Starting phenix.real_space_refine on Tue May 27 21:06:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q7e_18214/05_2025/8q7e_18214.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q7e_18214/05_2025/8q7e_18214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q7e_18214/05_2025/8q7e_18214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q7e_18214/05_2025/8q7e_18214.map" model { file = "/net/cci-nas-00/data/ceres_data/8q7e_18214/05_2025/8q7e_18214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q7e_18214/05_2025/8q7e_18214.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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: 3 Type Number sf(0) Gaussians C 17783 2.51 5 N 6016 2.21 5 O 6016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29815 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 947, 4692 Classifications: {'peptide': 947} Incomplete info: {'truncation_to_alanine': 837} Link IDs: {'PTRANS': 50, 'TRANS': 896} Chain breaks: 21 Unresolved chain link angles: 50 Unresolved non-hydrogen bonds: 3102 Unresolved non-hydrogen angles: 3996 Unresolved non-hydrogen dihedrals: 2611 Unresolved non-hydrogen chiralities: 279 Planarities with less than four sites: {'GLN:plan1': 63, 'ASP:plan': 33, 'TYR:plan': 24, 'ASN:plan1': 21, 'TRP:plan': 19, 'HIS:plan': 33, 'PHE:plan': 41, 'GLU:plan': 70, 'ARG:plan': 63} Unresolved non-hydrogen planarities: 1759 Chain: "B" Number of atoms: 5104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 5104 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 913} Link IDs: {'PTRANS': 52, 'TRANS': 977} Chain breaks: 24 Unresolved chain link angles: 52 Unresolved non-hydrogen bonds: 3376 Unresolved non-hydrogen angles: 4344 Unresolved non-hydrogen dihedrals: 2830 Unresolved non-hydrogen chiralities: 314 Planarities with less than four sites: {'GLN:plan1': 71, 'ASP:plan': 34, 'TYR:plan': 26, 'ASN:plan1': 22, 'TRP:plan': 20, 'HIS:plan': 34, 'PHE:plan': 42, 'GLU:plan': 74, 'ARG:plan': 71} Unresolved non-hydrogen planarities: 1887 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 378 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 6, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 195 Chain: "E" Number of atoms: 4643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 937, 4643 Classifications: {'peptide': 937} Incomplete info: {'truncation_to_alanine': 830} Link IDs: {'PTRANS': 49, 'TRANS': 887} Chain breaks: 23 Unresolved chain link angles: 49 Unresolved non-hydrogen bonds: 3084 Unresolved non-hydrogen angles: 3973 Unresolved non-hydrogen dihedrals: 2597 Unresolved non-hydrogen chiralities: 276 Planarities with less than four sites: {'GLN:plan1': 63, 'ASP:plan': 33, 'TYR:plan': 24, 'ASN:plan1': 21, 'TRP:plan': 19, 'HIS:plan': 33, 'PHE:plan': 41, 'GLU:plan': 69, 'ARG:plan': 63} Unresolved non-hydrogen planarities: 1755 Chain: "F" Number of atoms: 5019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 5019 Classifications: {'peptide': 1013} Incomplete info: {'truncation_to_alanine': 896} Link IDs: {'PTRANS': 50, 'TRANS': 962} Chain breaks: 24 Unresolved chain link angles: 50 Unresolved non-hydrogen bonds: 3319 Unresolved non-hydrogen angles: 4274 Unresolved non-hydrogen dihedrals: 2784 Unresolved non-hydrogen chiralities: 310 Planarities with less than four sites: {'GLN:plan1': 69, 'ASP:plan': 33, 'TYR:plan': 26, 'ASN:plan1': 21, 'TRP:plan': 20, 'HIS:plan': 34, 'PHE:plan': 42, 'GLU:plan': 73, 'ARG:plan': 69} Unresolved non-hydrogen planarities: 1859 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "H" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 378 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 6, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 195 Chain: "I" Number of atoms: 4580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 4580 Classifications: {'peptide': 924} Incomplete info: {'truncation_to_alanine': 817} Link IDs: {'PTRANS': 49, 'TRANS': 874} Chain breaks: 21 Unresolved chain link angles: 49 Unresolved non-hydrogen bonds: 3037 Unresolved non-hydrogen angles: 3916 Unresolved non-hydrogen dihedrals: 2558 Unresolved non-hydrogen chiralities: 273 Planarities with less than four sites: {'GLN:plan1': 63, 'ASP:plan': 31, 'TYR:plan': 24, 'ASN:plan1': 21, 'TRP:plan': 19, 'HIS:plan': 32, 'PHE:plan': 41, 'GLU:plan': 67, 'ARG:plan': 62} Unresolved non-hydrogen planarities: 1731 Chain: "J" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 895, 4433 Classifications: {'peptide': 895} Incomplete info: {'truncation_to_alanine': 790} Link IDs: {'PTRANS': 46, 'TRANS': 848} Chain breaks: 22 Unresolved chain link angles: 46 Unresolved non-hydrogen bonds: 2949 Unresolved non-hydrogen angles: 3796 Unresolved non-hydrogen dihedrals: 2481 Unresolved non-hydrogen chiralities: 265 Planarities with less than four sites: {'GLN:plan1': 66, 'ASP:plan': 29, 'TYR:plan': 23, 'ASN:plan1': 18, 'TRP:plan': 18, 'HIS:plan': 30, 'PHE:plan': 39, 'GLU:plan': 63, 'ARG:plan': 63} Unresolved non-hydrogen planarities: 1679 Chain: "K" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "L" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 378 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 6, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 195 Time building chain proxies: 21.57, per 1000 atoms: 0.72 Number of scatterers: 29815 At special positions: 0 Unit cell: (263.872, 258.765, 126.829, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 6016 8.00 N 6016 7.00 C 17783 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.39 Conformation dependent library (CDL) restraints added in 5.8 seconds 11420 Ramachandran restraints generated. 5710 Oldfield, 0 Emsley, 5710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11502 Finding SS restraints... Secondary structure from input PDB file: 277 helices and 30 sheets defined 70.8% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.30 Creating SS restraints... Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 109 through 132 Processing helix chain 'A' and resid 135 through 154 Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 158 through 165 Processing helix chain 'A' and resid 166 through 176 removed outlier: 4.072A pdb=" N LEU A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 195 removed outlier: 3.837A pdb=" N ALA A 195 " --> pdb=" O GLN A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 210 removed outlier: 3.619A pdb=" N GLN A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 235 Processing helix chain 'A' and resid 252 through 273 Processing helix chain 'A' and resid 295 through 318 Processing helix chain 'A' and resid 496 through 508 Processing helix chain 'A' and resid 510 through 524 Proline residue: A 516 - end of helix Processing helix chain 'A' and resid 540 through 552 Processing helix chain 'A' and resid 556 through 566 Processing helix chain 'A' and resid 566 through 572 removed outlier: 3.804A pdb=" N THR A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1023 Processing helix chain 'A' and resid 1036 through 1044 Processing helix chain 'A' and resid 1050 through 1065 Processing helix chain 'A' and resid 1069 through 1079 Processing helix chain 'A' and resid 1080 through 1091 Processing helix chain 'A' and resid 1099 through 1105 Processing helix chain 'A' and resid 1109 through 1141 Processing helix chain 'A' and resid 1148 through 1158 Processing helix chain 'A' and resid 1303 through 1332 removed outlier: 3.732A pdb=" N GLU A1331 " --> pdb=" O ARG A1327 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP A1332 " --> pdb=" O ASP A1328 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1358 Proline residue: A1341 - end of helix removed outlier: 3.528A pdb=" N LEU A1358 " --> pdb=" O ALA A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1360 through 1384 removed outlier: 3.612A pdb=" N ALA A1364 " --> pdb=" O ASP A1360 " (cutoff:3.500A) Proline residue: A1378 - end of helix Processing helix chain 'A' and resid 1392 through 1406 removed outlier: 3.601A pdb=" N LEU A1402 " --> pdb=" O LEU A1398 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A1403 " --> pdb=" O ASP A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1413 through 1431 removed outlier: 3.785A pdb=" N SER A1417 " --> pdb=" O SER A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1491 Processing helix chain 'A' and resid 1496 through 1517 removed outlier: 3.659A pdb=" N ARG A1500 " --> pdb=" O ASP A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1519 through 1536 removed outlier: 3.864A pdb=" N MET A1523 " --> pdb=" O ARG A1519 " (cutoff:3.500A) Processing helix chain 'A' and resid 1538 through 1563 Processing helix chain 'A' and resid 1566 through 1582 removed outlier: 4.630A pdb=" N GLU A1579 " --> pdb=" O GLN A1575 " (cutoff:3.500A) Proline residue: A1580 - end of helix Processing helix chain 'A' and resid 1583 through 1585 No H-bonds generated for 'chain 'A' and resid 1583 through 