU G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 68 removed outlier: 4.366A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.919A pdb=" N SER I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 28 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.826A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.009A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 removed outlier: 3.524A pdb=" N ARG B1170 " --> pdb=" O GLN A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 95 removed outlier: 3.522A pdb=" N LEU A 90 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.319A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.458A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 266 removed outlier: 3.734A pdb=" N ALA A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 331 removed outlier: 6.520A pdb=" N ARG A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.522A pdb=" N LYS A 357 " --> pdb=" O PHE B1086 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1060 through 1061 removed outlier: 3.623A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP A 454 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 380 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 484 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.081A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 419 " --> pdb=" O ILE A 427 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 427 " --> pdb=" O ILE A 419 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB1, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.659A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE H 99 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N SER H 113 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLY H 101 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG H 111 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA H 114 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP H 42 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.659A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 602 through 603 Processing sheet with id=AB4, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB5, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.577A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB7, first strand: chain 'A' and resid 1139 through 1140 Processing sheet with id=AB8, first strand: chain 'A' and resid 1172 through 1173 Processing sheet with id=AB9, first strand: chain 'A' and resid 1212 through 1215 Processing sheet with id=AC1, first strand: chain 'A' and resid 1307 through 1310 Processing sheet with id=AC2, first strand: chain 'A' and resid 1319 through 1322 removed outlier: 3.738A pdb=" N LYS A1319 " --> pdb=" O LEU A1331 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A1329 " --> pdb=" O ILE A1321 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.140A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR G 72 " --> pdb=" O LEU G 7 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.140A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.457A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS B 146 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 97 through 99 removed outlier: 3.598A pdb=" N HIS B 98 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER B 106 " --> pdb=" O HIS B 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 185 through 186 Processing sheet with id=AC8, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AC9, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.640A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD2, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AD3, first strand: chain 'B' and resid 572 through 577 removed outlier: 5.113A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.851A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.851A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD7, first strand: chain 'B' and resid 935 through 937 removed outlier: 4.489A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ILE B 965 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE B 779 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE B 967 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA B 781 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 935 through 937 Processing sheet with id=AD9, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AE1, first strand: chain 'B' and resid 1113 through 1119 Processing sheet with id=AE2, first strand: chain 'C' and resid 8 through 9 removed outlier: 3.700A pdb=" N THR C 8 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU C 24 " --> pdb=" O THR C 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 121 through 122 removed outlier: 3.557A pdb=" N VAL C 99 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE C 52 " --> pdb=" O VAL L 53 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL L 53 " --> pdb=" O ILE C 52 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 113 through 115 removed outlier: 3.624A pdb=" N ARG C 113 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 151 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 179 through 185 removed outlier: 4.742A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU C 234 " --> pdb=" O GLY C 181 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 74 through 75 removed outlier: 6.640A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AE8, first strand: chain 'G' and resid 149 through 153 removed outlier: 3.548A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU G 145 " --> pdb=" O VAL G 85 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 25 through 27 removed outlier: 3.799A pdb=" N LEU I 36 " --> pdb=" O LYS I 27 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 80 through 81 removed outlier: 3.806A pdb=" N ALA I 94 " --> pdb=" O THR I 81 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 111 through 113 Processing sheet with id=AF3, first strand: chain 'K' and resid 21 through 22 Processing sheet with id=AF4, first strand: chain 'L' and resid 16 through 18 1282 hydrogen bonds defined for protein. 3585 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 11.87 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5337 1.30 - 1.43: 8417 1.43 - 1.56: 18999 1.56 - 1.69: 125 1.69 - 1.83: 312 Bond restraints: 33190 Sorted by residual: bond pdb=" C12 PXZ M 6 " pdb=" C4 PXZ M 6 " ideal model delta sigma weight residual 1.354 1.541 -0.187 2.00e-02 2.50e+03 8.76e+01 bond pdb=" C1 PXZ M 6 " pdb=" C2 PXZ M 6 " ideal model delta sigma weight residual 1.372 1.520 -0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" C2 PXZ M 6 " pdb=" N2 PXZ M 6 " ideal model delta sigma weight residual 1.344 1.469 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C11 PXZ M 6 " pdb=" N10 PXZ M 6 " ideal model delta sigma weight residual 1.297 1.418 -0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" C13 PXZ M 6 " pdb=" O5 PXZ M 6 " ideal model delta sigma weight residual 1.353 1.471 -0.118 2.00e-02 2.50e+03 3.46e+01 ... (remaining 33185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 44485 2.56 - 5.11: 514 5.11 - 7.67: 94 7.67 - 10.22: 12 10.22 - 12.78: 5 Bond angle restraints: 45110 Sorted by residual: angle pdb=" N TYR A 859 " pdb=" CA TYR A 859 " pdb=" CB TYR A 859 " ideal model delta sigma weight residual 110.16 98.87 11.29 1.48e+00 4.57e-01 5.82e+01 angle pdb=" N VAL A 359 " pdb=" CA VAL A 359 " pdb=" C VAL A 359 " ideal model delta sigma weight residual 108.48 119.40 -10.92 1.44e+00 4.82e-01 5.75e+01 angle pdb=" CA TYR A 859 " pdb=" CB TYR A 859 " pdb=" CG TYR A 859 " ideal model delta sigma weight residual 113.90 101.12 12.78 1.80e+00 3.09e-01 5.04e+01 angle pdb=" N LYS A 866 " pdb=" CA LYS A 866 " pdb=" C LYS A 866 " ideal model delta sigma weight residual 111.36 104.85 6.51 1.09e+00 8.42e-01 3.57e+01 angle pdb=" C3' DT T 27 " pdb=" O3' DT T 27 " pdb=" P DT T 28 " ideal model delta sigma weight residual 119.70 126.79 -7.09 1.20e+00 6.94e-01 3.50e+01 ... (remaining 45105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 19893 35.32 - 70.64: 294 70.64 - 105.97: 17 105.97 - 141.29: 1 141.29 - 176.61: 9 Dihedral angle restraints: 20214 sinusoidal: 8860 harmonic: 11354 Sorted by residual: dihedral pdb=" CD ARG A 862 " pdb=" NE ARG A 862 " pdb=" CZ ARG A 862 " pdb=" NH1 ARG A 862 " ideal model delta sinusoidal sigma weight residual 0.00 -52.78 52.78 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CA LYS A 910 " pdb=" C LYS A 910 " pdb=" N PRO A 911 " pdb=" CA PRO A 911 " ideal model delta harmonic sigma weight residual 180.00 150.49 29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA LEU A 343 " pdb=" C LEU A 343 " pdb=" N LYS A 344 " pdb=" CA LYS A 344 " ideal model delta harmonic sigma weight residual 180.00 -153.71 -26.29 0 5.00e+00 4.00e-02 2.76e+01 ... (remaining 20211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 4966 0.127 - 0.255: 49 0.255 - 0.382: 2 0.382 - 0.509: 6 0.509 - 0.637: 25 Chirality restraints: 5048 Sorted by residual: chirality pdb=" P DT N 29 " pdb=" OP1 DT N 29 " pdb=" OP2 DT N 29 " pdb=" O5' DT N 29 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P DT T 6 " pdb=" OP1 DT T 6 " pdb=" OP2 DT T 6 " pdb=" O5' DT T 6 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P DC T 32 " pdb=" OP1 DC T 32 " pdb=" OP2 DC T 32 " pdb=" O5' DC T 32 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.62 2.00e-01 2.50e+01 9.76e+00 ... (remaining 5045 not shown) Planarity restraints: 5633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 862 " 0.874 9.50e-02 1.11e+02 3.92e-01 9.33e+01 pdb=" NE ARG A 862 " -0.053 2.00e-02 2.50e+03 pdb=" CZ ARG A 862 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 862 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 862 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C0 PXZ M 6 " -0.020 2.00e-02 2.50e+03 2.75e-02 3.77e+01 pdb=" C0' PXZ M 6 " 0.008 2.00e-02 2.50e+03 pdb=" C1 PXZ M 6 " 0.004 2.00e-02 2.50e+03 pdb=" C11 PXZ M 6 " -0.030 2.00e-02 2.50e+03 pdb=" C12 PXZ M 6 " -0.027 2.00e-02 2.50e+03 pdb=" C13 PXZ M 6 " -0.021 2.00e-02 2.50e+03 pdb=" C14 PXZ M 6 " -0.009 2.00e-02 2.50e+03 pdb=" C15 PXZ M 6 " -0.009 2.00e-02 2.50e+03 pdb=" C16 PXZ M 6 " 0.012 2.00e-02 2.50e+03 pdb=" C2 PXZ M 6 " 0.017 2.00e-02 2.50e+03 pdb=" C3 PXZ M 6 " 0.016 2.00e-02 2.50e+03 pdb=" C4 PXZ M 6 " -0.014 2.00e-02 2.50e+03 pdb=" C6 PXZ M 6 " 0.010 2.00e-02 2.50e+03 pdb=" C7 PXZ M 6 " 0.029 2.00e-02 2.50e+03 pdb=" C8 PXZ M 6 " 0.042 2.00e-02 2.50e+03 pdb=" C9 PXZ M 6 " 0.019 2.00e-02 2.50e+03 pdb=" N10 PXZ M 6 " -0.053 2.00e-02 2.50e+03 pdb=" N2 PXZ M 6 " 0.037 2.00e-02 2.50e+03 pdb=" O3 PXZ M 6 " 0.040 2.00e-02 2.50e+03 pdb=" O5 PXZ M 6 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 863 " -0.341 9.50e-02 1.11e+02 1.53e-01 1.43e+01 pdb=" NE ARG A 863 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 863 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 863 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 863 " -0.012 2.00e-02 2.50e+03 ... (remaining 5630 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 162 2.45 - 3.06: 21320 3.06 - 3.68: 50798 3.68 - 4.29: 76327 4.29 - 4.90: 124822 Nonbonded interactions: 273429 Sorted by model distance: nonbonded pdb=" O3' C P 12 " pdb="MG MG A2003 " model vdw 1.839 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2003 " model vdw 1.979 2.170 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG A2003 " model vdw 1.986 2.170 nonbonded pdb=" NH1 ARG B 897 " pdb=" OP1 DC T 26 " model vdw 2.010 3.120 nonbonded pdb=" NH1 ARG A 190 " pdb=" O5' DG N 37 " model vdw 2.028 3.120 ... (remaining 273424 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 41.730 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 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 0.408 33227 Z= 0.329 Angle : 0.715 12.776 45152 Z= 0.403 Chirality : 0.063 0.637 5048 Planarity : 0.007 0.392 5632 Dihedral : 12.103 176.610 12869 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.44 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.14), residues: 3858 helix: 0.77 (0.15), residues: 1290 sheet: -0.57 (0.22), residues: 562 loop : -0.72 (0.14), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 358 TYR 0.048 0.002 TYR A 859 PHE 0.023 0.002 PHE A 668 TRP 0.029 0.002 TRP A 988 HIS 0.007 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.24 (33190) covalent geometry : angle 0.70464 / 0.40 (45110) hydrogen bonds : bond 0.19236 / 12.88 ( 1311) hydrogen bonds : angle 7.59409 / 5.44 ( 3689) metal coordination : bond 0.00608 / 0.40 ( 31) metal coordination : angle 4.10561 / 2.95 ( 39) Misc. bond : bond 0.18271 / 9.62 ( 5) link_TRANS : bond 0.00080 / 0.04 ( 1) link_TRANS : angle 0.52714 / 0.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1020 time to evaluate : 1.308 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: A 234 PHE cc_start: 0.8041 (t80) cc_final: 0.7810 (t80) REVERT: A 266 MET cc_start: 0.2412 (mmm) cc_final: 0.2132 (mmm) REVERT: A 361 PHE cc_start: 0.6736 (m-80) cc_final: 0.6174 (m-80) REVERT: A 467 MET cc_start: 0.7141 (mmt) cc_final: 0.6742 (mpp) REVERT: A 744 ILE cc_start: 0.7809 (mt) cc_final: 0.7279 (mt) REVERT: A 962 ASP cc_start: 0.6758 (m-30) cc_final: 0.6453 (m-30) REVERT: B 177 CYS cc_start: 0.5946 (t) cc_final: 0.5204 (p) REVERT: B 208 PHE cc_start: 0.5976 (m-80) cc_final: 0.5776 (m-80) REVERT: B 296 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6554 (mm-30) REVERT: B 802 ASP cc_start: 0.6120 (m-30) cc_final: 0.5853 (m-30) REVERT: B 845 TYR cc_start: 0.4202 (m-80) cc_final: 0.3927 (m-10) REVERT: B 889 LYS cc_start: 0.8095 (mttt) cc_final: 0.7788 (mtmp) REVERT: C 105 VAL cc_start: 0.7841 (t) cc_final: 0.7625 (p) REVERT: C 260 GLN cc_start: 0.6959 (tt0) cc_final: 0.6435 (tp-100) REVERT: E 35 GLN cc_start: 0.6260 (mt0) cc_final: 0.5910 (mp10) REVERT: E 84 ILE cc_start: 0.3411 (mt) cc_final: 0.2820 (mt) REVERT: G 41 LYS cc_start: 0.7928 (tttt) cc_final: 0.7512 (tptp) REVERT: G 104 MET cc_start: 0.6099 (ttp) cc_final: 0.5680 (tpp) REVERT: G 143 ILE cc_start: 0.8084 (pt) cc_final: 0.7755 (mp) REVERT: H 78 THR cc_start: 0.8028 (p) cc_final: 0.7661 (p) REVERT: I 22 ASN cc_start: 0.7308 (m-40) cc_final: 0.7037 (m110) REVERT: I 23 MET cc_start: 0.4468 (ttm) cc_final: 0.4181 (ttm) REVERT: K 5 PRO cc_start: 0.6511 (Cg_exo) cc_final: 0.6310 (Cg_endo) outliers start: 0 outliers final: 1 residues processed: 1020 average time/residue: 0.7497 time to fit residues: 899.3254 Evaluate side-chains 525 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 524 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN A 288 ASN A 320 ASN A 472 HIS ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 ASN ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 HIS A 507 GLN A 562 ASN A 671 ASN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 GLN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1082 HIS ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1248 ASN A1310 HIS ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN B 245 GLN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 525 ASN ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 HIS B 654 GLN B 699 HIS B 718 GLN B 725 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN B 968 ASN B1007 ASN B1025 ASN B1097 HIS B1115 GLN ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN E 30 GLN E 138 ASN ** E 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 GLN H 76 ASN I 41 ASN I 87 GLN J 16 ASN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.183871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.154433 restraints weight = 55093.439| |-----------------------------------------------------------------------------| r_work (start): 0.4415 rms_B_bonded: 2.63 r_work: 0.4323 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33227 Z= 0.199 Angle : 0.792 31.568 45152 Z= 0.395 Chirality : 0.049 0.419 5048 Planarity : 0.006 0.066 5632 Dihedral : 14.537 176.357 5019 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.70 % Favored : 94.22 % Rotamer: Outliers : 3.53 % Allowed : 13.74 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.05 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.13), residues: 3858 helix: 0.50 (0.14), residues: 1330 sheet: -0.68 (0.21), residues: 579 loop : -0.88 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1286 TYR 0.030 0.002 TYR E 90 PHE 0.032 0.002 PHE B 422 TRP 0.019 0.002 TRP A 988 HIS 0.015 0.002 HIS B 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (33190) covalent geometry : angle 0.75193 / 0.39 (45110) hydrogen bonds : bond 0.05960 / 3.86 ( 1311) hydrogen bonds : angle 6.11543 / 4.34 ( 3689) metal coordination : bond 0.01180 / 0.85 ( 31) metal coordination : angle 8.46783 / 6.02 ( 39) Misc. bond : bond 0.00166 / 0.10 ( 5) link_TRANS : bond 0.00001 / 0.00 ( 1) link_TRANS : angle 0.73187 / 0.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 557 time to evaluate : 0.772 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: A 16 ARG cc_start: 0.7685 (mmt90) cc_final: 0.7225 (mpt180) REVERT: A 58 MET cc_start: 0.7101 (ttm) cc_final: 0.6882 (ttt) REVERT: A 65 ILE cc_start: 0.7285 (mp) cc_final: 0.7044 (mp) REVERT: A 67 ARG cc_start: 0.6749 (tpm170) cc_final: 0.6450 (tpm170) REVERT: A 78 MET cc_start: 0.7261 (tpt) cc_final: 0.6805 (tpt) REVERT: A 293 ASN cc_start: 0.7941 (m-40) cc_final: 0.7637 (m-40) REVERT: A 361 PHE cc_start: 0.6930 (m-80) cc_final: 0.6526 (m-80) REVERT: A 388 MET cc_start: 0.6130 (mmm) cc_final: 0.5513 (mmm) REVERT: A 407 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7201 (ttp80) REVERT: A 467 MET cc_start: 0.7210 (mmt) cc_final: 0.6624 (mpp) REVERT: A 643 LYS cc_start: 0.7960 (mttp) cc_final: 0.7652 (mtpt) REVERT: A 803 LYS cc_start: 0.7647 (mttt) cc_final: 0.7123 (mtmm) REVERT: A 872 MET cc_start: 0.8050 (ttt) cc_final: 0.7584 (ttt) REVERT: A 962 ASP cc_start: 0.6737 (m-30) cc_final: 0.6342 (m-30) REVERT: A 1054 MET cc_start: 0.6389 (mmp) cc_final: 0.6169 (mmt) REVERT: A 1228 MET cc_start: 0.5744 (OUTLIER) cc_final: 0.5503 (tpp) REVERT: B 49 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7067 (tp30) REVERT: B 173 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7466 (pt0) REVERT: B 177 CYS cc_start: 0.5800 (t) cc_final: 0.4926 (p) REVERT: B 208 PHE cc_start: 0.6908 (m-80) cc_final: 0.6464 (m-10) REVERT: B 296 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6674 (mm-30) REVERT: B 297 MET cc_start: 0.5528 (mtt) cc_final: 0.5276 (mtt) REVERT: B 323 SER cc_start: 0.8656 (t) cc_final: 0.8375 (p) REVERT: B 347 MET cc_start: 0.5366 (OUTLIER) cc_final: 0.5076 (tmm) REVERT: B 413 