Starting phenix.real_space_refine on Thu Dec 14 08:37:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e05_27817/12_2023/8e05_27817_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e05_27817/12_2023/8e05_27817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e05_27817/12_2023/8e05_27817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e05_27817/12_2023/8e05_27817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e05_27817/12_2023/8e05_27817_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e05_27817/12_2023/8e05_27817_neut.pdb" } resolution = 4.6 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= 0.001 sd= 0.023 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 174 5.16 5 C 17680 2.51 5 N 4774 2.21 5 O 5098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 120": "OD1" <-> "OD2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 541": "OE1" <-> "OE2" Residue "A PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A GLU 969": "OE1" <-> "OE2" Residue "A PHE 1076": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1123": "OE1" <-> "OE2" Residue "A PHE 1132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1199": "OE1" <-> "OE2" Residue "A GLU 1221": "OE1" <-> "OE2" Residue "A PHE 1223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1442": "OD1" <-> "OD2" Residue "A PHE 1448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 386": "OD1" <-> "OD2" Residue "B PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 541": "OE1" <-> "OE2" Residue "B PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 575": "OE1" <-> "OE2" Residue "B GLU 969": "OE1" <-> "OE2" Residue "B PHE 1076": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1123": "OE1" <-> "OE2" Residue "B PHE 1132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1199": "OE1" <-> "OE2" Residue "B PHE 1223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1442": "OD1" <-> "OD2" Residue "B PHE 1448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1775": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 27730 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1749, 13837 Classifications: {'peptide': 1749} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 89, 'TRANS': 1657} Chain breaks: 8 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 13837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1749, 13837 Classifications: {'peptide': 1749} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 89, 'TRANS': 1657} Chain breaks: 8 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.52, per 1000 atoms: 0.52 Number of scatterers: 27730 At special positions: 0 Unit cell: (170.52, 154.28, 107.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 174 16.00 P 4 15.00 O 5098 8.00 N 4774 7.00 C 17680 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: 10.81 Conformation dependent library (CDL) restraints added in 4.7 seconds 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6616 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 36 sheets defined 39.3% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.24 Creating SS restraints... Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.535A pdb=" N GLU A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 83 through 98 Proline residue: A 94 - end of helix Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 122 through 130 Processing helix chain 'A' and resid 132 through 142 removed outlier: 3.685A pdb=" N SER A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 164 Processing helix chain 'A' and resid 165 through 176 Processing helix chain 'A' and resid 192 through 195 Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 228 through 239 Processing helix chain 'A' and resid 269 through 274 removed outlier: 4.360A pdb=" N LEU A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 345 through 351 removed outlier: 3.592A pdb=" N PHE A 348 " --> pdb=" O PRO A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 removed outlier: 3.534A pdb=" N LEU A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 466 through 471 removed outlier: 4.423A pdb=" N PHE A 470 " --> pdb=" O PRO A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 494 Processing helix chain 'A' and resid 543 through 548 Processing helix chain 'A' and resid 564 through 570 Processing helix chain 'A' and resid 588 through 594 Processing helix chain 'A' and resid 611 through 618 Processing helix chain 'A' and resid 618 through 631 Processing helix chain 'A' and resid 650 through 661 Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 706 through 711 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 729 through 745 removed outlier: 3.892A pdb=" N ASN A 735 " --> pdb=" O GLU A 731 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN A 737 " --> pdb=" O VAL A 733 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP A 739 " --> pdb=" O ASN A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 762 Processing helix chain 'A' and resid 763 through 781 removed outlier: 4.456A pdb=" N VAL A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLU A 769 " --> pdb=" O LYS A 765 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 773 " --> pdb=" O GLU A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 799 No H-bonds generated for 'chain 'A' and resid 