1585' Processing helix chain 'A' and resid 1587 through 1608 removed outlier: 4.078A pdb=" N THR A1591 " --> pdb=" O LEU A1587 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS A1595 " --> pdb=" O THR A1591 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE A1596 " --> pdb=" O THR A1592 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A1603 " --> pdb=" O HIS A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1612 through 1622 removed outlier: 3.719A pdb=" N ALA A1616 " --> pdb=" O TRP A1612 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN A1620 " --> pdb=" O ALA A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1623 through 1625 No H-bonds generated for 'chain 'A' and resid 1623 through 1625' Processing helix chain 'A' and resid 1628 through 1664 removed outlier: 3.700A pdb=" N LEU A1634 " --> pdb=" O PRO A1630 " (cutoff:3.500A) Processing helix chain 'A' and resid 1708 through 1710 No H-bonds generated for 'chain 'A' and resid 1708 through 1710' Processing helix chain 'A' and resid 1721 through 1739 Processing helix chain 'A' and resid 1773 through 1782 removed outlier: 3.873A pdb=" N PHE A1782 " --> pdb=" O LEU A1778 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1798 Processing helix chain 'A' and resid 1800 through 1812 removed outlier: 3.584A pdb=" N LEU A1804 " --> pdb=" O SER A1800 " (cutoff:3.500A) Proline residue: A1810 - end of helix Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 110 through 132 removed outlier: 3.784A pdb=" N ARG B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 154 removed outlier: 3.620A pdb=" N ALA B 140 " --> pdb=" O PRO B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 165 removed outlier: 3.721A pdb=" N VAL B 161 " --> pdb=" O PRO B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 removed outlier: 3.967A pdb=" N LEU B 170 " --> pdb=" O GLY B 166 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS B 176 " --> pdb=" O MET B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 197 Processing helix chain 'B' and resid 197 through 210 Processing helix chain 'B' and resid 219 through 234 Processing helix chain 'B' and resid 252 through 273 Processing helix chain 'B' and resid 295 through 318 Processing helix chain 'B' and resid 319 through 323 Processing helix chain 'B' and resid 496 through 509 Processing helix chain 'B' and resid 510 through 522 Proline residue: B 516 - end of helix Processing helix chain 'B' and resid 540 through 553 Processing helix chain 'B' and resid 560 through 565 Processing helix chain 'B' and resid 567 through 572 Processing helix chain 'B' and resid 983 through 991 Processing helix chain 'B' and resid 991 through 1003 removed outlier: 3.842A pdb=" N PHE B 995 " --> pdb=" O GLU B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1024 removed outlier: 4.074A pdb=" N LEU B1012 " --> pdb=" O ASN B1008 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP B1024 " --> pdb=" O THR B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1030 removed outlier: 3.514A pdb=" N ALA B1028 " --> pdb=" O PHE B1025 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B1030 " --> pdb=" O GLU B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1043 removed outlier: 3.569A pdb=" N CYS B1040 " --> pdb=" O VAL B1036 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B1041 " --> pdb=" O LEU B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1068 Processing helix chain 'B' and resid 1068 through 1078 Processing helix chain 'B' and resid 1079 through 1087 removed outlier: 4.060A pdb=" N ILE B1083 " --> pdb=" O GLY B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1106 removed outlier: 3.633A pdb=" N ASP B1103 " --> pdb=" O CYS B1099 " (cutoff:3.500A) Processing helix chain 'B' and resid 1111 through 1141 removed outlier: 4.201A pdb=" N ARG B1139 " --> pdb=" O GLU B1135 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR B1140 " --> pdb=" O ASP B1136 " (cutoff:3.500A) Processing helix chain 'B' and resid 1148 through 1158 Processing helix chain 'B' and resid 1303 through 1332 removed outlier: 3.818A pdb=" N GLU B1331 " --> pdb=" O ARG B1327 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP B1332 " --> pdb=" O ASP B1328 " (cutoff:3.500A) Processing helix chain 'B' and resid 1335 through 1358 Proline residue: B1341 - end of helix Processing helix chain 'B' and resid 1360 through 1384 removed outlier: 4.477A pdb=" N SER B1377 " --> pdb=" O GLU B1373 " (cutoff:3.500A) Proline residue: B1378 - end of helix Processing helix chain 'B' and resid 1392 through 1405 Processing helix chain 'B' and resid 1413 through 1431 removed outlier: 3.652A pdb=" N SER B1417 " --> pdb=" O SER B1413 " (cutoff:3.500A) Processing helix chain 'B' and resid 1467 through 1491 removed outlier: 4.178A pdb=" N ASN B1471 " --> pdb=" O SER B1467 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE B1472 " --> pdb=" O SER B1468 " (cutoff:3.500A) Processing helix chain 'B' and resid 1496 through 1517 Processing helix chain 'B' and resid 1519 through 1536 removed outlier: 4.110A pdb=" N MET B1523 " --> pdb=" O ARG B1519 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B1524 " --> pdb=" O ALA B1520 " (cutoff:3.500A) Processing helix chain 'B' and resid 1538 through 1563 Processing helix chain 'B' and resid 1564 through 1577 removed outlier: 3.765A pdb=" N GLY B1572 " --> pdb=" O VAL B1568 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN B1573 " --> pdb=" O GLU B1569 " (cutoff:3.500A) Processing helix chain 'B' and resid 1577 through 1582 removed outlier: 3.917A pdb=" N ILE B1581 " --> pdb=" O HIS B1577 " (cutoff:3.500A) Processing helix chain 'B' and resid 1583 through 1585 No H-bonds generated for 'chain 'B' and resid 1583 through 1585' Processing helix chain 'B' and resid 1589 through 1608 removed outlier: 3.631A pdb=" N HIS B1599 " --> pdb=" O HIS B1595 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B1600 " --> pdb=" O PHE B1596 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP B1603 " --> pdb=" O HIS B1599 " (cutoff:3.500A) Processing helix chain 'B' and resid 1611 through 1622 removed outlier: 3.979A pdb=" N GLY B1615 " --> pdb=" O SER B1611 " (cutoff:3.500A) Processing helix chain 'B' and resid 1623 through 1625 No H-bonds generated for 'chain 'B' and resid 1623 through 1625' Processing helix chain 'B' and resid 1628 through 1668 removed outlier: 3.623A pdb=" N LEU B1632 " --> pdb=" O ARG B1628 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B1638 " --> pdb=" O LEU B1634 " (cutoff:3.500A) Processing helix chain 'B' and resid 1715 through 1720 Processing helix chain 'B' and resid 1721 through 1739 removed outlier: 3.582A pdb=" N GLN B1739 " --> pdb=" O TYR B1735 " (cutoff:3.500A) Processing helix chain 'B' and resid 1773 through 1782 Processing helix chain 'B' and resid 1790 through 1798 Processing helix chain 'B' and resid 1800 through 1813 removed outlier: 3.552A pdb=" N LEU B1804 " --> pdb=" O SER B1800 " (cutoff:3.500A) Proline residue: B1810 - end of helix Processing helix chain 'B' and resid 1864 through 1884 Processing helix chain 'B' and resid 1885 through 1887 No H-bonds generated for 'chain 'B' and resid 1885 through 1887' Processing helix chain 'B' and resid 1890 through 1902 removed outlier: 3.860A pdb=" N GLN B1902 " --> pdb=" O LEU B1898 " (cutoff:3.500A) Processing helix chain 'B' and resid 1922 through 1937 Processing helix chain 'D' and resid 81 through 91 Processing helix chain 'E' and resid 69 through 76 Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 138 through 154 Processing helix chain 'E' and resid 155 through 157 No H-bonds generated for 'chain 'E' and resid 155 through 157' Processing helix chain 'E' and resid 158 through 165 Processing helix chain 'E' and resid 166 through 176 removed outlier: 4.072A pdb=" N LEU E 170 " --> pdb=" O GLY E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 195 removed outlier: 3.838A pdb=" N ALA E 195 " --> pdb=" O GLN E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 210 removed outlier: 3.621A pdb=" N GLN E 210 " --> pdb=" O LEU E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 235 Processing helix chain 'E' and resid 252 through 273 Processing helix chain 'E' and resid 295 through 318 Processing helix chain 'E' and resid 496 through 508 Processing helix chain 'E' and resid 510 through 524 Proline residue: E 516 - end of helix Processing helix chain 'E' and resid 540 through 552 Processing helix chain 'E' and resid 556 through 566 Processing helix chain 'E' and resid 566 through 572 removed outlier: 3.803A pdb=" N THR E 570 " --> pdb=" O SER E 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 1014 through 1023 Processing helix chain 'E' and resid 1036 through 1044 Processing helix chain 'E' and resid 1050 through 1065 Processing helix chain 'E' and resid 1069 through 1079 Processing helix chain 'E' and resid 1080 through 1091 Processing helix chain 'E' and