LYS cc_start: 0.6667 (mmpt) cc_final: 0.6430 (mmpt) REVERT: B 463 ARG cc_start: 0.5240 (ttp-110) cc_final: 0.4821 (ptt180) REVERT: B 566 LYS cc_start: 0.3616 (OUTLIER) cc_final: 0.3330 (mttp) REVERT: B 802 ASP cc_start: 0.6260 (m-30) cc_final: 0.5973 (m-30) REVERT: B 889 LYS cc_start: 0.8042 (mttt) cc_final: 0.7822 (mtmp) REVERT: B 911 LEU cc_start: 0.5195 (mp) cc_final: 0.4659 (mm) REVERT: C 105 VAL cc_start: 0.7894 (t) cc_final: 0.7458 (p) REVERT: C 128 ILE cc_start: 0.5769 (pt) cc_final: 0.5531 (tp) REVERT: C 227 GLU cc_start: 0.5319 (OUTLIER) cc_final: 0.4797 (mt-10) REVERT: C 260 GLN cc_start: 0.7179 (tt0) cc_final: 0.6338 (tp-100) REVERT: D 57 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.6776 (mt) REVERT: D 62 MET cc_start: 0.6834 (mmp) cc_final: 0.6615 (tmm) REVERT: D 112 LYS cc_start: 0.6966 (pttp) cc_final: 0.6448 (mttp) REVERT: D 129 GLN cc_start: 0.8298 (tp40) cc_final: 0.8069 (tp-100) REVERT: E 35 GLN cc_start: 0.6475 (mt0) cc_final: 0.5857 (mp10) REVERT: E 88 LYS cc_start: 0.8781 (mttt) cc_final: 0.8561 (mttt) REVERT: F 75 MET cc_start: 0.7843 (mtt) cc_final: 0.7428 (mtp) REVERT: F 84 GLU cc_start: 0.7466 (mp0) cc_final: 0.7088 (mp0) REVERT: F 116 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7235 (mt-10) REVERT: G 14 HIS cc_start: 0.5821 (t70) cc_final: 0.5446 (t-90) REVERT: G 41 LYS cc_start: 0.7756 (tttt) cc_final: 0.7157 (tptp) REVERT: G 63 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6342 (ptp-170) REVERT: G 73 LYS cc_start: 0.7974 (mmmm) cc_final: 0.7656 (mmmm) REVERT: G 101 ILE cc_start: 0.6536 (OUTLIER) cc_final: 0.6333 (pt) REVERT: G 104 MET cc_start: 0.5807 (ttp) cc_final: 0.5496 (tpp) REVERT: G 142 GLU cc_start: 0.6482 (mp0) cc_final: 0.5934 (mp0) REVERT: I 23 MET cc_start: 0.4747 (ttm) cc_final: 0.4224 (ttm) REVERT: K 93 ASP cc_start: 0.6817 (m-30) cc_final: 0.6497 (m-30) outliers start: 121 outliers final: 40 residues processed: 630 average time/residue: 0.6701 time to fit residues: 501.7178 Evaluate side-chains 490 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 440 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 566 LYS Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 55 GLN Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 28 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 179 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 315 optimal weight: 0.9980 chunk 312 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 280 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 HIS A 662 HIS ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 ASN B1025 ASN ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 ASN H 44 ASN H 76 ASN I 87 GLN ** I 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.179056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.148630 restraints weight = 54992.196| |-----------------------------------------------------------------------------| r_work (start): 0.4341 rms_B_bonded: 2.59 r_work: 0.4250 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 33227 Z= 0.244 Angle : 0.782 23.377 45152 Z= 0.393 Chirality : 0.049 0.411 5048 Planarity : 0.006 0.086 5632 Dihedral : 14.462 179.738 5017 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.25 % Favored : 93.62 % Rotamer: Outliers : 4.23 % Allowed : 14.61 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.05 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.13), residues: 3858 helix: 0.38 (0.14), residues: 1344 sheet: -0.89 (0.21), residues: 573 loop : -1.04 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 931 TYR 0.053 0.002 TYR E 90 PHE 0.026 0.003 PHE B 422 TRP 0.021 0.002 TRP A 988 HIS 0.012 0.002 HIS B 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (33190) covalent geometry : angle 0.75121 / 0.39 (45110) hydrogen bonds : bond 0.05544 / 3.59 ( 1311) hydrogen bonds : angle 5.87977 / 4.17 ( 3689) metal coordination : bond 0.01051 / 0.64 ( 31) metal coordination : angle 7.45700 / 5.41 ( 39) Misc. bond : bond 0.00179 / 0.10 ( 5) link_TRANS : bond 0.00392 / 0.21 ( 1) link_TRANS : angle 0.10843 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 494 time to evaluate : 1.268 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 16 ARG cc_start: 0.7759 (mmt90) cc_final: 0.7228 (mpt180) REVERT: A 58 MET cc_start: 0.7269 (ttm) cc_final: 0.7030 (ttm) REVERT: A 65 ILE cc_start: 0.7547 (mp) cc_final: 0.7301 (mp) REVERT: A 78 MET cc_start: 0.7310 (tpt) cc_final: 0.7004 (tpt) REVERT: A 293 ASN cc_start: 0.7910 (m-40) cc_final: 0.7594 (m-40) REVERT: A 404 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7905 (tm-30) REVERT: A 408 ARG cc_start: 0.7318 (ttt90) cc_final: 0.7006 (ttt180) REVERT: A 803 LYS cc_start: 0.7698 (mttt) cc_final: 0.7202 (mtmm) REVERT: A 919 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6920 (tttt) REVERT: A 962 ASP cc_start: 0.6957 (m-30) cc_final: 0.6484 (m-30) REVERT: A 1071 GLU cc_start: 0.5903 (OUTLIER) cc_final: 0.5374 (mm-30) REVERT: A 1135 LYS cc_start: 0.5622 (ptmm) cc_final: 0.5246 (ptmm) REVERT: A 1228 MET cc_start: 0.5697 (OUTLIER) cc_final: 0.5304 (tpp) REVERT: A 1422 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7688 (mm-40) REVERT: B 49 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7226 (tp30) REVERT: B 173 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7515 (pt0) REVERT: B 177 CYS cc_start: 0.5742 (t) cc_final: 0.4942 (p) REVERT: B 184 TYR cc_start: 0.7448 (p90) cc_final: 0.6990 (p90) REVERT: B 208 PHE cc_start: 0.6820 (m-80) cc_final: 0.6285 (m-10) REVERT: B 296 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6728 (mm-30) REVERT: B 323 SER cc_start: 0.8642 (t) cc_final: 0.8366 (p) REVERT: B 340 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7892 (tptp) REVERT: B 368 MET cc_start: 0.4910 (ttt) cc_final: 0.4657 (ttt) REVERT: B 463 ARG cc_start: 0.5192 (ttp-110) cc_final: 0.4826 (ptt180) REVERT: B 566 LYS cc_start: 0.3784 (OUTLIER) cc_final: 0.2766 (mtpp) REVERT: B 802 ASP cc_start: 0.6746 (m-30) cc_final: 0.6456 (m-30) REVERT: B 889 LYS cc_start: 0.8047 (mttt) cc_final: 0.7779 (mtmp) REVERT: B 911 LEU cc_start: 0.5302 (mp) cc_final: 0.4747 (mm) REVERT: B 1092 ASP cc_start: 0.7899 (m-30) cc_final: 0.7651 (m-30) REVERT: C 100 GLU cc_start: 0.7524 (tt0) cc_final: 0.6834 (mp0) REVERT: C 105 VAL cc_start: 0.7924 (t) cc_final: 0.7486 (p) REVERT: C 260 GLN cc_start: 0.7202 (tt0) cc_final: 0.6399 (tp-100) REVERT: D 57 LEU cc_start: 0.7650 (mm) cc_final: 0.6790 (mt) REVERT: D 62 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6593 (tmm) REVERT: D 84 ARG cc_start: 0.8658 (tpt90) cc_final: 0.8426 (tpt-90) REVERT: D 94 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7466 (ptmt) REVERT: D 128 GLN cc_start: 0.6882 (tp-100) cc_final: 0.6583 (tp-100) REVERT: D 129 GLN cc_start: 0.8247 (tp40) cc_final: 0.7963 (tp40) REVERT: D 132 ASP cc_start: 0.8039 (m-30) cc_final: 0.7802 (m-30) REVERT: E 35 GLN cc_start: 0.6512 (mt0) cc_final: 0.5901 (mp10) REVERT: F 61 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6547 (mt-10) REVERT: F 80 MET cc_start: 0.5860 (pmm) cc_final: 0.5328 (pmm) REVERT: F 84 GLU cc_start: 0.7846 (mp0) cc_final: 0.7538 (mp0) REVERT: F 95 LYS cc_start: 0.7598 (tttp) cc_final: 0.7276 (mtmm) REVERT: G 14 HIS cc_start: 0.5838 (t70) cc_final: 0.5189 (t-90) REVERT: G 41 LYS cc_start: 0.7799 (tttt) cc_final: 0.7247 (tptp) REVERT: G 44 PHE cc_start: 0.5255 (m-80) cc_final: 0.4591 (m-80) REVERT: G 63 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6394 (ptp-170) REVERT: G 73 LYS cc_start: 0.8045 (mmmm) cc_final: 0.7746 (mmmm) REVERT: G 83 GLU cc_start: 0.6960 (tt0) cc_final: 0.6347 (pt0) REVERT: G 143 ILE cc_start: 0.7707 (tt) cc_final: 0.7500 (mp) REVERT: I 23 MET cc_start: 0.5087 (ttm) cc_final: 0.4496 (ttm) REVERT: L 25 GLU cc_start: 0.7220 (tt0) cc_final: 0.6878 (tm-30) outliers start: 145 outliers final: 59 residues processed: 579 average time/residue: 0.6422 time to fit residues: 443.8920 Evaluate side-chains 498 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 427 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 919 LYS Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1346 VAL Chi-restraints excluded: chain A residue 1422 GLN Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 566 LYS Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1046 THR Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 176 TRP Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 55 GLN Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 28 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 84 optimal weight: 0.9990 chunk 71 optimal weight: 0.0030 chunk 272 optimal weight: 0.4980 chunk 108 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 105 optimal weight: 0.0980 chunk 342 optimal weight: 0.9990 chunk 195 optimal weight: 8.9990 chunk 335 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 HIS ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1117 HIS E 148 HIS G 93 ASN H 44 ASN H 76 ASN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN ** I 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.182849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.153006 restraints weight = 54823.589| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 2.62 r_work: 0.4308 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 33227 Z= 0.147 Angle : 0.711 21.725 45152 Z= 0.353 Chirality : 0.046 0.423 5048 Planarity : 0.005 0.062 5632 Dihedral : 14.305 177.026 5017 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.37 % Favored : 94.50 % Rotamer: Outliers : 4.00 % Allowed : 16.36 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.05 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 3858 helix: 0.55 (0.14), residues: 1347 sheet: -0.85 (0.21), residues: 571 loop : -0.94 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 37 TYR 0.025 0.002 TYR E 90 PHE 0.023 0.002 PHE B 918 TRP 0.018 0.002 TRP A1334 HIS 0.013 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (33190) covalent geometry : angle 0.68457 / 0.35 (45110) hydrogen bonds : bond 0.04735 / 2.98 ( 1311) hydrogen bonds : angle 5.61918 / 3.98 ( 3689) metal coordination : bond 0.00690 / 0.45 ( 31) metal coordination : angle 6.61160 / 4.61 ( 39) Misc. bond : bond 0.00129 / 0.08 ( 5) link_TRANS : bond 0.00098 / 0.05 ( 1) link_TRANS : angle 0.47173 / 0.