Starting phenix.real_space_refine on Sat Aug 10 19:03:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7e_18214/08_2024/8q7e_18214.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7e_18214/08_2024/8q7e_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7e_18214/08_2024/8q7e_18214.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7e_18214/08_2024/8q7e_18214.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7e_18214/08_2024/8q7e_18214.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7e_18214/08_2024/8q7e_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 Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 19.81, per 1000 atoms: 0.66 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 - 3.50 Amino acid : False - 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: 14.62 Conformation dependent library (CDL) restraints added in 8.2 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: 4.66 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: 17.93 Time building geometry restraints manager: 15.74 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: 102.06 - 107.26: 323 107.26 - 112.46: 16259 112.46 - 117.66: 5511 117.66 - 122.86: 17783 122.86 - 128.06: 1247 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.350 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 100.400 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.220 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 113.890 ------------------------------------------------------------------------------- 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.533 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2482 time to fit residues: 68.0759 Evaluate side-chains 132 residues out of total 5320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.666 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 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= 0.173 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.273 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2651 time to fit residues: 70.2226 Evaluate side-chains 132 residues out of total 5320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 300 optimal weight: 50.0000 chunk 167 optimal weight: 10.0000 chunk 450 optimal weight: 30.0000 chunk 368 optimal weight: 30.0000 chunk 149 optimal weight: 20.0000 chunk 542 optimal weight: 20.0000 chunk 585 optimal weight: 0.9990 chunk 482 optimal weight: 30.0000 chunk 537 optimal weight: 0.0770 chunk 184 optimal weight: 50.0000 chunk 434 optimal weight: 10.0000 overall best weight: 8.2152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29662 Z= 0.194 Angle : 0.422 15.303 41123 Z= 0.265 Chirality : 0.035 0.127 5751 Planarity : 0.002 0.018 5863 Dihedral : 3.440 15.330 5863 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: 2.81 (0.12), residues: 5710 helix: 2.89 (0.08), residues: 4068 sheet: -2.11 (0.35), residues: 186 loop : -0.67 (0.17), residues: 1456 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.382 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2782 time to fit residues: 74.9012 Evaluate side-chains 132 residues out of total 5320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 535 optimal weight: 30.0000 chunk 407 optimal weight: 60.0000 chunk 281 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 chunk 258 optimal weight: 6.9990 chunk 364 optimal weight: 8.9990 chunk 544 optimal weight: 20.0000 chunk 576 optimal weight: 50.0000 chunk 284 optimal weight: 20.0000 chunk 515 optimal weight: 50.0000 chunk 155 optimal weight: 0.2980 overall best weight: 11.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29662 Z= 0.243 Angle : 0.489 16.712 41123 Z= 0.308 Chirality : 0.035 0.120 5751 Planarity : 0.003 0.015 5863 Dihedral : 4.088 19.260 5863 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 1.93 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: 1.98 (0.11), residues: 5710 helix: 2.19 (0.08), residues: 4072 sheet: -2.45 (0.33), residues: 202 loop : -0.70 (0.17), residues: 1436 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.756 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2572 time to fit residues: 69.5424 Evaluate side-chains 132 residues out of total 5320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 479 optimal weight: 5.9990 chunk 327 optimal weight: 50.0000 chunk 8 optimal weight: 0.1980 chunk 428 optimal weight: 40.0000 chunk 237 optimal weight: 30.0000 chunk 491 optimal weight: 50.0000 chunk 398 optimal weight: 50.0000 chunk 0 optimal weight: 60.0000 chunk 294 optimal weight: 30.0000 chunk 517 optimal weight: 0.0070 chunk 145 optimal weight: 30.0000 overall best weight: 13.2408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29662 Z= 0.277 Angle : 0.496 15.997 41123 Z= 0.323 Chirality : 0.036 0.124 5751 Planarity : 0.003 0.015 5863 Dihedral : 4.127 20.254 5863 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % 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: 1.58 (0.11), residues: 5710 helix: 1.93 (0.08), residues: 4076 sheet: -2.49 (0.33), residues: 206 loop : -0.97 (0.17), residues: 1428 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.471 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2669 time to fit residues: 71.4466 Evaluate side-chains 132 residues out of total 5320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 193 optimal weight: 20.0000 chunk 518 optimal weight: 20.0000 chunk 113 optimal weight: 30.0000 chunk 338 optimal weight: 50.0000 chunk 142 optimal weight: 40.0000 chunk 576 optimal weight: 50.0000 chunk 478 optimal weight: 5.9990 chunk 266 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 190 optimal weight: 30.0000 chunk 302 optimal weight: 50.0000 overall best weight: 11.