797 through 799' Processing helix chain 'A' and resid 811 through 825 Processing helix chain 'A' and resid 844 through 865 Processing helix chain 'A' and resid 872 through 882 Processing helix chain 'A' and resid 889 through 903 removed outlier: 3.834A pdb=" N LEU A 893 " --> pdb=" O ASP A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 916 removed outlier: 3.536A pdb=" N GLY A 915 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 937 removed outlier: 3.550A pdb=" N ILE A 937 " --> pdb=" O ARG A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 958 Processing helix chain 'A' and resid 967 through 978 Processing helix chain 'A' and resid 992 through 995 removed outlier: 3.652A pdb=" N LEU A 995 " --> pdb=" O PRO A 992 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 992 through 995' Processing helix chain 'A' and resid 1026 through 1047 Processing helix chain 'A' and resid 1107 through 1111 Processing helix chain 'A' and resid 1127 through 1145 removed outlier: 3.657A pdb=" N ALA A1131 " --> pdb=" O PHE A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1149 Processing helix chain 'A' and resid 1165 through 1173 Processing helix chain 'A' and resid 1190 through 1200 removed outlier: 4.110A pdb=" N GLU A1199 " --> pdb=" O LEU A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1223 Processing helix chain 'A' and resid 1228 through 1232 Processing helix chain 'A' and resid 1234 through 1238 Processing helix chain 'A' and resid 1243 through 1245 No H-bonds generated for 'chain 'A' and resid 1243 through 1245' Processing helix chain 'A' and resid 1286 through 1313 Processing helix chain 'A' and resid 1341 through 1351 removed outlier: 3.587A pdb=" N VAL A1345 " --> pdb=" O SER A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1380 Processing helix chain 'A' and resid 1442 through 1460 Processing helix chain 'A' and resid 1468 through 1478 Processing helix chain 'A' and resid 1486 through 1491 Processing helix chain 'A' and resid 1492 through 1503 Processing helix chain 'A' and resid 1506 through 1510 Processing helix chain 'A' and resid 1512 through 1521 removed outlier: 3.929A pdb=" N LYS A1521 " --> pdb=" O VAL A1517 " (cutoff:3.500A) Processing helix chain 'A' and resid 1522 through 1527 removed outlier: 3.509A pdb=" N ALA A1526 " --> pdb=" O ASP A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1559 Processing helix chain 'A' and resid 1609 through 1611 No H-bonds generated for 'chain 'A' and resid 1609 through 1611' Processing helix chain 'A' and resid 1670 through 1678 Processing helix chain 'A' and resid 1685 through 1689 Processing helix chain 'A' and resid 1904 through 1908 Processing helix chain 'A' and resid 1950 through 1957 Proline residue: A1955 - end of helix Processing helix chain 'A' and resid 1990 through 2007 Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.535A pdb=" N GLU B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 81 Processing helix chain 'B' and resid 83 through 98 Proline residue: B 94 - end of helix Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 122 through 130 Processing helix chain 'B' and resid 132 through 142 removed outlier: 3.686A pdb=" N SER B 142 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 165 through 176 Processing helix chain 'B' and resid 192 through 195 Processing helix chain 'B' and resid 196 through 204 Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 228 through 239 Processing helix chain 'B' and resid 269 through 274 removed outlier: 4.360A pdb=" N LEU B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 322 through 326 Processing helix chain 'B' and resid 345 through 351 removed outlier: 3.592A pdb=" N PHE B 348 " --> pdb=" O PRO B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.534A pdb=" N LEU B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 466 through 471 removed outlier: 4.422A pdb=" N PHE B 470 " --> pdb=" O PRO B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 543 through 548 Processing helix chain 'B' and resid 564 through 570 Processing helix chain 'B' and resid 588 through 594 Processing helix chain 'B' and resid 611 through 618 Processing helix chain 'B' and resid 618 through 631 Processing helix chain 'B' and resid 650 through 661 Processing helix chain 'B' and resid 703 through 705 No H-bonds generated for 'chain 'B' and resid 703 through 705' Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 712 through 714 No H-bonds generated for 'chain 'B' and resid 712 through 714' Processing helix chain 'B' and resid 729 through 745 removed outlier: 3.892A pdb=" N ASN B 735 " --> pdb=" O GLU B 731 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 737 " --> pdb=" O VAL B 733 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP B 739 " --> pdb=" O ASN B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 781 removed outlier: 4.456A pdb=" N VAL B 768 " --> pdb=" O ALA B 764 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N GLU B 769 " --> pdb=" O LYS B 765 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR B 773 " --> pdb=" O GLU B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 799 No H-bonds generated for 'chain 'B' and resid 797 through 799' Processing helix chain 'B' and resid 811 through 825 Processing helix chain 'B' and