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 493 time to evaluate : 1.417 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: A 16 ARG cc_start: 0.7579 (mmt90) cc_final: 0.7132 (mpt180) REVERT: A 58 MET cc_start: 0.7144 (ttm) cc_final: 0.6876 (ttm) REVERT: A 65 ILE cc_start: 0.7483 (mp) cc_final: 0.7223 (mp) REVERT: A 67 ARG cc_start: 0.6495 (tpm170) cc_final: 0.5872 (tpm170) REVERT: A 78 MET cc_start: 0.7180 (tpt) cc_final: 0.6531 (tpt) REVERT: A 293 ASN cc_start: 0.7902 (m-40) cc_final: 0.7607 (m-40) REVERT: A 361 PHE cc_start: 0.7171 (m-80) cc_final: 0.6923 (m-80) REVERT: A 388 MET cc_start: 0.6006 (mmm) cc_final: 0.5645 (mmm) REVERT: A 803 LYS cc_start: 0.7629 (mttt) cc_final: 0.7102 (mtmm) REVERT: A 1228 MET cc_start: 0.5830 (OUTLIER) cc_final: 0.5511 (tpp) REVERT: A 1422 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7614 (mm-40) REVERT: A 1428 MET cc_start: 0.7614 (ttm) cc_final: 0.6669 (tmm) REVERT: B 173 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7554 (pt0) REVERT: B 177 CYS cc_start: 0.5402 (t) cc_final: 0.4642 (p) REVERT: B 208 PHE cc_start: 0.6838 (m-80) cc_final: 0.6351 (m-10) REVERT: B 296 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6715 (mm-30) REVERT: B 323 SER cc_start: 0.8621 (t) cc_final: 0.8353 (p) REVERT: B 357 CYS cc_start: 0.5397 (OUTLIER) cc_final: 0.3756 (m) REVERT: B 407 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.7123 (mtt) REVERT: B 463 ARG cc_start: 0.5170 (ttp-110) cc_final: 0.4740 (pmt170) REVERT: B 566 LYS cc_start: 0.3858 (OUTLIER) cc_final: 0.2878 (mtpp) REVERT: B 802 ASP cc_start: 0.6309 (m-30) cc_final: 0.6031 (m-30) REVERT: B 889 LYS cc_start: 0.8027 (mttt) cc_final: 0.7788 (mtmp) REVERT: B 911 LEU cc_start: 0.5035 (mp) cc_final: 0.4575 (mm) REVERT: B 1081 ASP cc_start: 0.8194 (t70) cc_final: 0.7900 (t70) REVERT: C 100 GLU cc_start: 0.7455 (tt0) cc_final: 0.6786 (mp0) REVERT: C 105 VAL cc_start: 0.7926 (t) cc_final: 0.7478 (p) REVERT: C 106 ARG cc_start: 0.7009 (mtp-110) cc_final: 0.6610 (ttm-80) REVERT: C 260 GLN cc_start: 0.7234 (tt0) cc_final: 0.6433 (tp-100) REVERT: D 57 LEU cc_start: 0.7706 (mm) cc_final: 0.6903 (mt) REVERT: D 62 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6627 (tmm) REVERT: D 94 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7472 (ptmt) REVERT: D 128 GLN cc_start: 0.6990 (tp-100) cc_final: 0.6779 (tp-100) REVERT: D 129 GLN cc_start: 0.8312 (tp40) cc_final: 0.7992 (tp40) REVERT: D 132 ASP cc_start: 0.8040 (m-30) cc_final: 0.7828 (m-30) REVERT: E 35 GLN cc_start: 0.6394 (mt0) cc_final: 0.5950 (mp10) REVERT: E 116 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8346 (mt0) REVERT: E 199 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7886 (t) REVERT: F 75 MET cc_start: 0.7684 (mtt) cc_final: 0.7113 (mtp) REVERT: F 80 MET cc_start: 0.6315 (pmm) cc_final: 0.5655 (pmm) REVERT: F 84 GLU cc_start: 0.7934 (mp0) cc_final: 0.7650 (mp0) REVERT: F 95 LYS cc_start: 0.7569 (tttp) cc_final: 0.7268 (mtmm) REVERT: G 14 HIS cc_start: 0.5798 (t70) cc_final: 0.5091 (t-90) REVERT: G 30 LEU cc_start: 0.5813 (tm) cc_final: 0.5610 (tm) REVERT: G 41 LYS cc_start: 0.7798 (tttt) cc_final: 0.7179 (tptp) REVERT: G 44 PHE cc_start: 0.5165 (m-80) cc_final: 0.4479 (m-80) REVERT: G 63 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6284 (ptp-170) REVERT: G 73 LYS cc_start: 0.8078 (mmmm) cc_final: 0.7722 (mmmm) REVERT: G 164 MET cc_start: 0.5863 (ppp) cc_final: 0.5469 (pp-130) REVERT: H 44 ASN cc_start: 0.6666 (OUTLIER) cc_final: 0.6417 (t160) REVERT: H 146 LYS cc_start: 0.7347 (ttmm) cc_final: 0.7102 (ttmm) REVERT: I 23 MET cc_start: 0.5097 (ttm) cc_final: 0.4521 (ttm) REVERT: I 92 LYS cc_start: 0.7778 (mmtm) cc_final: 0.7532 (mppt) REVERT: K 55 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6938 (tp40) REVERT: K 93 ASP cc_start: 0.6761 (m-30) cc_final: 0.6354 (m-30) REVERT: L 32 ASP cc_start: 0.7945 (t0) cc_final: 0.7694 (t0) outliers start: 137 outliers final: 50 residues processed: 579 average time/residue: 0.6555 time to fit residues: 456.8368 Evaluate side-chains 492 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 430 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1302 GLU Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1422 GLN Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 357 CYS Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 566 LYS Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 176 TRP Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 44 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 55 GLN Chi-restraints excluded: chain K residue 78 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 139 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 95 optimal weight: 0.2980 chunk 376 optimal weight: 5.9990 chunk 312 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 360 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS A 711 GLN ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS B 518 HIS B 649 ASN B 650 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 790 GLN B1007 ASN ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 ASN H 44 ASN H 76 ASN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN ** I 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.181646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.151654 restraints weight = 54658.889| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 2.61 r_work: 0.4287 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 33227 Z= 0.159 Angle : 0.704 21.199 45152 Z= 0.350 Chirality : 0.046 0.410 5048 Planarity : 0.005 0.060 5632 Dihedral : 14.220 176.408 5017 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.60 % Favored : 94.25 % Rotamer: Outliers : 3.88 % Allowed : 17.88 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.05 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 3858 helix: 0.58 (0.14), residues: 1343 sheet: -0.85 (0.21), residues: 575 loop : -0.96 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 37 TYR 0.046 0.002 TYR E 90 PHE 0.024 0.002 PHE B 918 TRP 0.014 0.002 TRP C 49 HIS 0.010 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (33190) covalent geometry : angle 0.67972 / 0.35 (45110) hydrogen bonds : bond 0.04637 / 2.94 ( 1311) hydrogen bonds : angle 5.51852 / 3.92 ( 3689) metal coordination : bond 0.00757 / 0.48 ( 31) metal coordination : angle 6.33751 / 4.41 ( 39) Misc. bond : bond 0.00126 / 0.08 ( 5) link_TRANS : bond 0.00162 / 0.09 ( 1) link_TRANS : angle 0.25895 / 0.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 437 time to evaluate : 1.351 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 16 ARG cc_start: 0.7605 (mmt90) cc_final: 0.7135 (mpt180) REVERT: A 57 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6218 (mp) REVERT: A 58 MET cc_start: 0.7134 (ttm) cc_final: 0.6796 (ttm) REVERT: A 65 ILE cc_start: 0.7480 (mp) cc_final: 0.7230 (mp) REVERT: A 67 ARG cc_start: 0.6644 (tpm170) cc_final: 0.6329 (tpm170) REVERT: A 78 MET cc_start: 0.7206 (tpt) cc_final: 0.6656 (tpt) REVERT: A 293 ASN cc_start: 0.7919 (m-40) cc_final: 0.7641 (m-40) REVERT: A 361 PHE cc_start: 0.7156 (m-80) cc_final: 0.6907 (m-80) REVERT: A 388 MET cc_start: 0.6153 (mmm) cc_final: 0.5833 (mmm) REVERT: A 467 MET cc_start: 0.6941 (mmt) cc_final: 0.6529 (mpp) REVERT: A 711 GLN cc_start: 0.6303 (mt0) cc_final: 0.6091 (mt0) REVERT: A 803 LYS cc_start: 0.7596 (mttt) cc_final: 0.7085 (mtmm) REVERT: A 1071 GLU cc_start: 0.5973 (OUTLIER) cc_final: 0.5426 (mm-30) REVERT: A 1078 GLN cc_start: 0.6559 (OUTLIER) cc_final: 0.6350 (mp10) REVERT: A 1228 MET cc_start: 0.5954 (OUTLIER) cc_final: 0.5651 (tpp) REVERT: A 1310 HIS cc_start: 0.6671 (OUTLIER) cc_final: 0.6307 (p-80) REVERT: A 1422 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7663 (mm-40) REVERT: A 1428 MET cc_start: 0.7604 (ttm) cc_final: 0.6678 (tmm) REVERT: A 1433 GLU cc_start: 0.6797 (tp30) cc_final: 0.6249 (tp30) REVERT: B 173 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7574 (pt0) REVERT: B 177 CYS cc_start: 0.5623 (t) cc_final: 0.4888 (p) REVERT: B 208 PHE cc_start: 0.6878 (m-80) cc_final: 0.6311 (m-10) REVERT: B 296 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6695 (mm-30) REVERT: B 323 SER cc_start: 0.8613 (t) cc_final: 0.8349 (p) REVERT: B 357 CYS cc_start: 0.5392 (OUTLIER) cc_final: 