resid 1099 through 1105 Processing helix chain 'E' and resid 1109 through 1141 Processing helix chain 'E' and resid 1148 through 1158 Processing helix chain 'E' and resid 1303 through 1332 removed outlier: 3.733A pdb=" N GLU E1331 " --> pdb=" O ARG E1327 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP E1332 " --> pdb=" O ASP E1328 " (cutoff:3.500A) Processing helix chain 'E' and resid 1335 through 1358 Proline residue: E1341 - end of helix removed outlier: 3.527A pdb=" N LEU E1358 " --> pdb=" O ALA E1354 " (cutoff:3.500A) Processing helix chain 'E' and resid 1360 through 1384 removed outlier: 3.611A pdb=" N ALA E1364 " --> pdb=" O ASP E1360 " (cutoff:3.500A) Proline residue: E1378 - end of helix Processing helix chain 'E' and resid 1392 through 1406 removed outlier: 3.601A pdb=" N LEU E1402 " --> pdb=" O LEU E1398 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU E1403 " --> pdb=" O ASP E1399 " (cutoff:3.500A) Processing helix chain 'E' and resid 1413 through 1431 removed outlier: 3.786A pdb=" N SER E1417 " --> pdb=" O SER E1413 " (cutoff:3.500A) Processing helix chain 'E' and resid 1468 through 1491 Processing helix chain 'E' and resid 1496 through 1517 removed outlier: 3.659A pdb=" N ARG E1500 " --> pdb=" O ASP E1496 " (cutoff:3.500A) Processing helix chain 'E' and resid 1519 through 1536 removed outlier: 3.864A pdb=" N MET E1523 " --> pdb=" O ARG E1519 " (cutoff:3.500A) Processing helix chain 'E' and resid 1538 through 1563 Processing helix chain 'E' and resid 1566 through 1582 removed outlier: 4.631A pdb=" N GLU E1579 " --> pdb=" O GLN E1575 " (cutoff:3.500A) Proline residue: E1580 - end of helix Processing helix chain 'E' and resid 1583 through 1585 No H-bonds generated for 'chain 'E' and resid 1583 through 1585' Processing helix chain 'E' and resid 1587 through 1608 removed outlier: 4.078A pdb=" N THR E1591 " --> pdb=" O LEU E1587 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS E1595 " --> pdb=" O THR E1591 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE E1596 " --> pdb=" O THR E1592 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP E1603 " --> pdb=" O HIS E1599 " (cutoff:3.500A) Processing helix chain 'E' and resid 1612 through 1622 removed outlier: 3.719A pdb=" N ALA E1616 " --> pdb=" O TRP E1612 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN E1620 " --> pdb=" O ALA E1616 " (cutoff:3.500A) Processing helix chain 'E' and resid 1623 through 1625 No H-bonds generated for 'chain 'E' and resid 1623 through 1625' Processing helix chain 'E' and resid 1628 through 1664 removed outlier: 3.700A pdb=" N LEU E1634 " --> pdb=" O PRO E1630 " (cutoff:3.500A) Processing helix chain 'E' and resid 1708 through 1710 No H-bonds generated for 'chain 'E' and resid 1708 through 1710' Processing helix chain 'E' and resid 1721 through 1739 Processing helix chain 'E' and resid 1773 through 1782 removed outlier: 3.873A pdb=" N PHE E1782 " --> pdb=" O LEU E1778 " (cutoff:3.500A) Processing helix chain 'E' and resid 1790 through 1798 Processing helix chain 'E' and resid 1800 through 1812 removed outlier: 3.584A pdb=" N LEU E1804 " --> pdb=" O SER E1800 " (cutoff:3.500A) Proline residue: E1810 - end of helix Processing helix chain 'F' and resid 69 through 76 Processing helix chain 'F' and resid 110 through 132 removed outlier: 3.784A pdb=" N ARG F 128 " --> pdb=" O ARG F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 154 removed outlier: 3.620A pdb=" N ALA F 140 " --> pdb=" O PRO F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 165 removed outlier: 3.721A pdb=" N VAL F 161 " --> pdb=" O PRO F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 176 removed outlier: 3.967A pdb=" N LEU F 170 " --> pdb=" O GLY F 166 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS F 176 " --> pdb=" O MET F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 197 Processing helix chain 'F' and resid 197 through 210 Processing helix chain 'F' and resid 219 through 234 Processing helix chain 'F' and resid 252 through 273 Processing helix chain 'F' and resid 295 through 318 Processing helix chain 'F' and resid 319 through 323 Processing helix chain 'F' and resid 496 through 509 Processing helix chain 'F' and resid 510 through 522 Proline residue: F 516 - end of helix Processing helix chain 'F' and resid 540 through 553 Processing helix chain 'F' and resid 560 through 565 Processing helix chain 'F' and resid 567 through 572 Processing helix chain 'F' and resid 992 through 1003 Processing helix chain 'F' and resid 1012 through 1024 removed outlier: 3.755A pdb=" N ASP F1024 " --> pdb=" O THR F1020 " (cutoff:3.500A) Processing helix chain 'F' and resid 1025 through 1030 removed outlier: 3.515A pdb=" N ALA F1028 " --> pdb=" O PHE F1025 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL F1030 " --> pdb=" O GLU F1027 " (cutoff:3.500A) Processing helix chain 'F' and resid 1036 through 1043 removed outlier: 3.570A pdb=" N CYS F1040 " --> pdb=" O VAL F1036 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU F1041 " --> pdb=" O LEU F1037 " (cutoff:3.500A) Processing helix chain 'F' and resid 1054 through 1068 Processing helix chain 'F' and resid 1068 through 1078 Processing helix chain 'F' and resid 1079 through 1087 removed outlier: 4.060A pdb=" N ILE F1083 " --> pdb=" O GLY F1079 " (cutoff:3.500A) Processing helix chain 'F' and resid 1099 through 1106 removed outlier: 3.633A pdb=" N ASP F1103 " --> pdb=" O CYS F1099 " (cutoff:3.500A) Processing helix chain 'F' and resid 1111 through 1141 removed outlier: 4.202A pdb=" N ARG F1139 " --> pdb=" O GLU F1135 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR F1140 " --> pdb=" O ASP F1136 " (cutoff:3.500A) Processing helix chain 'F' and resid 1148 through 1158 Processing helix chain 'F' and resid 1303 through 1332 removed outlier: 3.818A pdb=" N GLU F1331 " --> pdb=" O ARG F1327 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP F1332 " --> pdb=" O ASP F1328 " (cutoff:3.500A) Processing helix chain 'F' and resid 1335 through 1358 Proline residue: F1341 - end of helix Processing helix chain 'F' and resid 1360 through 1384 removed outlier: 4.478A pdb=" N SER F1377 " --> pdb=" O GLU F1373 " (cutoff:3.500A) Proline residue: F1378 - end of helix Processing helix chain 'F' and resid 1392 through 1405 Processing helix chain 'F' and resid 1413 through 1431 removed outlier: 3.652A pdb=" N SER F1417 " --> pdb=" O SER F1413 " (cutoff:3.500A) Processing helix chain 'F' and resid 1467 through 1491 removed outlier: 4.177A pdb=" N ASN F1471 " --> pdb=" O SER F1467 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE F1472 " --> pdb=" O SER F1468 " (cutoff:3.500A) Processing helix chain 'F' and resid 1496 through 1517 Processing helix chain 'F' and resid 1519 through 1536 removed outlier: 4.111A pdb=" N MET F1523 " --> pdb=" O ARG F1519 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU F1524 " --> pdb=" O ALA F1520 " (cutoff:3.500A) Processing helix chain 'F' and resid 1538 through 1563 Processing helix chain 'F' and resid 1564 through 1577 removed outlier: 3.765A pdb=" N GLY F1572 " --> pdb=" O VAL F1568 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN F1573 " --> pdb=" O GLU F1569 " (cutoff:3.500A) Processing helix chain 'F' and resid 1577 through 1582 removed outlier: 3.917A pdb=" N ILE F1581 " --> pdb=" O HIS F1577 " (cutoff:3.500A) Processing helix chain 'F' and resid 1583 through 1585 No H-bonds generated for 'chain 'F' and resid 1583 through 1585' Processing helix chain 'F' and resid 1589 through 1608 removed outlier: 3.630A pdb=" N HIS F1599 " --> pdb=" O HIS F1595 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR F1600 " --> pdb=" O PHE F1596 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP F1603 " --> pdb=" O HIS F1599 " (cutoff:3.500A) Processing helix chain 'F' and resid 1611 through 1622 removed outlier: 3.979A pdb=" N GLY F1615 " --> pdb=" O SER F1611 " (cutoff:3.500A) Processing helix chain 'F' and resid 1623 through 1625 No H-bonds generated for 'chain 'F' and resid 1623 through 1625' Processing helix chain 'F' and resid 1628 through 1668 removed outlier: 3.623A pdb=" N LEU F1632 " --> pdb=" O ARG F1628 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER F1638 " --> pdb=" O LEU F1634 " (cutoff:3.500A) Processing helix chain 'F' and resid 1715 through 1720 Processing helix chain 'F' and resid 1721 through 1739 removed outlier: 3.581A pdb=" N GLN F1739 " --> pdb=" O TYR F1735 " (cutoff:3.500A) Processing helix chain 'F' and resid 1773 through 1782 Processing helix chain 'F' and resid 1790 through 1798 Processing helix chain 'F' and resid 1800 through 1813 removed outlier: 3.552A pdb=" N LEU F1804 " --> pdb=" O SER F1800 " (cutoff:3.500A) Proline residue: F1810 - end of helix Processing helix chain 'F' and resid 1864 through 1884 Processing helix chain 'F' and resid 1885 through 1887 No H-bonds generated for 'chain 'F' and resid 1885 through 