resid 844 through 865 Processing helix chain 'B' and resid 872 through 882 Processing helix chain 'B' and resid 889 through 903 removed outlier: 3.833A pdb=" N LEU B 893 " --> pdb=" O ASP B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 916 removed outlier: 3.536A pdb=" N GLY B 915 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 937 removed outlier: 3.550A pdb=" N ILE B 937 " --> pdb=" O ARG B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 958 Processing helix chain 'B' and resid 967 through 978 Processing helix chain 'B' and resid 992 through 995 removed outlier: 3.652A pdb=" N LEU B 995 " --> pdb=" O PRO B 992 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 992 through 995' Processing helix chain 'B' and resid 1026 through 1047 Processing helix chain 'B' and resid 1107 through 1111 Processing helix chain 'B' and resid 1127 through 1145 removed outlier: 3.658A pdb=" N ALA B1131 " --> pdb=" O PHE B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1146 through 1149 Processing helix chain 'B' and resid 1165 through 1173 Processing helix chain 'B' and resid 1190 through 1200 removed outlier: 4.110A pdb=" N GLU B1199 " --> pdb=" O LEU B1195 " (cutoff:3.500A) Processing helix chain 'B' and resid 1219 through 1223 Processing helix chain 'B' and resid 1228 through 1232 Processing helix chain 'B' and resid 1234 through 1238 Processing helix chain 'B' and resid 1243 through 1245 No H-bonds generated for 'chain 'B' and resid 1243 through 1245' Processing helix chain 'B' and resid 1286 through 1313 Processing helix chain 'B' and resid 1341 through 1351 removed outlier: 3.588A pdb=" N VAL B1345 " --> pdb=" O SER B1341 " (cutoff:3.500A) Processing helix chain 'B' and resid 1359 through 1380 Processing helix chain 'B' and resid 1442 through 1460 Processing helix chain 'B' and resid 1468 through 1478 Processing helix chain 'B' and resid 1486 through 1491 Processing helix chain 'B' and resid 1492 through 1503 Processing helix chain 'B' and resid 1506 through 1510 Processing helix chain 'B' and resid 1512 through 1521 removed outlier: 3.929A pdb=" N LYS B1521 " --> pdb=" O VAL B1517 " (cutoff:3.500A) Processing helix chain 'B' and resid 1522 through 1527 removed outlier: 3.509A pdb=" N ALA B1526 " --> pdb=" O ASP B1522 " (cutoff:3.500A) Processing helix chain 'B' and resid 1556 through 1559 Processing helix chain 'B' and resid 1609 through 1611 No H-bonds generated for 'chain 'B' and resid 1609 through 1611' Processing helix chain 'B' and resid 1670 through 1678 Processing helix chain 'B' and resid 1685 through 1689 Processing helix chain 'B' and resid 1904 through 1908 Processing helix chain 'B' and resid 1950 through 1957 Proline residue: B1955 - end of helix Processing helix chain 'B' and resid 1990 through 2007 Processing sheet with id=AA1, first strand: chain 'A' and resid 241 through 242 Processing sheet with id=AA2, first strand: chain 'A' and resid 306 through 308 removed outlier: 6.743A pdb=" N LEU A 307 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE A 334 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU A 357 " --> pdb=" O ASP A 386 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 385 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU A 409 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU A 478 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU A 502 " --> pdb=" O CYS A 554 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N LEU A 576 " --> pdb=" O ASP A 601 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 634 through 636 Processing sheet with id=AA4, first strand: chain 'A' and resid 673 through 681 removed outlier: 6.718A pdb=" N MET A 639 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N TRP A 698 " --> pdb=" O MET A 639 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N MET A 641 " --> pdb=" O TRP A 698 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE A 700 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE A 643 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N LEU A 719 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS A 640 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL A 721 " --> pdb=" O LYS A 640 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 642 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N VAL A 723 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL A 644 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ASN A 725 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR A 720 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL A 755 " --> pdb=" O TYR A 720 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 722 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N THR A 757 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TRP A 724 " --> pdb=" O THR A 757 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 870 through 871 Processing sheet with id=AA6, first strand: chain 'A' and resid 948 through 950 Processing sheet with id=AA7, first strand: chain 'A' and resid 1080 through 1086 removed outlier: 6.663A pdb=" N THR A1093 " --> pdb=" O ASN A1081 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR A1083 " --> pdb=" O LEU A1091 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU A1091 " --> pdb=" O THR A1083 