0.3705 (m) REVERT: B 407 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.7158 (mtt) REVERT: B 463 ARG cc_start: 0.5177 (ttp-110) cc_final: 0.4752 (pmt170) REVERT: B 566 LYS cc_start: 0.3884 (OUTLIER) cc_final: 0.3007 (mtpm) REVERT: B 579 ASP cc_start: 0.7384 (t0) cc_final: 0.7177 (t0) REVERT: B 802 ASP cc_start: 0.6361 (m-30) cc_final: 0.6055 (m-30) REVERT: B 889 LYS cc_start: 0.8093 (mttt) cc_final: 0.7824 (mtmp) REVERT: B 911 LEU cc_start: 0.4963 (mp) cc_final: 0.4464 (mm) REVERT: C 6 GLN cc_start: 0.8004 (mm110) cc_final: 0.7691 (mm-40) REVERT: C 100 GLU cc_start: 0.7492 (tt0) cc_final: 0.6739 (mm-30) REVERT: C 105 VAL cc_start: 0.7869 (t) cc_final: 0.7474 (p) REVERT: C 227 GLU cc_start: 0.5180 (OUTLIER) cc_final: 0.4585 (mt-10) REVERT: C 260 GLN cc_start: 0.7314 (tt0) cc_final: 0.6827 (tp-100) REVERT: D 57 LEU cc_start: 0.7753 (mm) cc_final: 0.6995 (mt) REVERT: D 62 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6663 (tmm) REVERT: D 94 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7618 (ptmm) REVERT: D 112 LYS cc_start: 0.6727 (pttp) cc_final: 0.5991 (mttt) REVERT: D 128 GLN cc_start: 0.6995 (tp-100) cc_final: 0.6769 (tp-100) REVERT: D 129 GLN cc_start: 0.8246 (tp40) cc_final: 0.7957 (tp40) REVERT: D 132 ASP cc_start: 0.7921 (m-30) cc_final: 0.7704 (m-30) REVERT: E 35 GLN cc_start: 0.6468 (mt0) cc_final: 0.5843 (mp10) REVERT: E 108 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.7213 (tp40) REVERT: E 181 ARG cc_start: 0.6614 (OUTLIER) cc_final: 0.6388 (mtm180) REVERT: E 199 THR cc_start: 0.8240 (OUTLIER) cc_final: 0.7933 (t) REVERT: F 80 MET cc_start: 0.6515 (pmm) cc_final: 0.6153 (pmm) REVERT: F 84 GLU cc_start: 0.7910 (mp0) cc_final: 0.7602 (mp0) REVERT: F 95 LYS cc_start: 0.7600 (tttp) cc_final: 0.7289 (mtmm) REVERT: G 14 HIS cc_start: 0.5830 (t70) cc_final: 0.5087 (t-90) REVERT: G 41 LYS cc_start: 0.7785 (tttt) cc_final: 0.7221 (tptp) REVERT: G 63 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6350 (ptp-170) REVERT: G 73 LYS cc_start: 0.8085 (mmmm) cc_final: 0.7732 (mmmm) REVERT: G 164 MET cc_start: 0.5909 (ppp) cc_final: 0.5480 (pp-130) REVERT: H 118 TYR cc_start: 0.7073 (m-80) cc_final: 0.6665 (m-80) REVERT: H 146 LYS cc_start: 0.7382 (ttmm) cc_final: 0.7051 (ttmm) REVERT: I 23 MET cc_start: 0.5011 (ttm) cc_final: 0.4511 (ttm) REVERT: I 92 LYS cc_start: 0.7740 (mmtm) cc_final: 0.7415 (mppt) REVERT: K 55 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6916 (tp40) REVERT: L 28 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6831 (tt) outliers start: 133 outliers final: 54 residues processed: 521 average time/residue: 0.6802 time to fit residues: 426.3484 Evaluate side-chains 488 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 415 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1078 GLN Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1310 HIS Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1422 GLN Chi-restraints excluded: chain A residue 1470 CYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 357 CYS Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 566 LYS Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 176 TRP Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 181 ARG Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 55 GLN Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 28 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 116 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 266 optimal weight: 0.8980 chunk 222 optimal weight: 0.6980 chunk 193 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 310 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 209 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 518 HIS B 649 ASN B 749 HIS ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1007 ASN ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN H 76 ASN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN I 118 HIS ** K 2 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 = 0.4722 r_free = 0.4722 target = 0.179721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.149244 restraints weight = 54833.267| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 2.61 r_work: 0.4257 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33227 Z= 0.186 Angle : 0.712 20.466 45152 Z= 0.354 Chirality : 0.047 0.403 5048 Planarity : 0.005 0.070 5632 Dihedral : 14.187 176.769 5017 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.86 % Favored : 94.01 % Rotamer: Outliers : 4.43 % Allowed : 17.67 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.05 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.13), residues: 3858 helix: 0.59 (0.14), residues: 1341 sheet: -0.94 (0.21), residues: 559 loop : -0.98 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 859 TYR 0.034 0.002 TYR E 90 PHE 0.023 0.002 PHE B 918 TRP 0.030 0.002 TRP A1334 HIS 0.008 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (33190) covalent geometry : angle 0.68688 / 0.35 (45110) hydrogen bonds : bond 0.04659 / 2.97 ( 1311) hydrogen bonds : angle 5.47094 / 3.88 ( 3689) metal coordination : bond 0.00881 / 0.53 ( 31) metal coordination : angle 6.39651 / 4.55 ( 39) Misc. bond : bond 0.00116 / 0.07 ( 5) link_TRANS : bond 0.00204 / 0.11 ( 1) link_TRANS : angle 0.14915 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 440 time to evaluate : 1.267 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 16 ARG cc_start: 0.7644 (mmt90) cc_final: 0.7148 (mpt180) REVERT: A 58 MET cc_start: 0.7181 (ttm) cc_final: 0.6893 (ttm) REVERT: A 65 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.6964 (mp) REVERT: A 67 ARG cc_start: 0.6954 (tpm170) cc_final: 0.6749 (tpm170) REVERT: A 78 MET cc_start: 0.7279 (tpt) cc_final: 0.6793 (tpt) REVERT: A 293 ASN cc_start: 0.7889 (m-40) cc_final: 0.7604 (m-40) REVERT: A 361 PHE cc_start: 0.7177 (m-80) cc_final: 0.6857 (m-80) REVERT: A 407 ARG cc_start: 0.7553 (mmt-90) cc_final: 0.7309 (mmm-85) REVERT: A 467 MET cc_start: 0.6977 (mmt) cc_final: 0.6663 (mpp) REVERT: A 803 LYS cc_start: 0.7746 (mttt) cc_final: 0.7289 (mtmm) REVERT: A 1034 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6352 (tp40) REVERT: A 1071 GLU cc_start: 0.5906 (OUTLIER) cc_final: 0.5359 (mm-30) REVERT: A 1228 MET cc_start: 0.6018 (OUTLIER) cc_final: 0.5738 (tpp) REVERT: A 1310 HIS cc_start: 0.6763 (OUTLIER) cc_final: 0.6293 (p-80) REVERT: A 1422 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7612 (mm-40) REVERT: A 1433 GLU cc_start: 0.6808 (tp30) cc_final: 0.6291 (tp30) REVERT: B 49 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.6280 (tm-30) REVERT: B 145 GLN cc_start: 0.8303 (mt0) cc_final: 0.8034 (mp10) REVERT: B 173 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7611 (pt0) REVERT: B 177 CYS cc_start: 0.5621 (t) cc_final: 0.4897 (p) REVERT: B 208 PHE cc_start: 0.6886 (m-80) cc_final: 0.6387 (m-10) REVERT: B 323 SER cc_start: 0.8584 (t) cc_final: 0.8301 (p) REVERT: B 357 CYS cc_start: 0.5373 (OUTLIER) cc_final: 0.3711 (m) REVERT: B 407 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.7081 (mtt) REVERT: B 429 PHE cc_start: 0.6140 (t80) cc_final: 0.5774 (t80) REVERT: B 463 ARG cc_start: 0.5188 (ttp-110) cc_final: 0.4781 (pmt170) REVERT: B 566 LYS cc_start: 0.3994 (OUTLIER) cc_final: 0.3106 (mtpm) REVERT: B 802 ASP cc_start: 0.6559 (m-30) cc_final: 0.6288 (m-30) REVERT: B 889 LYS cc_start: 0.8077 (mttt) cc_final: 0.7835 (mtmt) REVERT: B 911 LEU cc_start: 0.5062 (mp) cc_final: 0.4578 (mm) REVERT: C 6 GLN cc_start: 0.8030 (mm110) cc_final: 0.7741 (mm-40) REVERT: C 106 ARG cc_start: 0.7217 (mtp-110) cc_final: 0.6771 (ttm110) REVERT: C 260 GLN cc_start: 0.7321 (tt0) cc_final: 0.6900 (tp-100) REVERT: D 57 LEU cc_start: 0.7657 (mm) cc_final: 0.6837 (mt) REVERT: D 62 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6678 (tmm) REVERT: D 94 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8033 (ptmm) REVERT: D 112 LYS cc_start: 0.6812 (pttp) cc_final: 0.6065 (mttp) REVERT: D 128 GLN cc_start: 0.6968 (tp-100) cc_final: 0.6740 (tp-100) REVERT: D 129 GLN cc_start: 0.8242 (tp40) cc_final: 0.7921 (tp40) REVERT: D 132 ASP cc_start: 0.7753 (m-30) cc_final: 0.7488 (m-30) REVERT: E 35 GLN cc_start: 0.6416 (mt0) cc_final: 0.5941 (mp10) REVERT: F 80 MET cc_start: 0.6511 (pmm) cc_final: 0.6010 (pmm) REVERT: F 84 GLU cc_start: 0.7836 (mp0) cc_final: 0.7527 (mp0) REVERT: F 95 LYS cc_start: 0.7597 (tttp) cc_final: 0.7280 (mtmm) REVERT: G 41 LYS cc_start: 0.7815 (tttt) cc_final: 0.7213 (tptp) REVERT: G 73 LYS cc_start: 0.8167 (mmmm) cc_final: 0.7834 (mmmm) REVERT: G 83 GLU cc_start: 0.7064 (tt0) cc_final: 0.6372 (pt0) REVERT: G 164 MET cc_start: 0.5857 (ppp) cc_final: 0.5462 (pp-130) REVERT: H 146 LYS cc_start: 0.7413 (ttmm) cc_final: 0.7119 (ttmm) REVERT: I 23 MET cc_start: 0.4844 (ttm) cc_final: 0.4334 (ttm) REVERT: K 55 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6992 (tp40) REVERT: K 93 ASP cc_start: 0.6736 (m-30) cc_final: 0.6129 (m-30) REVERT: L 28 ILE cc_start: 0.7127 (OUTLIER) cc_final: 0.6810 (tt) REVERT: L 32 ASP cc_start: 0.7975 (t0) cc_final: 0.7531 (t0) outliers start: 152 outliers final: 65 residues processed: 543 average time/residue: 0.6448 time to fit residues: 423.5208 Evaluate side-chains 480 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 400 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1310 