1887' Processing helix chain 'F' and resid 1890 through 1902 removed outlier: 3.860A pdb=" N GLN F1902 " --> pdb=" O LEU F1898 " (cutoff:3.500A) Processing helix chain 'F' and resid 1922 through 1937 Processing helix chain 'H' and resid 81 through 91 Processing helix chain 'I' and resid 69 through 76 Processing helix chain 'I' and resid 109 through 132 Processing helix chain 'I' and resid 135 through 154 Processing helix chain 'I' and resid 155 through 157 No H-bonds generated for 'chain 'I' and resid 155 through 157' Processing helix chain 'I' and resid 158 through 165 Processing helix chain 'I' and resid 166 through 176 removed outlier: 4.073A pdb=" N LEU I 170 " --> pdb=" O GLY I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 195 removed outlier: 3.837A pdb=" N ALA I 195 " --> pdb=" O GLN I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 210 removed outlier: 3.620A pdb=" N GLN I 210 " --> pdb=" O LEU I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 219 through 235 Processing helix chain 'I' and resid 252 through 273 Processing helix chain 'I' and resid 295 through 318 Processing helix chain 'I' and resid 496 through 508 Processing helix chain 'I' and resid 510 through 524 Proline residue: I 516 - end of helix Processing helix chain 'I' and resid 540 through 552 Processing helix chain 'I' and resid 556 through 566 Processing helix chain 'I' and resid 566 through 572 removed outlier: 3.803A pdb=" N THR I 570 " --> pdb=" O SER I 566 " (cutoff:3.500A) Processing helix chain 'I' and resid 1014 through 1023 Processing helix chain 'I' and resid 1036 through 1044 Processing helix chain 'I' and resid 1050 through 1065 Processing helix chain 'I' and resid 1069 through 1079 Processing helix chain 'I' and resid 1109 through 1141 Processing helix chain 'I' and resid 1148 through 1158 Processing helix chain 'I' and resid 1303 through 1332 removed outlier: 3.732A pdb=" N GLU I1331 " --> pdb=" O ARG I1327 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP I1332 " --> pdb=" O ASP I1328 " (cutoff:3.500A) Processing helix chain 'I' and resid 1335 through 1358 Proline residue: I1341 - end of helix removed outlier: 3.529A pdb=" N LEU I1358 " --> pdb=" O ALA I1354 " (cutoff:3.500A) Processing helix chain 'I' and resid 1360 through 1384 removed outlier: 3.611A pdb=" N ALA I1364 " --> pdb=" O ASP I1360 " (cutoff:3.500A) Proline residue: I1378 - end of helix Processing helix chain 'I' and resid 1392 through 1406 removed outlier: 3.601A pdb=" N LEU I1402 " --> pdb=" O LEU I1398 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU I1403 " --> pdb=" O ASP I1399 " (cutoff:3.500A) Processing helix chain 'I' and resid 1413 through 1431 removed outlier: 3.786A pdb=" N SER I1417 " --> pdb=" O SER I1413 " (cutoff:3.500A) Processing helix chain 'I' and resid 1468 through 1491 Processing helix chain 'I' and resid 1496 through 1517 removed outlier: 3.660A pdb=" N ARG I1500 " --> pdb=" O ASP I1496 " (cutoff:3.500A) Processing helix chain 'I' and resid 1519 through 1536 removed outlier: 3.864A pdb=" N MET I1523 " --> pdb=" O ARG I1519 " (cutoff:3.500A) Processing helix chain 'I' and resid 1538 through 1563 Processing helix chain 'I' and resid 1566 through 1582 removed outlier: 4.630A pdb=" N GLU I1579 " --> pdb=" O GLN I1575 " (cutoff:3.500A) Proline residue: I1580 - end of helix Processing helix chain 'I' and resid 1583 through 1585 No H-bonds generated for 'chain 'I' and resid 1583 through 1585' Processing helix chain 'I' and resid 1587 through 1608 removed outlier: 4.078A pdb=" N THR I1591 " --> pdb=" O LEU I1587 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS I1595 " --> pdb=" O THR I1591 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE I1596 " --> pdb=" O THR I1592 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP I1603 " --> pdb=" O HIS I1599 " (cutoff:3.500A) Processing helix chain 'I' and resid 1612 through 1622 removed outlier: 3.719A pdb=" N ALA I1616 " --> pdb=" O TRP I1612 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN I1620 " --> pdb=" O ALA I1616 " (cutoff:3.500A) Processing helix chain 'I' and resid 1623 through 1625 No H-bonds generated for 'chain 'I' and resid 1623 through 1625' Processing helix chain 'I' and resid 1628 through 1664 removed outlier: 3.700A pdb=" N LEU I1634 " --> pdb=" O PRO I1630 " (cutoff:3.500A) Processing helix chain 'I' and resid 1708 through 1710 No H-bonds generated for 'chain 'I' and resid 1708 through 1710' Processing helix chain 'I' and resid 1721 through 1739 Processing helix chain 'I' and resid 1773 through 1782 removed outlier: 3.873A pdb=" N PHE I1782 " --> pdb=" O LEU I1778 " (cutoff:3.500A) Processing helix chain 'I' and resid 1790 through 1798 Processing helix chain 'I' and resid 1800 through 1812 removed outlier: 3.584A pdb=" N LEU I1804 " --> pdb=" O SER I1800 " (cutoff:3.500A) Proline residue: I1810 - end of helix Processing helix chain 'J' and resid 69 through 76 Processing helix chain 'J' and resid 110 through 132 removed outlier: 3.784A pdb=" N ARG J 128 " --> pdb=" O ARG J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 154 removed outlier: 3.621A pdb=" N ALA J 140 " --> pdb=" O PRO J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 165 removed outlier: 3.720A pdb=" N VAL J 161 " --> pdb=" O PRO J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 176 removed outlier: 3.967A pdb=" N LEU J 170 " --> pdb=" O GLY J 166 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS J 176 " --> pdb=" O MET J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 197 Processing helix chain 'J' and resid 197 through 210 Processing helix chain 'J' and resid 219 through 234 Processing helix chain 'J' and resid 252 through 273 Processing helix chain 'J' and resid 295 through 318 Processing helix chain 'J' and resid 496 through 509 Processing helix chain 'J' and resid 510 through 522 Proline residue: J 516 - end of helix Processing helix chain 'J' and resid 540 through 553 Processing helix chain 'J' and resid 560 through 565 Processing helix chain 'J' and resid 567 through 572 Processing helix chain 'J' and resid 1122 through 1141 removed outlier: 4.201A pdb=" N ARG J1139 " --> pdb=" O GLU J1135 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR J1140 " --> pdb=" O ASP J1136 " (cutoff:3.500A) Processing helix chain 'J' and resid 1148 through 1158 Processing helix chain 'J' and resid 1303 through 1332 removed outlier: 3.818A pdb=" N GLU J1331 " --> pdb=" O ARG J1327 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP J1332 " --> pdb=" O ASP J1328 " (cutoff:3.500A) Processing helix chain 'J' and resid 1335 through 1358 Proline residue: J1341 - end of helix Processing helix chain 'J' and resid 1360 through 1384 removed outlier: 4.478A pdb=" N SER J1377 " --> pdb=" O GLU J1373 " (cutoff:3.500A) Proline residue: J1378 - end of helix Processing helix chain 'J' and resid 1392 through 1405 Processing helix chain 'J' and resid 1413 through 1431 removed outlier: 3.652A pdb=" N SER J1417 " --> pdb=" O SER J1413 " (cutoff:3.500A) Processing helix chain 'J' and resid 1467 through 1491 removed outlier: 4.177A pdb=" N ASN J1471 " --> pdb=" O SER J1467 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE J1472 " --> pdb=" O SER J1468 " (cutoff:3.500A) Processing helix chain 'J' and resid 1496 through 1517 Processing helix chain 'J' and resid 1519 through 1536 removed outlier: 4.111A pdb=" N MET J1523 " --> pdb=" O ARG J1519 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU J1524 " --> pdb=" O ALA J1520 " (cutoff:3.500A) Processing helix chain 'J' and resid 1538 through 1563 Processing helix chain 'J' and resid 1564 through 1577 removed outlier: 3.765A pdb=" N GLY J1572 " --> pdb=" O VAL J1568 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN J1573 " --> pdb=" O GLU J1569 " (cutoff:3.500A) Processing helix chain 'J' and resid 1577 through 1582 removed outlier: 3.916A pdb=" N ILE J1581 " --> pdb=" O HIS J1577 " (cutoff:3.500A) Processing helix chain 'J' and resid 1583 through 1585 No H-bonds generated for 'chain 'J' and resid 1583 through 1585' Processing helix chain 'J' and resid 1589 through 1608 removed outlier: 3.631A pdb=" N HIS J1599 " --> pdb=" O HIS J1595 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR J1600 " --> pdb=" O PHE J1596 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP J1603 " --> pdb=" O HIS J1599 " (cutoff:3.500A) Processing helix chain 'J' and resid 1611 through 1622 removed outlier: 3.980A pdb=" N GLY J1615 " --> pdb=" O SER J1611 " (cutoff:3.500A) Processing helix chain 'J' and resid 1623 through 1625 No H-bonds generated for 'chain 'J' and resid 1623 through 1625' Processing helix chain 'J' and resid 1628 through 1668 removed outlier: 3.622A pdb=" N LEU J1632 " --> pdb=" O ARG J1628 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER J1638 " --> pdb=" O LEU J1634 " (cutoff:3.500A) Processing helix chain 'J' and resid 1715 through 