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N TYR A1085 " --> pdb=" O GLY A1089 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY A1089 " --> pdb=" O TYR A1085 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLN A1015 " --> pdb=" O PRO A1164 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1202 through 1203 removed outlier: 4.032A pdb=" N ILE A1203 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL A1213 " --> pdb=" O ILE A1203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 1247 through 1250 removed outlier: 6.716A pdb=" N ILE A1257 " --> pdb=" O LEU A1248 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY A1324 " --> pdb=" O ALA A1333 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU A1335 " --> pdb=" O LEU A1322 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LEU A1322 " --> pdb=" O GLU A1335 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1392 through 1394 Processing sheet with id=AB2, first strand: chain 'A' and resid 1528 through 1536 removed outlier: 6.209A pdb=" N PHE A1528 " --> pdb=" O ARG A1987 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARG A1987 " --> pdb=" O PHE A1528 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR A1530 " --> pdb=" O VAL A1985 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N TRP A1981 " --> pdb=" O CYS A1534 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR A1969 " --> pdb=" O VAL A1965 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLU A1975 " --> pdb=" O LEU A1959 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU A1959 " --> pdb=" O GLU A1975 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1539 through 1542 removed outlier: 7.083A pdb=" N VAL A1564 " --> pdb=" O GLN A1575 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLN A1575 " --> pdb=" O VAL A1564 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N ASN A1566 " --> pdb=" O GLU A1573 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLU A1573 " --> pdb=" O ASN A1566 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1584 through 1590 removed outlier: 4.145A pdb=" N CYS A1586 " --> pdb=" O ALA A1597 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS A1602 " --> pdb=" O THR A1598 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1627 through 1635 removed outlier: 6.789A pdb=" N GLY A1646 " --> pdb=" O THR A1628 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE A1630 " --> pdb=" O LEU A1644 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU A1644 " --> pdb=" O PHE A1630 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA A1632 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU A1642 " --> pdb=" O ALA A1632 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER A1640 " --> pdb=" O PRO A1634 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1627 through 1635 removed outlier: 6.789A pdb=" N GLY A1646 " --> pdb=" O THR A1628 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE A1630 " --> pdb=" O LEU A1644 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU A1644 " --> pdb=" O PHE A1630 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA A1632 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU A1642 " --> pdb=" O ALA A1632 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER A1640 " --> pdb=" O PRO A1634 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1696 through 1699 removed outlier: 6.266A pdb=" N ASP A1717 " --> pdb=" O ILE A1723 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A1723 " --> pdb=" O ASP A1717 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1736 through 1743 removed outlier: 3.614A pdb=" N SER A1738 " --> pdb=" O LEU A1754 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A1760 " --> pdb=" O ASP A1755 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU A1761 " --> pdb=" O ARG A1774 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ARG A1774 " --> pdb=" O LEU A1761 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N MET A1763 " --> pdb=" O CYS A1772 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1786 through 1789 removed outlier: 7.208A pdb=" N VAL A1930 " --> pdb=" O ILE A1945 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N VAL A1947 " --> pdb=" O VAL A1928 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A1928 " --> pdb=" O VAL A1947 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 241 through 242 Processing sheet with id=AC2, first strand: chain 'B' and resid 306 through 308 removed outlier: 6.744A pdb=" N LEU B 307 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE B 334 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B 357 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 385 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 409 " --> pdb=" O LYS B 431 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU B 478 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU B 502 " --> pdb=" O CYS B 554 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU B 576 " --> pdb=" O ASP B 601 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 634 through 636 Processing sheet with id=AC4, first strand: chain 'B' and resid 673 through 681 removed outlier: 6.718A pdb=" N MET B 639 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N TRP B 698 " --> pdb=" O MET B 639 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N