HIS Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1346 VAL Chi-restraints excluded: chain A residue 1422 GLN Chi-restraints excluded: chain A residue 1470 CYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 357 CYS Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 566 LYS Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1046 THR Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 176 TRP Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 55 GLN Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 28 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 230 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 325 optimal weight: 3.9990 chunk 245 optimal weight: 0.9990 chunk 207 optimal weight: 7.9990 chunk 298 optimal weight: 8.9990 chunk 123 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 649 ASN ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1007 ASN ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN ** K 2 ASN ** 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 = 0.4730 r_free = 0.4730 target = 0.180462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.150171 restraints weight = 55030.030| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 2.61 r_work: 0.4268 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33227 Z= 0.163 Angle : 0.713 20.036 45152 Z= 0.352 Chirality : 0.046 0.404 5048 Planarity : 0.005 0.055 5632 Dihedral : 14.138 176.055 5017 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.78 % Favored : 94.09 % Rotamer: Outliers : 3.88 % Allowed : 18.64 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.05 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.13), residues: 3858 helix: 0.64 (0.14), residues: 1334 sheet: -0.96 (0.21), residues: 562 loop : -0.94 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 37 TYR 0.034 0.002 TYR E 90 PHE 0.044 0.002 PHE G 44 TRP 0.033 0.002 TRP A1334 HIS 0.008 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (33190) covalent geometry : angle 0.68882 / 0.35 (45110) hydrogen bonds : bond 0.04489 / 2.85 ( 1311) hydrogen bonds : angle 5.41761 / 3.84 ( 3689) metal coordination : bond 0.00791 / 0.50 ( 31) metal coordination : angle 6.35071 / 4.46 ( 39) Misc. bond : bond 0.00114 / 0.07 ( 5) link_TRANS : bond 0.00164 / 0.09 ( 1) link_TRANS : angle 0.29282 / 0.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 428 time to evaluate : 1.208 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 16 ARG cc_start: 0.7610 (mmt90) cc_final: 0.7382 (mpt-90) REVERT: A 58 MET cc_start: 0.7190 (ttm) cc_final: 0.6855 (ttm) REVERT: A 65 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.7174 (mp) REVERT: A 67 ARG cc_start: 0.7101 (tpm170) cc_final: 0.6787 (tpm170) REVERT: A 77 ASN cc_start: 0.7044 (t0) cc_final: 0.6734 (t160) REVERT: A 78 MET cc_start: 0.7225 (tpt) cc_final: 0.6703 (tpt) REVERT: A 293 ASN cc_start: 0.7867 (m-40) cc_final: 0.7592 (m-40) REVERT: A 361 PHE cc_start: 0.7201 (m-80) cc_final: 0.6941 (m-80) REVERT: A 388 MET cc_start: 0.5943 (mmm) cc_final: 0.5177 (mmm) REVERT: A 407 ARG cc_start: 0.7537 (mmt-90) cc_final: 0.7291 (mmm-85) REVERT: A 803 LYS cc_start: 0.7719 (mttt) cc_final: 0.7259 (mtmm) REVERT: A 1034 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6432 (tp40) REVERT: A 1071 GLU cc_start: 0.5895 (OUTLIER) cc_final: 0.5323 (mm-30) REVERT: A 1228 MET cc_start: 0.6008 (OUTLIER) cc_final: 0.5730 (tpp) REVERT: A 1334 TRP cc_start: 0.6514 (OUTLIER) cc_final: 0.5888 (m100) REVERT: A 1422 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7606 (mm-40) REVERT: A 1433 GLU cc_start: 0.6844 (tp30) cc_final: 0.6233 (tp30) REVERT: B 145 GLN cc_start: 0.8324 (mt0) cc_final: 0.8038 (mp10) REVERT: B 177 CYS cc_start: 0.5590 (t) cc_final: 0.4876 (p) REVERT: B 208 PHE cc_start: 0.6916 (m-80) cc_final: 0.6424 (m-10) REVERT: B 323 SER cc_start: 0.8572 (t) cc_final: 0.8281 (p) REVERT: B 407 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.7033 (mtt) REVERT: B 463 ARG cc_start: 0.5217 (ttp-110) cc_final: 0.4777 (pmt170) REVERT: B 566 LYS cc_start: 0.4014 (OUTLIER) cc_final: 0.3174 (mtpm) REVERT: B 802 ASP cc_start: 0.6524 (m-30) cc_final: 0.6244 (m-30) REVERT: B 854 ILE cc_start: 0.5572 (OUTLIER) cc_final: 0.5361 (mm) REVERT: B 889 LYS cc_start: 0.8077 (mttt) cc_final: 0.7834 (mtmt) REVERT: B 911 LEU cc_start: 0.5059 (mp) cc_final: 0.4621 (mm) REVERT: C 6 GLN cc_start: 0.7951 (mm110) cc_final: 0.7655 (mm-40) REVERT: C 106 ARG cc_start: 0.7236 (mtp-110) cc_final: 0.6768 (ttm110) REVERT: C 260 GLN cc_start: 0.7320 (tt0) cc_final: 0.6890 (tp-100) REVERT: D 57 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7023 (mt) REVERT: D 94 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.7881 (ptmm) REVERT: D 112 LYS cc_start: 0.6814 (pttp) cc_final: 0.6066 (mttp) REVERT: D 128 GLN cc_start: 0.7004 (tp-100) cc_final: 0.6768 (tp-100) REVERT: D 129 GLN cc_start: 0.8278 (tp40) cc_final: 0.7982 (tp40) REVERT: D 132 ASP cc_start: 0.7715 (m-30) cc_final: 0.7478 (m-30) REVERT: E 35 GLN cc_start: 0.6407 (mt0) cc_final: 0.5945 (mp10) REVERT: E 72 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7302 (ttp) REVERT: E 116 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8420 (mt0) REVERT: E 199 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.8017 (t) REVERT: F 80 MET cc_start: 0.6464 (pmm) cc_final: 0.6084 (pmm) REVERT: F 84 GLU cc_start: 0.7819 (mp0) cc_final: 0.7489 (mp0) REVERT: F 95 LYS cc_start: 0.7535 (tttp) cc_final: 0.7268 (mtmm) REVERT: F 100 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6375 (mmt90) REVERT: G 41 LYS cc_start: 0.7758 (tttt) cc_final: 0.7130 (tptp) REVERT: G 44 PHE cc_start: 0.5010 (OUTLIER) cc_final: 0.4661 (m-80) REVERT: G 73 LYS cc_start: 0.8079 (mmmm) cc_final: 0.7745 (mmmm) REVERT: G 83 GLU cc_start: 0.7066 (tt0) cc_final: 0.6402 (pt0) REVERT: G 164 MET cc_start: 0.5856 (ppp) cc_final: 0.5473 (pp-130) REVERT: H 146 LYS cc_start: 0.7351 (ttmm) cc_final: 0.7119 (ttmm) REVERT: I 23 MET cc_start: 0.4885 (ttm) cc_final: 0.4415 (ttm) REVERT: I 92 LYS cc_start: 0.7601 (mmtm) cc_final: 0.7274 (mmmm) REVERT: K 93 ASP cc_start: 0.6737 (m-30) cc_final: 0.6249 (m-30) REVERT: L 28 ILE cc_start: 0.7087 (OUTLIER) cc_final: 0.6767 (tt) outliers start: 133 outliers final: 67 residues processed: 514 average time/residue: 0.6689 time to fit residues: 415.4074 Evaluate side-chains 479 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 396 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1334 TRP Chi-restraints excluded: chain A residue 1346 VAL Chi-restraints excluded: chain A residue 1422 GLN Chi-restraints excluded: chain A residue 1470 CYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 566 LYS Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 176 TRP Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 28 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 185 optimal weight: 9.9990 chunk 276 optimal weight: 5.9990 chunk 143 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 272 optimal weight: 0.6980 chunk 343 optimal weight: 0.2980 chunk 385 optimal weight: 10.9990 chunk 4 optimal weight: 4.9990 chunk 320 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 GLN B 518 HIS B 718 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1007 ASN ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.181645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.151827 restraints weight = 54653.765| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 2.60 r_work: 0.4286 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 33227 Z= 0.147 Angle : 0.713 18.961 45152 Z= 0.350 Chirality : 0.046 0.399 5048 Planarity : 0.004 0.055 5632 Dihedral : 14.077 174.938 5017 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.73 % Favored : 94.14 % Rotamer: Outliers : 3.15 % Allowed : 19.86 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.05 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 3858 helix: 0.73 (0.14), residues: 1337 sheet: -0.90 (0.21), residues: 564 loop : -0.92 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 859 TYR 0.030 0.002 TYR E 90 PHE 0.035 0.002 PHE G 44 TRP 0.031 0.002 TRP A1334 HIS 0.011 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (33190) covalent geometry : angle 0.68829 / 0.35 (45110) hydrogen bonds : bond 0.04323 / 2.72 ( 1311) hydrogen bonds : angle 5.31696 / 3.77 ( 3689) metal coordination : bond 0.00707 / 0.44 ( 31) metal coordination : angle 6.32716 / 4.58 ( 39) Misc. bond : bond 0.00125 / 0.08 ( 5) link_TRANS : bond 0.00136 / 0.07 ( 1) link_TRANS : angle 0.37067 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 435 time to evaluate : 1.205 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 16 ARG cc_start: 0.7531 (mmt90) cc_final: 0.7317 (mpt-90) REVERT: A 58 MET cc_start: 0.7142 (ttm) cc_final: 0.6802 (ttm) REVERT: A 77 ASN cc_start: 0.6994 (t0) cc_final: 0.6696 (t160) REVERT: A 293 ASN cc_start: 0.7843 (m-40) cc_final: 0.7589 (m-40) REVERT: A 388 MET cc_start: 0.5890 (mmm) cc_final: 0.5453 (mmm) REVERT: A 407 ARG cc_start: 0.7529 (mmt-90) cc_final: 0.7302 (mmm-85) REVERT: A 561 MET cc_start: 0.5898 (OUTLIER) cc_final: 0.4893 (mpt) REVERT: A 803 LYS cc_start: 0.7632 (mttt) cc_final: 0.7168 (mtmm) REVERT: A 1034 GLN cc_start: 0.7148 (OUTLIER) cc_final: 0.6258 (tp40) REVERT: A 