1720 Processing helix chain 'J' and resid 1721 through 1739 removed outlier: 3.581A pdb=" N GLN J1739 " --> pdb=" O TYR J1735 " (cutoff:3.500A) Processing helix chain 'J' and resid 1773 through 1782 Processing helix chain 'J' and resid 1790 through 1798 Processing helix chain 'J' and resid 1800 through 1813 removed outlier: 3.551A pdb=" N LEU J1804 " --> pdb=" O SER J1800 " (cutoff:3.500A) Proline residue: J1810 - end of helix Processing helix chain 'J' and resid 1864 through 1881 Processing helix chain 'J' and resid 1890 through 1902 removed outlier: 3.860A pdb=" N GLN J1902 " --> pdb=" O LEU J1898 " (cutoff:3.500A) Processing helix chain 'J' and resid 1922 through 1937 Processing helix chain 'L' and resid 81 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 25 removed outlier: 6.528A pdb=" N ARG A 41 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU A 25 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A 39 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1695 through 1699 removed outlier: 4.517A pdb=" N VAL C 30 " --> pdb=" O THR A1755 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TRP A1754 " --> pdb=" O LEU A1713 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1695 through 1699 removed outlier: 6.455A pdb=" N GLU A1761 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TRP C 27 " --> pdb=" O ARG A1759 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG A1759 " --> pdb=" O TRP C 27 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A1768 " --> pdb=" O LEU A1846 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1788 through 1789 removed outlier: 3.730A pdb=" N VAL A1788 " --> pdb=" O LEU A1832 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 12 through 13 removed outlier: 7.022A pdb=" N ARG B 41 " --> pdb=" O GLU B 23 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU B 25 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU B 39 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 38 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1696 through 1700 removed outlier: 4.072A pdb=" N TRP D 33 " --> pdb=" O LEU B1700 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL D 30 " --> pdb=" O THR B1755 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1696 through 1700 removed outlier: 4.072A pdb=" N TRP D 33 " --> pdb=" O LEU B1700 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLU B1761 " --> pdb=" O LYS D 25 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TRP D 27 " --> pdb=" O ARG B1759 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG B1759 " --> pdb=" O TRP D 27 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B1768 " --> pdb=" O LEU B1846 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU B1848 " --> pdb=" O ILE B1768 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N HIS B1770 " --> pdb=" O LEU B1848 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1788 through 1789 Processing sheet with id=AA9, first strand: chain 'B' and resid 1888 through 1889 removed outlier: 3.980A pdb=" N LEU B1888 " --> pdb=" O LEU B1949 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 70 through 72 Processing sheet with id=AB2, first strand: chain 'E' and resid 19 through 25 removed outlier: 6.528A pdb=" N ARG E 41 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU E 25 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU E 39 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 1694 through 1700 removed outlier: 3.748A pdb=" N ALA E1694 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL G 30 " --> pdb=" O THR E1755 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TRP E1754 " --> pdb=" O LEU E1713 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 1694 through 1700 removed outlier: 3.748A pdb=" N ALA E1694 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLU E1761 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TRP G 27 " --> pdb=" O ARG E1759 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ARG E1759 " --> pdb=" O TRP G 27 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE E1768 " --> pdb=" O LEU E1846 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 1788 through 1789 removed outlier: 3.730A pdb=" N VAL E1788 " --> pdb=" O LEU E1832 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 12 through 13 removed outlier: 7.023A pdb=" N ARG F 41 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU F 25 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU F 39 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR F 38 " --> pdb=" O LEU F 67 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 1696 through 1700 removed outlier: 3.557A pdb=" N ALA H 29 " --> pdb=" O SER F1696 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA H 31 " --> pdb=" O LEU F1698 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL H 30 " --> pdb=" O THR F1755 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 1845 through 1848 removed outlier: 6.427A pdb=" N ILE F1768 " --> pdb=" O LEU F1846 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU F1848 " --> pdb=" O ILE F1768 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N HIS F1770 " --> pdb=" O LEU F1848 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU F1761 " --> pdb=" O LYS H 25 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 1788 through 1789 Processing sheet with id=AC1, first strand: chain 'F' and resid 1888 through 1889 removed outlier: 3.981A pdb=" N LEU F1888 " --> pdb=" O LEU F1949 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 70 through 72 Processing sheet with id=AC3, first strand: chain 'I' and resid 19 through 25 removed outlier: 6.528A pdb=" N ARG I 41 " --> pdb=" O GLU I 23 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU I 25 " --> pdb=" O LEU I 39 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU I 39 " --> pdb=" O LEU I 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 1695 through 1699 removed outlier: 4.562A pdb=" N VAL K 30 " --> pdb=" O THR I1755 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TRP I1754 " --> pdb=" O LEU I1713 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 1695 through 1699 removed outlier: 6.691A pdb=" N GLU I1761 " --> pdb=" O LYS K 25 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TRP K 27 " --> pdb=" O ARG I1759 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ARG I1759 " --> pdb=" O TRP K 27 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE I1768 " --> pdb=" O LEU I1846 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 1788 through 1789 removed outlier: 3.730A pdb=" N VAL I1788 " --> pdb=" O LEU I1832 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 12 through 13 removed outlier: 7.022A pdb=" N ARG J 41 " --> pdb=" O GLU J 23 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU J 25 " --> pdb=" O LEU J 39 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU J 39 " --> pdb=" O LEU J 25 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR J 38 " --> pdb=" O LEU J 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 1696 through 1700 removed outlier: 3.603A pdb=" N ALA L 31 " --> pdb=" O LEU J1698 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP L 33 " --> pdb=" O LEU J1700 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL L 30 " --> pdb=" O THR J1755 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 1845 through 1848 removed outlier: 6.427A pdb=" N ILE J1768 " --> pdb=" O LEU J1846 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU J1848 " --> pdb=" O ILE J1768 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N HIS J1770 " --> pdb=" O LEU J1848 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU J1761 " --> pdb=" O LYS L 25 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU L 23 " --> pdb=" O GLN J1763 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 1788 through 1789 Processing sheet with id=AD2, first strand: chain 'J' and resid 1939 through 1941 Processing sheet with id=AD3, first strand: chain 'L' and resid 70 through 72 3148 hydrogen bonds defined for protein. 9333 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.55 Time building geometry restraints manager: 11.