MET B 641 " --> pdb=" O TRP B 698 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE B 700 " --> pdb=" O MET B 641 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE B 643 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N LEU B 719 " --> pdb=" O LEU B 638 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LYS B 640 " --> pdb=" O LEU B 719 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL B 721 " --> pdb=" O LYS B 640 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE B 642 " --> pdb=" O VAL B 721 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N VAL B 723 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 644 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N ASN B 725 " --> pdb=" O VAL B 644 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR B 720 " --> pdb=" O LEU B 753 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL B 755 " --> pdb=" O TYR B 720 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL B 722 " --> pdb=" O VAL B 755 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N THR B 757 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TRP B 724 " --> pdb=" O THR B 757 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 870 through 871 Processing sheet with id=AC6, first strand: chain 'B' and resid 948 through 950 Processing sheet with id=AC7, first strand: chain 'B' and resid 1080 through 1086 removed outlier: 6.663A pdb=" N THR B1093 " --> pdb=" O ASN B1081 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR B1083 " --> pdb=" O LEU B1091 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU B1091 " --> pdb=" O THR B1083 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR B1085 " --> pdb=" O GLY B1089 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY B1089 " --> pdb=" O TYR B1085 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N GLN B1015 " --> pdb=" O PRO B1164 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1202 through 1203 removed outlier: 4.032A pdb=" N ILE B1203 " --> pdb=" O VAL B1213 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL B1213 " --> pdb=" O ILE B1203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 1247 through 1250 removed outlier: 6.715A pdb=" N ILE B1257 " --> pdb=" O LEU B1248 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY B1324 " --> pdb=" O ALA B1333 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU B1335 " --> pdb=" O LEU B1322 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LEU B1322 " --> pdb=" O GLU B1335 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1392 through 1394 Processing sheet with id=AD2, first strand: chain 'B' and resid 1528 through 1536 removed outlier: 6.209A pdb=" N PHE B1528 " --> pdb=" O ARG B1987 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARG B1987 " --> pdb=" O PHE B1528 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B1530 " --> pdb=" O VAL B1985 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N TRP B1981 " --> pdb=" O CYS B1534 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR B1969 " --> pdb=" O VAL B1965 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLU B1975 " --> pdb=" O LEU B1959 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU B1959 " --> pdb=" O GLU B1975 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1539 through 1542 removed outlier: 7.083A pdb=" N VAL B1564 " --> pdb=" O GLN B1575 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLN B1575 " --> pdb=" O VAL B1564 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N ASN B1566 " --> pdb=" O GLU B1573 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLU B1573 " --> pdb=" O ASN B1566 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1584 through 1590 removed outlier: 4.144A pdb=" N CYS B1586 " --> pdb=" O ALA B1597 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS B1602 " --> pdb=" O THR B1598 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1627 through 1635 removed outlier: 6.789A pdb=" N GLY B1646 " --> pdb=" O THR B1628 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHE B1630 " --> pdb=" O LEU B1644 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU B1644 " --> pdb=" O PHE B1630 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA B1632 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU B1642 " --> pdb=" O ALA B1632 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER B1640 " --> pdb=" O PRO B1634 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1627 through 1635 removed outlier: 6.789A pdb=" N GLY B1646 " --> pdb=" O THR B1628 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHE B1630 " --> pdb=" O LEU B1644 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU B1644 " --> pdb=" O PHE B1630 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA B1632 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU B1642 " --> pdb=" O ALA B1632 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER B1640 " --> pdb=" O PRO B1634 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1696 through 1699 removed outlier: 6.267A pdb=" N ASP B1717 " --> pdb=" O ILE B1723 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE B1723 " --> pdb=" O ASP B1717 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1736 through 1743 removed outlier: 3.614A pdb=" N SER B1738 " --> pdb=" O LEU B1754 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B1760 " --> pdb=" O ASP B1755 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU B1761 " --> pdb=" O ARG B1774 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ARG B1774 " --> pdb=" O LEU B1761 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N MET B1763 " --> pdb=" O CYS B1772 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1786 through 1789 removed outlier: 7.209A pdb=" N VAL B1930 " --> pdb=" O ILE B1945 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N VAL B1947 " --> pdb=" O VAL B1928 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B1928 " --> pdb=" O VAL B1947 " (cutoff:3.500A) 1160 hydrogen bonds defined for protein. 