1071 GLU cc_start: 0.5931 (OUTLIER) cc_final: 0.5373 (mm-30) REVERT: A 1215 GLU cc_start: 0.6965 (tm-30) cc_final: 0.6616 (tm-30) REVERT: A 1228 MET cc_start: 0.6040 (OUTLIER) cc_final: 0.5792 (tpp) REVERT: A 1334 TRP cc_start: 0.6487 (OUTLIER) cc_final: 0.5869 (m100) REVERT: A 1422 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7767 (mm-40) REVERT: A 1428 MET cc_start: 0.7581 (ttm) cc_final: 0.6670 (tmm) REVERT: A 1433 GLU cc_start: 0.6774 (tp30) cc_final: 0.6170 (tp30) REVERT: B 126 VAL cc_start: 0.8456 (t) cc_final: 0.8208 (p) REVERT: B 145 GLN cc_start: 0.8365 (mt0) cc_final: 0.8101 (mp10) REVERT: B 173 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7621 (pt0) REVERT: B 177 CYS cc_start: 0.5569 (t) cc_final: 0.4890 (p) REVERT: B 208 PHE cc_start: 0.6901 (m-80) cc_final: 0.6460 (m-10) REVERT: B 323 SER cc_start: 0.8562 (t) cc_final: 0.8271 (p) REVERT: B 357 CYS cc_start: 0.5382 (OUTLIER) cc_final: 0.3682 (m) REVERT: B 407 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6918 (mtt) REVERT: B 463 ARG cc_start: 0.5219 (ttp-110) cc_final: 0.4744 (pmt170) REVERT: B 508 MET cc_start: 0.7935 (mtt) cc_final: 0.7572 (mtt) REVERT: B 566 LYS cc_start: 0.4187 (OUTLIER) cc_final: 0.3246 (mtpm) REVERT: B 802 ASP cc_start: 0.6401 (m-30) cc_final: 0.6114 (m-30) REVERT: B 889 LYS cc_start: 0.8064 (mttt) cc_final: 0.7804 (mtmt) REVERT: B 911 LEU cc_start: 0.4985 (mp) cc_final: 0.4684 (mm) REVERT: C 6 GLN cc_start: 0.7929 (mm110) cc_final: 0.7655 (mm-40) REVERT: C 106 ARG cc_start: 0.7151 (mtp-110) cc_final: 0.6684 (ttm110) REVERT: C 227 GLU cc_start: 0.5115 (OUTLIER) cc_final: 0.4496 (mt-10) REVERT: C 260 GLN cc_start: 0.7317 (tt0) cc_final: 0.6854 (tp-100) REVERT: D 57 LEU cc_start: 0.7269 (mm) cc_final: 0.6987 (mt) REVERT: D 94 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.7904 (ptmm) REVERT: D 112 LYS cc_start: 0.6796 (pttp) cc_final: 0.6070 (mttp) REVERT: D 128 GLN cc_start: 0.7089 (tp-100) cc_final: 0.6845 (tp-100) REVERT: D 129 GLN cc_start: 0.8255 (tp40) cc_final: 0.7959 (tp40) REVERT: D 132 ASP cc_start: 0.7693 (m-30) cc_final: 0.7458 (m-30) REVERT: E 35 GLN cc_start: 0.6340 (mt0) cc_final: 0.5893 (mp10) REVERT: E 72 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7307 (ttp) REVERT: E 116 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8451 (mt0) REVERT: E 199 THR cc_start: 0.8338 (OUTLIER) cc_final: 0.8053 (t) REVERT: F 61 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.6210 (mt-10) REVERT: F 80 MET cc_start: 0.6530 (pmm) cc_final: 0.6245 (pmm) REVERT: F 84 GLU cc_start: 0.7795 (mp0) cc_final: 0.7475 (mp0) REVERT: F 100 ARG cc_start: 0.6948 (OUTLIER) cc_final: 0.6338 (mmt90) REVERT: G 41 LYS cc_start: 0.7699 (tttt) cc_final: 0.7083 (tptp) REVERT: G 44 PHE cc_start: 0.4862 (OUTLIER) cc_final: 0.4572 (m-10) REVERT: G 73 LYS cc_start: 0.8042 (mmmm) cc_final: 0.7682 (mmmm) REVERT: G 83 GLU cc_start: 0.7043 (tt0) cc_final: 0.6393 (pt0) REVERT: G 164 MET cc_start: 0.5940 (ppp) cc_final: 0.5550 (pp-130) REVERT: H 36 LYS cc_start: 0.7833 (tppt) cc_final: 0.7565 (tppp) REVERT: H 146 LYS cc_start: 0.7360 (ttmm) cc_final: 0.7138 (ttmm) REVERT: I 23 MET cc_start: 0.5016 (ttm) cc_final: 0.4492 (ttm) REVERT: K 93 ASP cc_start: 0.6678 (m-30) cc_final: 0.6189 (m-30) REVERT: L 28 ILE cc_start: 0.7033 (OUTLIER) cc_final: 0.6700 (tt) REVERT: L 32 ASP cc_start: 0.7883 (t0) cc_final: 0.7483 (t0) outliers start: 108 outliers final: 57 residues processed: 504 average time/residue: 0.6659 time to fit residues: 402.7988 Evaluate side-chains 478 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 403 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1334 TRP Chi-restraints excluded: chain A residue 1346 VAL Chi-restraints excluded: chain A residue 1422 GLN Chi-restraints excluded: chain A residue 1470 CYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 357 CYS Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 566 LYS Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 176 TRP Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain L residue 28 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 363 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 225 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 281 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 228 optimal weight: 0.0770 chunk 2 optimal weight: 5.9990 overall best weight: 2.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 HIS ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN B 518 HIS ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 GLN B1007 ASN ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 ASN K 55 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.178634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.148522 restraints weight = 55383.433| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 2.60 r_work: 0.4270 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 33227 Z= 0.221 Angle : 0.771 19.906 45152 Z= 0.384 Chirality : 0.048 0.385 5048 Planarity : 0.005 0.073 5632 Dihedral : 14.104 176.225 5017 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.12 % Favored : 93.75 % Rotamer: Outliers : 3.27 % Allowed : 20.36 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.05 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.13), residues: 3858 helix: 0.52 (0.14), residues: 1356 sheet: -1.02 (0.21), residues: 564 loop : -1.06 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 859 TYR 0.051 0.002 TYR E 90 PHE 0.033 0.003 PHE A1284 TRP 0.030 0.002 TRP A1334 HIS 0.010 0.002 HIS A1310 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.22 (33190) covalent geometry : angle 0.74726 / 0.38 (45110) hydrogen bonds : bond 0.04725 / 3.06 ( 1311) hydrogen bonds : angle 5.43772 / 3.86 ( 3689) metal coordination : bond 0.00914 / 0.56 ( 31) metal coordination : angle 6.48414 / 4.76 ( 39) Misc. bond : bond 0.00109 / 0.07 ( 5) link_TRANS : bond 0.00254 / 0.13 ( 1) link_TRANS : angle 0.16126 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 424 time to evaluate : 1.301 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 16 ARG cc_start: 0.7656 (mmt90) cc_final: 0.7441 (mpt-90) REVERT: A 58 MET cc_start: 0.7228 (ttm) cc_final: 0.6908 (ttm) REVERT: A 77 ASN cc_start: 0.6993 (t0) cc_final: 0.6718 (t160) REVERT: A 293 ASN cc_start: 0.7877 (m-40) cc_final: 0.7595 (m-40) REVERT: A 388 MET cc_start: 0.6040 (mmm) cc_final: 0.5473 (mmm) REVERT: A 407 ARG cc_start: 0.7543 (mmt-90) cc_final: 0.7314 (mmm-85) REVERT: A 500 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6733 (mt-10) REVERT: A 561 MET cc_start: 0.6129 (OUTLIER) cc_final: 0.5094 (mpt) REVERT: A 803 LYS cc_start: 0.7801 (mttt) cc_final: 0.7372 (mtmm) REVERT: A 1034 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6251 (tp40) REVERT: A 1071 GLU cc_start: 0.6094 (OUTLIER) cc_final: 0.5482 (mm-30) REVERT: A 1162 GLU cc_start: 0.7316 (tt0) cc_final: 0.7014 (tt0) REVERT: A 1215 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6709 (tm-30) REVERT: A 1228 MET cc_start: 0.6068 (OUTLIER) cc_final: 0.5823 (tpp) REVERT: A 1422 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7873 (mm-40) REVERT: A 1433 GLU cc_start: 0.6872 (tp30) cc_final: 0.6330 (tp30) REVERT: B 145 GLN cc_start: 0.8390 (mt0) cc_final: 0.8136 (mp10) REVERT: B 169 ARG cc_start: 0.6127 (ppp80) cc_final: 0.5806 (ppp80) REVERT: B 177 CYS cc_start: 0.5518 (t) cc_final: 0.4896 (p) REVERT: B 208 PHE cc_start: 0.6941 (m-80) cc_final: 0.6449 (m-10) REVERT: B 323 SER cc_start: 0.8590 (t) cc_final: 0.8281 (p) REVERT: B 357 CYS cc_start: 0.5311 (OUTLIER) cc_final: 0.3622 (m) REVERT: B 407 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.7053 (mtt) REVERT: B 463 ARG cc_start: 0.5339 (ttp-110) cc_final: 0.4863 (pmt170) REVERT: B 508 MET cc_start: 0.8017 (mtt) cc_final: 0.7680 (mtt) REVERT: B 529 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8101 (mpt) REVERT: B 566 LYS cc_start: 0.4179 (OUTLIER) cc_final: 0.3193 (mtpm) REVERT: B 677 MET cc_start: 0.7674 (tpp) cc_final: 0.7470 (mmp) REVERT: B 802 ASP cc_start: 0.6723 (m-30) cc_final: 0.6405 (m-30) REVERT: B 889 LYS cc_start: 0.8092 (mttt) cc_final: 0.7816 (mtmt) REVERT: B 911 LEU cc_start: 0.5281 (mp) cc_final: 0.4981 (mm) REVERT: C 6 GLN cc_start: 0.7956 (mm110) cc_final: 0.7675 (mm-40) REVERT: C 260 GLN cc_start: 0.7259 (tt0) cc_final: 0.6856 (tp-100) REVERT: D 94 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.7959 (ptmm) REVERT: D 112 LYS cc_start: 0.6938 (pttp) cc_final: 0.6240 (mttp) REVERT: D 128 GLN cc_start: 0.7109 (tp-100) cc_final: 0.6860 (tp-100) REVERT: D 129 GLN cc_start: 0.8256 (tp40) cc_final: 0.7942 (tp40) REVERT: D 132 ASP cc_start: 0.7768 (m-30) cc_final: 0.7499 (m-30) REVERT: E 35 GLN cc_start: 0.6540 (mt0) cc_final: 0.5901 (mp10) REVERT: E 72 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7405 (ttp) REVERT: E 199 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.8081 (t) REVERT: F 61 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.6276 (mt-10) REVERT: G 41 LYS cc_start: 0.7746 (tttt) cc_final: 0.7104 (tptp) REVERT: G 44 PHE cc_start: 0.5022 (OUTLIER) cc_final: 0.4647 (m-80) REVERT: G 73 LYS cc_start: 0.8041 (mmmm) cc_final: 0.7694 (mmmm) REVERT: G 83 GLU cc_start: 0.7157 (tt0) cc_final: 0.6645 (pt0) REVERT: G 164 MET cc_start: 0.6052 (ppp) cc_final: 