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 6016 1.29 - 1.35: 5863 1.35 - 1.42: 0 1.42 - 1.48: 6016 1.48 - 1.55: 11767 Bond restraints: 29662 Sorted by residual: bond pdb=" CA VAL E1809 " pdb=" CB VAL E1809 " ideal model delta sigma weight residual 1.537 1.528 0.009 5.00e-03 4.00e+04 3.37e+00 bond pdb=" CA VAL A1809 " pdb=" CB VAL A1809 " ideal model delta sigma weight residual 1.537 1.528 0.009 5.00e-03 4.00e+04 3.01e+00 bond pdb=" CA VAL I1809 " pdb=" CB VAL I1809 " ideal model delta sigma weight residual 1.537 1.528 0.008 5.00e-03 4.00e+04 2.84e+00 bond pdb=" C MET B1633 " pdb=" O MET B1633 " ideal model delta sigma weight residual 1.236 1.255 -0.018 1.15e-02 7.56e+03 2.54e+00 bond pdb=" C MET J1633 " pdb=" O MET J1633 " ideal model delta sigma weight residual 1.236 1.255 -0.018 1.15e-02 7.56e+03 2.54e+00 ... (remaining 29657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 38662 0.93 - 1.87: 2098 1.87 - 2.80: 277 2.80 - 3.74: 68 3.74 - 4.67: 18 Bond angle restraints: 41123 Sorted by residual: angle pdb=" O GLU I 498 " pdb=" C GLU I 498 " pdb=" N TRP I 499 " ideal model delta sigma weight residual 122.07 125.80 -3.73 1.03e+00 9.43e-01 1.31e+01 angle pdb=" O GLU A 498 " pdb=" C GLU A 498 " pdb=" N TRP A 499 " ideal model delta sigma weight residual 122.07 125.79 -3.72 1.03e+00 9.43e-01 1.31e+01 angle pdb=" O GLU E 498 " pdb=" C GLU E 498 " pdb=" N TRP E 499 " ideal model delta sigma weight residual 122.07 125.74 -3.67 1.03e+00 9.43e-01 1.27e+01 angle pdb=" CA GLU A 498 " pdb=" C GLU A 498 " pdb=" N TRP A 499 " ideal model delta sigma weight residual 117.07 113.62 3.45 1.14e+00 7.69e-01 9.16e+00 angle pdb=" CA GLU I 498 " pdb=" C GLU I 498 " pdb=" N TRP I 499 " ideal model delta sigma weight residual 117.07 113.67 3.40 1.14e+00 7.69e-01 8.89e+00 ... (remaining 41118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 3.96: 15374 3.96 - 7.91: 1488 7.91 - 11.87: 381 11.87 - 15.82: 102 15.82 - 19.78: 20 Dihedral angle restraints: 17365 sinusoidal: 0 harmonic: 17365 Sorted by residual: dihedral pdb=" CA LEU F1888 " pdb=" C LEU F1888 " pdb=" N HIS F1889 " pdb=" CA HIS F1889 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA LEU B1888 " pdb=" C LEU B1888 " pdb=" N HIS B1889 " pdb=" CA HIS B1889 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ALA I1490 " pdb=" C ALA I1490 " pdb=" N ALA I1491 " pdb=" CA ALA I1491 " ideal model delta harmonic sigma weight residual 180.00 -162.55 -17.45 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 17362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3809 0.034 - 0.068: 1403 0.068 - 0.103: 404 0.103 - 0.137: 122 0.137 - 0.171: 13 Chirality restraints: 5751 Sorted by residual: chirality pdb=" CA SER I1377 " pdb=" N SER I1377 " pdb=" C SER I1377 " pdb=" CB SER I1377 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA SER E1377 " pdb=" N SER E1377 " pdb=" C SER E1377 " pdb=" CB SER E1377 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA SER A1377 " pdb=" N SER A1377 " pdb=" C SER A1377 " pdb=" CB SER A1377 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 5748 not shown) Planarity restraints: 5863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A1368 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C GLY A1368 " 0.030 2.00e-02 2.50e+03 pdb=" O GLY A1368 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS A1369 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E1368 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C GLY E1368 " -0.030 2.00e-02 2.50e+03 pdb=" O GLY E1368 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS E1369 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY I1368 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C GLY I1368 " -0.030 2.00e-02 2.50e+03 pdb=" O GLY I1368 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS I1369 " 0.010 2.00e-02 2.50e+03 ... (remaining 5860 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 10198 2.82 - 3.34: 30752 3.34 - 3.86: 45364 3.86 - 4.38: 40654 4.38 - 4.90: 67934 Nonbonded interactions: 194902 Sorted by model distance: nonbonded pdb=" O SER J 236 " pdb=" N CYS J 240 " model vdw 2.298 3.120 nonbonded pdb=" O SER F 236 " pdb=" N CYS F 240 " model vdw 2.299 3.120 nonbonded pdb=" O SER B 236 " pdb=" N CYS B 240 " model vdw 2.299 3.120 nonbonded pdb=" O ASP E1361 " pdb=" N ALA E1364 " model vdw 2.399 3.120 nonbonded pdb=" O ASP I1361 " pdb=" N ALA I1364 " model vdw 2.399 3.120 ... (remaining 194897 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 46 or resid 61 through 79 or resid 109 through \ 129 or resid 137 through 318 or resid 335 through 340 or resid 476 through 522 o \ r resid 535 through 555 or resid 559 through 572 or resid 1121 through 1142 or r \ esid 1145 through 1739 or resid 1750 through 1821 or resid 1830 through 1836 or \ resid 1845 through 1858)) selection = (chain 'B' and (resid 10 through 14 or resid 17 through 129 or resid 137 through \ 318 or resid 335 through 572 or resid 1121 through 1608 or resid 1611 through 1 \ 665 or resid 1691 through 1836 or resid 1845 through 1858)) selection = (chain 'E' and (resid 10 through 46 or resid 61 through 79 or resid 109 through \ 318 or resid 335 through 340 or resid 476 through 522 or resid 535 through 555 o \ r resid 559 through 572 or resid 1121 through 1142 or resid 1145 through 1739 or \ resid 1750 through 1821 or resid 1830 through 1836 or resid 1845 through 1858)) \ selection = (chain 'F' and (resid 10 through 14 or resid 17 through 129 or resid 137 through \ 318 or resid 335 through 572 or resid 1121 through 1608 or resid 1611 through 1 \ 665 or resid 1691 through 1836 or resid 1845 through 1858)) selection = (chain 'I' and (resid 10 through 46 or resid 61 through 79 or resid 109 through \ 129 or resid 137 through 318 or resid 335 through 340 or resid 476 through 522 o \ r resid 535 through 555 or resid 559 through 572 or resid 1121 through 1142 or r \ esid 1145 through 1739 or resid 1750 through 1821 or resid 1830 through 1858)) selection = (chain 'J' and (resid 10 through 14 or resid 17 through 129 or resid 137 through \ 1608 or resid 1611 through 1665 or resid 1691 through 1836 or resid 1845 throug \ h 1858)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.470 Check model and map are aligned: 0.260 Set scattering table: 0.310 Process input model: 88.360 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 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 : 0.003 0.046 29662 Z= 0.216 Angle : 0.494 4.669 41123 Z= 0.328 Chirality : 0.040 0.171 5751 Planarity : 0.002 0.017 5863 Dihedral : 4.571 19.781 5863 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.11), residues: 5710 helix: 1.16 (0.08), residues: 3939 sheet: -2.03 (0.33), residues: 206 loop : -1.58 (0.16), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 42 PHE 0.000 0.000 PHE A 162 TYR 0.000 0.000 TYR A 21 Details of bonding type rmsd hydrogen bonds : bond 0.12158 ( 3129) hydrogen bonds : angle 5.80803 ( 9333) covalent geometry : bond 0.00298 (29662) covalent geometry : angle 0.49359 (41123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11420 Ramachandran restraints generated. 5710 Oldfield, 0 Emsley, 5710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11420 Ramachandran restraints generated. 5710 Oldfield, 0 Emsley, 5710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 5320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.407 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2493 time to fit residues: 66.8357 Evaluate side-chains 132 residues out of total 5320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 503 optimal weight: 10.0000 chunk 451 optimal weight: 0.0060 chunk 250 optimal weight: 50.0000 chunk 154 optimal weight: 6.9990 chunk 304 optimal weight: 7.9990 chunk 241 optimal weight: 50.0000 chunk 467 optimal weight: 20.0000 chunk 180 optimal weight: 30.0000 chunk 284 optimal weight: 40.0000 chunk 347 optimal weight: 8.9990 chunk 541 optimal weight: 30.0000 overall best weight: 6.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.055970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.030140 restraints weight = 348326.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.030122 restraints weight = 338332.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.030170 restraints weight = 323545.418| |-----------------------------------------------------------------------------| r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 29662 Z= 0.177 Angle : 0.422 14.048 41123 Z= 0.261 Chirality : 0.035 0.128 5751 Planarity : 0.002 0.016 5863 Dihedral : 3.585 18.642 5863 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.12), residues: 5710 helix: 2.64 (0.08), residues: 4005 sheet: -2.04 (0.33), residues: 206 loop : -0.99 (0.17), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 42 PHE 0.000 0.000 PHE A 162 TYR 0.000 0.000 TYR A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 3129) hydrogen bonds : angle 4.00023 ( 9333) covalent geometry : bond 0.00240 (29662) covalent geometry : angle 0.42160 (41123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11420 Ramachandran restraints generated. 5710 Oldfield, 0 Emsley, 5710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11420 Ramachandran restraints generated. 5710 Oldfield, 0 Emsley, 5710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 5320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.426 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2624 time to fit residues: 70.4006 Evaluate side-chains 132 residues out of total 5320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 243 optimal weight: 50.0000 chunk 520 optimal weight: 50.0000 chunk 377 optimal weight: 20.0000 chunk 403 optimal weight: 0.5980 chunk 79 optimal weight: 50.0000 chunk 211 optimal weight: 6.9990 chunk 502 optimal weight: 50.0000 chunk 179 optimal weight: 30.0000 chunk 111 optimal weight: 50.0000 chunk 250 optimal weight: 50.0000 chunk 239 optimal weight: 50.0000 overall best weight: 21.