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.6486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29662 Z= 0.232 Angle : 0.440 14.235 41123 Z= 0.284 Chirality : 0.035 0.124 5751 Planarity : 0.002 0.012 5863 Dihedral : 3.921 19.099 5863 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % 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: 1.84 (0.11), residues: 5710 helix: 2.15 (0.08), residues: 4084 sheet: -2.57 (0.33), residues: 213 loop : -0.95 (0.17), residues: 1413 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.740 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2643 time to fit residues: 72.0632 Evaluate side-chains 132 residues out of total 5320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 555 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 328 optimal weight: 50.0000 chunk 421 optimal weight: 50.0000 chunk 326 optimal weight: 50.0000 chunk 485 optimal weight: 20.0000 chunk 322 optimal weight: 0.9990 chunk 574 optimal weight: 50.0000 chunk 359 optimal weight: 30.0000 chunk 350 optimal weight: 30.0000 chunk 265 optimal weight: 7.9990 overall best weight: 11.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.7149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29662 Z= 0.246 Angle : 0.450 14.017 41123 Z= 0.295 Chirality : 0.035 0.129 5751 Planarity : 0.002 0.013 5863 Dihedral : 3.883 18.124 5863 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % 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: 1.78 (0.11), residues: 5710 helix: 2.16 (0.08), residues: 4102 sheet: -2.22 (0.33), residues: 219 loop : -1.25 (0.17), residues: 1389 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.333 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2680 time to fit residues: 72.0798 Evaluate side-chains 132 residues out of total 5320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 355 optimal weight: 20.0000 chunk 229 optimal weight: 50.0000 chunk 343 optimal weight: 50.0000 chunk 173 optimal weight: 30.0000 chunk 112 optimal weight: 30.0000 chunk 111 optimal weight: 30.0000 chunk 365 optimal weight: 20.0000 chunk 391 optimal weight: 40.0000 chunk 284 optimal weight: 30.0000 chunk 53 optimal weight: 30.0000 chunk 451 optimal weight: 40.0000 overall best weight: 26.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.7969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 29662 Z= 0.522 Angle : 0.726 18.396 41123 Z= 0.504 Chirality : 0.039 0.135 5751 Planarity : 0.005 0.029 5863 Dihedral : 5.606 24.335 5863 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.63 % Favored : 91.24 % 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: -1.04 (0.11), residues: 5710 helix: 0.00 (0.08), residues: 4035 sheet: -2.92 (0.31), residues: 191 loop : -2.07 (0.16), residues: 1484 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.352 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2731 time to fit residues: 73.1275 Evaluate side-chains 132 residues out of total 5320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 522 optimal weight: 7.9990 chunk 550 optimal weight: 20.0000 chunk 502 optimal weight: 30.0000 chunk 535 optimal weight: 6.9990 chunk 322 optimal weight: 40.0000 chunk 233 optimal weight: 30.0000 chunk 420 optimal weight: 50.0000 chunk 164 optimal weight: 20.0000 chunk 483 optimal weight: 30.0000 chunk 506 optimal weight: 40.0000 chunk 533 optimal weight: 50.0000 overall best weight: 16.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.8076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 29662 Z= 0.349 Angle : 0.550 16.368 41123 Z= 0.370 Chirality : 0.036 0.121 5751 Planarity : 0.003 0.019 5863 Dihedral : 4.754 22.931 5863 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % 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: -0.42 (0.11), residues: 5710 helix: 0.49 (0.08), residues: 4070 sheet: -2.69 (0.34), residues: 191 loop : -1.98 (0.17), residues: 1449 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.724 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2471 time to fit residues: 66.6067 Evaluate side-chains 132 residues out of total 5320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 351 optimal weight: 30.0000 chunk 566 optimal weight: 7.9990 chunk 345 optimal weight: 20.0000 chunk 268 optimal weight: 5.9990 chunk 393 optimal weight: 40.0000 chunk 593 optimal weight: 8.9990 chunk 546 optimal weight: 6.9990 chunk 472 optimal weight: 40.0000 chunk 49 optimal weight: 20.0000 chunk 365 optimal weight: 20.0000 chunk 289 optimal weight: 30.0000 overall best weight: 9.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.8075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29662 Z= 0.214 Angle : 0.425 12.880 41123 Z= 0.276 Chirality : 0.035 0.120 5751 Planarity : 0.002 0.016 5863 Dihedral : 4.092 18.102 5863 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % 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: 0.77 (0.11), residues: 5710 helix: 1.43 (0.08), residues: 4081 sheet: -2.39 (0.34), residues: 196 loop : -1.75 (0.17), residues: 1433 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 ********************** 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 fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.488 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2528 time to fit residues: 68.5223 Evaluate side-chains 132 residues out of total 5320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 375 optimal weight: 30.0000 chunk 503 optimal weight: 50.0000 chunk 144 optimal weight: 20.0000 chunk 435 optimal weight: 30.0000 chunk 69 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 473 optimal weight: 20.0000 chunk 198 optimal weight: 50.0000 chunk 486 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 87 optimal weight: 50.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.054038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.028930 restraints weight = 358479.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.028994 restraints weight = 331591.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.029010 restraints weight = 314778.019| |-----------------------------------------------------------------------------| r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.8094 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= 0.162 Angle : 0.370 10.628 41123 Z= 0.240 Chirality : 0.035 0.118 5751 Planarity : 0.002 0.011 5863 Dihedral : 3.666 15.796 5863 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % 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: 1.75 (0.12), residues: 5710 helix: 2.22 (0.08), residues: 4077 sheet: -2.22 (0.36), residues: 196 loop : -1.56 (0.17), residues: 1437 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4897.14 seconds wall clock time: 87 minutes 59.31 seconds (5279.31 seconds total)