0.5589 (pp-130) REVERT: H 36 LYS cc_start: 0.7818 (tppt) cc_final: 0.7549 (tppp) REVERT: H 118 TYR cc_start: 0.7318 (m-80) cc_final: 0.6477 (m-80) REVERT: H 146 LYS cc_start: 0.7416 (ttmm) cc_final: 0.7149 (ttmm) REVERT: I 23 MET cc_start: 0.4962 (ttm) cc_final: 0.4441 (ttm) REVERT: I 92 LYS cc_start: 0.7750 (mmtm) cc_final: 0.7437 (mppt) REVERT: K 55 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7323 (tp-100) REVERT: L 28 ILE cc_start: 0.7158 (OUTLIER) cc_final: 0.6840 (tt) outliers start: 112 outliers final: 60 residues processed: 492 average time/residue: 0.6578 time to fit residues: 390.1111 Evaluate side-chains 476 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 399 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1346 VAL Chi-restraints excluded: chain A residue 1422 GLN Chi-restraints excluded: chain A residue 1470 CYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 357 CYS Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 566 LYS Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 176 TRP Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 115 TYR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 55 GLN Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 166 optimal weight: 0.6980 chunk 245 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 313 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 chunk 270 optimal weight: 3.9990 chunk 230 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 326 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 GLN ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.178798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.148725 restraints weight = 55882.978| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 2.61 r_work: 0.4273 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 33227 Z= 0.233 Angle : 0.858 59.182 45152 Z= 0.447 Chirality : 0.048 0.385 5048 Planarity : 0.005 0.080 5632 Dihedral : 14.104 176.216 5017 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.01 % Favored : 93.86 % Rotamer: Outliers : 2.60 % Allowed : 21.55 % Favored : 75.85 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.05 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.13), residues: 3858 helix: 0.52 (0.14), residues: 1350 sheet: -1.04 (0.21), residues: 564 loop : -1.06 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG B1141 TYR 0.045 0.002 TYR A1395 PHE 0.039 0.002 PHE E 73 TRP 0.026 0.002 TRP A1334 HIS 0.008 0.002 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.23 (33190) covalent geometry : angle 0.83700 / 0.45 (45110) hydrogen bonds : bond 0.04699 / 3.05 ( 1311) hydrogen bonds : angle 5.45357 / 3.88 ( 3689) metal coordination : bond 0.01316 / 0.83 ( 31) metal coordination : angle 6.48545 / 4.78 ( 39) Misc. bond : bond 0.00105 / 0.07 ( 5) link_TRANS : bond 0.00207 / 0.11 ( 1) link_TRANS : angle 0.18307 / 0.10 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 400 time to evaluate : 1.279 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 16 ARG cc_start: 0.7672 (mmt90) cc_final: 0.7454 (mpt-90) REVERT: A 58 MET cc_start: 0.7231 (ttm) cc_final: 0.6910 (ttm) REVERT: A 293 ASN cc_start: 0.7883 (m-40) cc_final: 0.7599 (m-40) REVERT: A 388 MET cc_start: 0.6068 (mmm) cc_final: 0.5448 (mmm) REVERT: A 407 ARG cc_start: 0.7547 (mmt-90) cc_final: 0.7319 (mmm-85) REVERT: A 418 TYR cc_start: 0.5693 (m-80) cc_final: 0.5429 (m-80) REVERT: A 561 MET cc_start: 0.6122 (OUTLIER) cc_final: 0.5089 (mpt) REVERT: A 803 LYS cc_start: 0.7790 (mttt) cc_final: 0.7361 (mtmm) REVERT: A 1034 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6233 (tp40) REVERT: A 1071 GLU cc_start: 0.6083 (OUTLIER) cc_final: 0.5462 (mm-30) REVERT: A 1162 GLU cc_start: 0.7335 (tt0) cc_final: 0.7026 (tt0) REVERT: A 1215 GLU cc_start: 0.7107 (tm-30) cc_final: 0.6743 (tm-30) REVERT: A 1228 MET cc_start: 0.6077 (OUTLIER) cc_final: 0.5835 (tpp) REVERT: A 1422 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7895 (mm-40) REVERT: A 1433 GLU cc_start: 0.6853 (tp30) cc_final: 0.6319 (tp30) REVERT: B 49 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.6422 (tm-30) REVERT: B 145 GLN cc_start: 0.8396 (mt0) cc_final: 0.8139 (mp10) REVERT: B 177 CYS cc_start: 0.5562 (t) cc_final: 0.4898 (p) REVERT: B 208 PHE cc_start: 0.6938 (m-80) cc_final: 0.6451 (m-10) REVERT: B 323 SER cc_start: 0.8585 (t) cc_final: 0.8274 (p) REVERT: B 357 CYS cc_start: 0.5296 (OUTLIER) cc_final: 0.3619 (m) REVERT: B 368 MET cc_start: 0.4689 (ttt) cc_final: 0.4081 (ttt) REVERT: B 407 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.7044 (mtt) REVERT: B 463 ARG cc_start: 0.5332 (ttp-110) cc_final: 0.4854 (pmt170) REVERT: B 508 MET cc_start: 0.8021 (mtt) cc_final: 0.7672 (mtt) REVERT: B 529 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8099 (mpt) REVERT: B 566 LYS cc_start: 0.4165 (OUTLIER) cc_final: 0.3184 (mtpm) REVERT: B 802 ASP cc_start: 0.6695 (m-30) cc_final: 0.6377 (m-30) REVERT: B 889 LYS cc_start: 0.8095 (mttt) cc_final: 0.7817 (mtmt) REVERT: B 911 LEU cc_start: 0.5285 (mp) cc_final: 0.4971 (mm) REVERT: B 1141 ARG cc_start: 0.7001 (tpm170) cc_final: 0.6634 (tpp-160) REVERT: C 6 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7682 (mm-40) REVERT: C 260 GLN cc_start: 0.7254 (tt0) cc_final: 0.6853 (tp-100) REVERT: D 94 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.7960 (ptmm) REVERT: D 112 LYS cc_start: 0.6892 (pttp) cc_final: 0.6187 (mttp) REVERT: D 128 GLN cc_start: 0.7116 (tp-100) cc_final: 0.6865 (tp-100) REVERT: D 129 GLN cc_start: 0.8247 (tp40) cc_final: 0.7933 (tp40) REVERT: D 132 ASP cc_start: 0.7778 (m-30) cc_final: 0.7510 (m-30) REVERT: E 35 GLN cc_start: 0.6535 (mt0) cc_final: 0.5893 (mp10) REVERT: E 72 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7409 (ttp) REVERT: E 199 THR cc_start: 0.8378 (OUTLIER) cc_final: 0.8081 (t) REVERT: F 61 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.6249 (mt-10) REVERT: G 41 LYS cc_start: 0.7743 (tttt) cc_final: 0.7087 (tptp) REVERT: G 44 PHE cc_start: 0.5041 (OUTLIER) cc_final: 0.4671 (m-80) REVERT: G 73 LYS cc_start: 0.8036 (mmmm) cc_final: 0.7688 (mmmm) REVERT: G 83 GLU cc_start: 0.7154 (tt0) cc_final: 0.6658 (pt0) REVERT: G 164 MET cc_start: 0.6066 (ppp) cc_final: 0.5592 (pp-130) REVERT: H 36 LYS cc_start: 0.7805 (tppt) cc_final: 0.7552 (tppp) REVERT: H 118 TYR cc_start: 0.7320 (m-80) cc_final: 0.6475 (m-80) REVERT: H 146 LYS cc_start: 0.7401 (ttmm) cc_final: 0.7096 (ttmm) REVERT: I 23 MET cc_start: 0.4974 (ttm) cc_final: 0.4445 (ttm) REVERT: I 92 LYS cc_start: 0.7753 (mmtm) cc_final: 0.7439 (mppt) REVERT: L 28 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6851 (tt) REVERT: L 35 ARG cc_start: 0.5837 (ttt-90) cc_final: 0.5347 (tmt170) outliers start: 89 outliers final: 56 residues processed: 452 average time/residue: 0.6741 time to fit residues: 367.3936 Evaluate side-chains 465 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 392 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1346 VAL Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1422 GLN Chi-restraints excluded: chain A residue 1470 CYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 357 CYS Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 566 LYS Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 176 TRP Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 115 TYR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain L residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 75 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 377 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 282 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 164 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1310 HIS B 518 HIS ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 GLN B1007 ASN ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 ASN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.178805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.148764 restraints weight = 55591.988| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 2.60 r_work: 0.4273 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 33227 Z= 0.233 Angle : 0.858 59.182 45152 Z= 0.447 Chirality : 0.048 0.385 5048 Planarity : 0.005 0.080 5632 Dihedral : 14.104 176.216 5017 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.01 % Favored : 93.86 % Rotamer: Outliers : 2.27 % Allowed : 21.87 % Favored : 75.85 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.05 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.13), residues: 3858 helix: 0.52 (0.14), residues: 1350 sheet: -1.04 (0.21), residues: 564 loop : -1.06 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG B1141 TYR 0.045 0.002 TYR A1395 PHE 0.039 0.002 PHE E 73 TRP 0.026 0.002 TRP A1334 HIS 0.008 0.002 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.23 (33190) covalent geometry : angle 0.83700 / 0.45 (45110) hydrogen bonds : bond 0.04699 / 3.05 ( 1311) hydrogen bonds : angle 5.45357 / 3.88 ( 3689) metal coordination : bond 0.01316 / 0.83 ( 31) metal coordination : angle 6.48545 / 4.78 ( 39) Misc. bond : bond 0.00105 / 0.07 ( 5) link_TRANS : bond 0.00207 / 0.11 ( 1) link_TRANS : angle 0.18307 / 0.10 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15971.92 seconds wall clock time: 271 minutes 55.13 seconds (16315.13 seconds total)