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.054972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.029264 restraints weight = 363689.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.029162 restraints weight = 376691.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.029243 restraints weight = 351411.581| |-----------------------------------------------------------------------------| r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 29662 Z= 0.479 Angle : 0.730 19.481 41123 Z= 0.494 Chirality : 0.039 0.140 5751 Planarity : 0.005 0.032 5863 Dihedral : 5.780 24.298 5863 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.80 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.11), residues: 5710 helix: 0.34 (0.08), residues: 4032 sheet: -2.88 (0.29), residues: 230 loop : -1.62 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 42 PHE 0.000 0.000 PHE A 162 TYR 0.000 0.000 TYR A 21 Details of bonding type rmsd hydrogen bonds : bond 0.06994 ( 3129) hydrogen bonds : angle 6.26668 ( 9333) covalent geometry : bond 0.00647 (29662) covalent geometry : angle 0.72953 (41123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11420 Ramachandran restraints generated. 5710 Oldfield, 0 Emsley, 5710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11420 Ramachandran restraints generated. 5710 Oldfield, 0 Emsley, 5710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 5320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.512 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2641 time to fit residues: 70.8664 Evaluate side-chains 132 residues out of total 5320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 57 optimal weight: 40.0000 chunk 160 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 424 optimal weight: 50.0000 chunk 467 optimal weight: 20.0000 chunk 479 optimal weight: 5.9990 chunk 572 optimal weight: 5.9990 chunk 386 optimal weight: 50.0000 chunk 189 optimal weight: 30.0000 chunk 156 optimal weight: 7.9990 chunk 312 optimal weight: 10.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.054852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.029268 restraints weight = 356045.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.029319 restraints weight = 328198.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.029333 restraints weight = 305809.145| |-----------------------------------------------------------------------------| r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 29662 Z= 0.157 Angle : 0.391 13.802 41123 Z= 0.242 Chirality : 0.035 0.125 5751 Planarity : 0.002 0.011 5863 Dihedral : 3.812 17.294 5863 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.12), residues: 5710 helix: 2.16 (0.08), residues: 4046 sheet: -2.82 (0.32), residues: 202 loop : -0.83 (0.18), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 42 PHE 0.000 0.000 PHE A 162 TYR 0.000 0.000 TYR A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 3129) hydrogen bonds : angle 4.32962 ( 9333) covalent geometry : bond 0.00211 (29662) covalent geometry : angle 0.39124 (41123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11420 Ramachandran restraints generated. 5710 Oldfield, 0 Emsley, 5710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11420 Ramachandran restraints generated. 5710 Oldfield, 0 Emsley, 5710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 5320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.768 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2799 time to fit residues: 75.5785 Evaluate side-chains 132 residues out of total 5320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 265 optimal weight: 6.9990 chunk 304 optimal weight: 9.9990 chunk 380 optimal weight: 40.0000 chunk 107 optimal weight: 10.0000 chunk 425 optimal weight: 0.7980 chunk 5 optimal weight: 50.0000 chunk 174 optimal weight: 7.9990 chunk 432 optimal weight: 50.0000 chunk 128 optimal weight: 50.0000 chunk 272 optimal weight: 20.0000 chunk 90 optimal weight: 30.0000 overall best weight: 7.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.054591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.029283 restraints weight = 355164.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.029323 restraints weight = 327639.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.029282 restraints weight = 306298.799| |-----------------------------------------------------------------------------| r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29662 Z= 0.169 Angle : 0.385 13.679 41123 Z= 0.242 Chirality : 0.035 0.120 5751 Planarity : 0.002 0.012 5863 Dihedral : 3.376 14.771 5863 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.12), residues: 5710 helix: 2.82 (0.08), residues: 4053 sheet: -2.71 (0.32), residues: 202 loop : -0.74 (0.18), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 42 PHE 0.000 0.000 PHE A 162 TYR 0.000 0.000 TYR A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 3129) hydrogen bonds : angle 3.97677 ( 9333) covalent geometry : bond 0.00231 (29662) covalent geometry : angle 0.38454 (41123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11420 Ramachandran restraints generated. 5710 Oldfield, 0 Emsley, 5710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11420 Ramachandran restraints generated. 5710 Oldfield, 0 Emsley, 5710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 5320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.355 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2737 time to fit residues: 74.0764 Evaluate side-chains 132 residues out of total 5320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 595 optimal weight: 50.0000 chunk 556 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 512 optimal weight: 10.0000 chunk 28 optimal weight: 50.0000 chunk 159 optimal weight: 20.0000 chunk 451 optimal weight: 50.0000 chunk 363 optimal weight: 9.9990 chunk 246 optimal weight: 50.0000 chunk 135 optimal weight: 10.0000 chunk 385 optimal weight: 40.0000 overall best weight: 11.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.054307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.028962 restraints weight = 361186.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.029097 restraints weight = 340787.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.029098 restraints weight = 313857.785| |-----------------------------------------------------------------------------| r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.6220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29662 Z= 0.259 Angle : 0.455 14.086 41123 Z= 0.302 Chirality : 0.035 0.123 5751 Planarity : 0.002 0.013 5863 Dihedral : 3.872 17.719 5863 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.12), residues: 5710 helix: 2.27 (0.08), residues: 4088 sheet: -2.68 (0.34), residues: 190 loop : -1.08 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 42 PHE 0.000 0.000 PHE A 162 TYR 0.000 0.000 TYR A 21 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 3129) hydrogen bonds : angle 4.50512 ( 9333) covalent geometry : bond 0.00350 (29662) covalent geometry : angle 0.45535 (41123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11420 Ramachandran restraints generated. 5710 Oldfield, 0 Emsley, 5710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11420 Ramachandran restraints generated. 5710 Oldfield, 0 Emsley, 5710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 5320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.510 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2711 time to fit residues: 73.1914 Evaluate side-chains 132 residues out of total 5320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 358 optimal weight: 10.0000 chunk 474 optimal weight: 30.0000 chunk 547 optimal weight: 0.9980 chunk 21 optimal weight: 50.0000 chunk 113 optimal weight: 50.0000 chunk 423 optimal weight: 50.0000 chunk 489 optimal weight: 20.0000 chunk 135 optimal weight: 50.0000 chunk 139 optimal weight: 5.9990 chunk 306 optimal weight: 8.9990 chunk 226 optimal weight: 40.0000 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.054178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.029069 restraints weight = 359215.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.029142 restraints weight = 338840.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.029189 restraints weight = 306940.473| |-----------------------------------------------------------------------------| r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.6573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29662 Z= 0.197 Angle : 0.392 12.766 41123 Z= 0.252 Chirality : 0.035 0.117 5751 Planarity : 0.002 0.012 5863 Dihedral : 3.490 14.972 5863 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.12), residues: 5710 helix: 2.65 (0.08), residues: 4090 sheet: -2.63 (0.34), residues: 198 loop : -0.91 (0.18), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 42 PHE 0.000 0.000 PHE A 162 TYR 0.000 0.000 TYR A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 3129) hydrogen bonds : angle 4.13043 ( 9333) covalent geometry : bond 0.00266 (29662) covalent geometry : angle 0.39172 (41123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11420 Ramachandran restraints generated. 5710 Oldfield, 0 Emsley, 5710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11420 Ramachandran restraints generated. 5710 Oldfield, 0 Emsley, 5710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 5320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.347 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2623 time to fit residues: 70.5484 Evaluate side-chains 132 residues out of total 5320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 306 optimal weight: 7.9990 chunk 304 optimal weight: 10.0000 chunk 362 optimal weight: 10.0000 chunk 330 optimal weight: 50.0000 chunk 397 optimal weight: 50.0000 chunk 222 optimal weight: 50.0000 chunk 246 optimal weight: 50.0000 chunk 273 optimal weight: 20.0000 chunk 332 optimal weight: 50.0000 chunk 9 optimal weight: 50.0000 chunk 195 optimal weight: 50.0000 overall best weight: 19.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.054198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.029205 restraints weight = 367811.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.029174 restraints weight = 339052.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.029106 restraints weight = 335535.224| |-----------------------------------------------------------------------------| r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.7283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 29662 Z= 0.412 Angle : 0.601 16.763 41123 Z= 0.409 Chirality : 0.037 0.128 5751 Planarity : 0.004 0.020 5863 Dihedral : 4.774 21.925 5863 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.90 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.11), residues: 5710 helix: 1.03 (0.08), residues: 4097 sheet: -2.71 (0.31), residues: 210 loop : -1.75 (0.17), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 42 PHE 0.000 0.000 PHE A 162 TYR 0.000 0.000 TYR A 21 Details of bonding type rmsd hydrogen bonds : bond 0.05639 ( 3129) hydrogen bonds : angle 5.59231 ( 9333) covalent geometry : bond 0.00557 (29662) covalent geometry : angle 0.60115 (41123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11420 Ramachandran restraints generated. 5710 Oldfield, 0 Emsley, 5710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11420 Ramachandran restraints generated. 5710 Oldfield, 0 Emsley, 5710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 5320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.532 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2777 time to fit residues: 74.1486 Evaluate side-chains 132 residues out of total 5320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 128 optimal weight: 9.9990 chunk 184 optimal weight: 50.0000 chunk 95 optimal weight: 5.9990 chunk 348 optimal weight: 30.0000 chunk 191 optimal weight: 50.0000 chunk 304 optimal weight: 10.0000 chunk 496 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 82 optimal weight: 40.0000 chunk 335 optimal weight: 50.0000 chunk 565 optimal weight: 20.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.054043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.028956 restraints weight = 359801.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.029125 restraints weight = 326612.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.029153 restraints weight = 293040.153| |-----------------------------------------------------------------------------| r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.7270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29662 Z= 0.200 Angle : 0.403 13.161 41123 Z= 0.260 Chirality : 0.035 0.120 5751 Planarity : 0.002 0.011 5863 Dihedral : 3.847 17.452 5863 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.12), residues: 5710 helix: 2.03 (0.08), residues: 4100 sheet: -2.66 (0.31), residues: 226 loop : -1.30 (0.18), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 42 PHE 0.000 0.000 PHE A 162 TYR 0.000 0.000 TYR A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 3129) hydrogen bonds : angle 4.49961 ( 9333) covalent geometry : bond 0.00269 (29662) covalent geometry : angle 0.40345 (41123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11420 Ramachandran restraints generated. 5710 Oldfield, 0 Emsley, 5710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11420 Ramachandran restraints generated. 5710 Oldfield, 0 Emsley, 5710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 5320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.423 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2917 time to fit residues: 77.8146 Evaluate side-chains 132 residues out of total 5320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 136 optimal weight: 50.0000 chunk 110 optimal weight: 50.0000 chunk 46 optimal weight: 30.0000 chunk 160 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 chunk 36 optimal weight: 60.0000 chunk 192 optimal weight: 50.0000 chunk 260 optimal weight: 30.0000 chunk 460 optimal weight: 30.0000 chunk 355 optimal weight: 30.0000 chunk 67 optimal weight: 50.0000 overall best weight: 24.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.035464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.022594 restraints weight = 457433.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.022594 restraints weight = 448603.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.022594 restraints weight = 448971.121| |-----------------------------------------------------------------------------| r_work (final): 0.2382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.7955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 29662 Z= 0.491 Angle : 0.677 17.790 41123 Z= 0.466 Chirality : 0.038 0.131 5751 Planarity : 0.005 0.022 5863 Dihedral : 5.334 22.726 5863 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.18 % Favored : 90.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.11), residues: 5710 helix: 0.23 (0.08), residues: 4048 sheet: -3.09 (0.32), residues: 198 loop : -2.10 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 42 PHE 0.000 0.000 PHE A 162 TYR 0.000 0.000 TYR A 21 Details of bonding type rmsd hydrogen bonds : bond 0.06371 ( 3129) hydrogen bonds : angle 6.17979 ( 9333) covalent geometry : bond 0.00665 (29662) covalent geometry : angle 0.67655 (41123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11420 Ramachandran restraints generated. 5710 Oldfield, 0 Emsley, 5710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11420 Ramachandran restraints generated. 5710 Oldfield, 0 Emsley, 5710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 5320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.312 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2619 time to fit residues: 70.0194 Evaluate side-chains 132 residues out of total 5320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 155 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 431 optimal weight: 50.0000 chunk 270 optimal weight: 6.9990 chunk 514 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 247 optimal weight: 50.0000 chunk 225 optimal weight: 8.9990 chunk 288 optimal weight: 20.0000 chunk 536 optimal weight: 10.0000 chunk 251 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.054075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.028919 restraints weight = 358803.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.029022 restraints weight = 331218.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.029071 restraints weight = 305665.991| |-----------------------------------------------------------------------------| r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.7764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 29662 Z= 0.152 Angle : 0.378 11.997 41123 Z= 0.238 Chirality : 0.035 0.122 5751 Planarity : 0.002 0.012 5863 Dihedral : 3.932 17.802 5863 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.12), residues: 5710 helix: 1.90 (0.08), residues: 4092 sheet: -2.43 (0.37), residues: 176 loop : -1.59 (0.17), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 42 PHE 0.000 0.000 PHE A 162 TYR 0.000 0.000 TYR A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 3129) hydrogen bonds : angle 4.51308 ( 9333) covalent geometry : bond 0.00204 (29662) covalent geometry : angle 0.37819 (41123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11972.10 seconds wall clock time: 206 minutes 35.33 seconds (12395.33 seconds total)