3096 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: 15.07 Time building geometry restraints manager: 11.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4589 1.31 - 1.44: 7277 1.44 - 1.56: 16210 1.56 - 1.69: 6 1.69 - 1.81: 250 Bond restraints: 28332 Sorted by residual: bond pdb=" C PRO A1220 " pdb=" O PRO A1220 " ideal model delta sigma weight residual 1.238 1.187 0.051 1.36e-02 5.41e+03 1.41e+01 bond pdb=" N MET A1224 " pdb=" CA MET A1224 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.28e-02 6.10e+03 7.01e+00 bond pdb=" N ARG A1016 " pdb=" CA ARG A1016 " ideal model delta sigma weight residual 1.455 1.481 -0.026 1.25e-02 6.40e+03 4.41e+00 bond pdb=" N VAL A1219 " pdb=" CA VAL A1219 " ideal model delta sigma weight residual 1.461 1.485 -0.024 1.23e-02 6.61e+03 3.89e+00 bond pdb=" N PRO A1220 " pdb=" CD PRO A1220 " ideal model delta sigma weight residual 1.473 1.447 0.026 1.40e-02 5.10e+03 3.50e+00 ... (remaining 28327 not shown) Histogram of bond angle deviations from ideal: 98.73 - 106.22: 885 106.22 - 113.70: 15759 113.70 - 121.19: 13786 121.19 - 128.68: 7681 128.68 - 136.17: 323 Bond angle restraints: 38434 Sorted by residual: angle pdb=" N THR A1225 " pdb=" CA THR A1225 " pdb=" C THR A1225 " ideal model delta sigma weight residual 112.88 104.73 8.15 1.29e+00 6.01e-01 3.99e+01 angle pdb=" N ASP A1226 " pdb=" CA ASP A1226 " pdb=" C ASP A1226 " ideal model delta sigma weight residual 113.97 107.60 6.37 1.28e+00 6.10e-01 2.48e+01 angle pdb=" C PRO A1220 " pdb=" CA PRO A1220 " pdb=" CB PRO A1220 " ideal model delta sigma weight residual 113.06 105.23 7.83 1.59e+00 3.96e-01 2.42e+01 angle pdb=" N PHE A1223 " pdb=" CA PHE A1223 " pdb=" C PHE A1223 " ideal model delta sigma weight residual 110.32 103.57 6.75 1.59e+00 3.96e-01 1.80e+01 angle pdb=" N ILE A 377 " pdb=" CA ILE A 377 " pdb=" C ILE A 377 " ideal model delta sigma weight residual 113.53 109.89 3.64 9.80e-01 1.04e+00 1.38e+01 ... (remaining 38429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 15915 16.93 - 33.86: 1011 33.86 - 50.79: 157 50.79 - 67.71: 61 67.71 - 84.64: 20 Dihedral angle restraints: 17164 sinusoidal: 6974 harmonic: 10190 Sorted by residual: dihedral pdb=" CA ARG A1592 " pdb=" C ARG A1592 " pdb=" N SER A1593 " pdb=" CA SER A1593 " ideal model delta harmonic sigma weight residual -180.00 -157.51 -22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ARG B1592 " pdb=" C ARG B1592 " pdb=" N SER B1593 " pdb=" CA SER B1593 " ideal model delta harmonic sigma weight residual -180.00 -157.51 -22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA GLN B1591 " pdb=" C GLN B1591 " pdb=" N ARG B1592 " pdb=" CA ARG B1592 " ideal model delta harmonic sigma weight residual 180.00 157.97 22.03 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 17161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3887 0.074 - 0.148: 439 0.148 - 0.223: 12 0.223 - 0.297: 4 0.297 - 0.371: 2 Chirality restraints: 4344 Sorted by residual: chirality pdb=" CA ARG A1016 " pdb=" N ARG A1016 " pdb=" C ARG A1016 " pdb=" CB ARG A1016 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA VAL A1219 " pdb=" N VAL A1219 " pdb=" C VAL A1219 " pdb=" CB VAL A1219 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA THR A1225 " pdb=" N THR A1225 " pdb=" C THR A1225 " pdb=" CB THR A1225 " both_signs ideal model delta sigma weight residual False 2.53 2.81 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 4341 not shown) Planarity restraints: 4922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B1655 " -0.066 5.00e-02 4.00e+02 9.94e-02 1.58e+01 pdb=" N PRO B1656 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO B1656 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO B1656 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1655 " 0.066 5.00e-02 4.00e+02 9.94e-02 1.58e+01 pdb=" N PRO A1656 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO A1656 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A1656 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1784 " 0.256 9.50e-02 1.11e+02 1.15e-01 9.66e+00 pdb=" NE ARG B1784 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG B1784 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG B1784 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B1784 " 0.002 2.00e-02 2.50e+03 ... (remaining 4919 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1094 2.72 - 3.26: 29014 3.26 - 3.81: 46086 3.81 - 4.35: 59849 4.35 - 4.90: 95874 Nonbonded interactions: 231917 Sorted by model distance: nonbonded pdb=" OG SER A 458 " pdb=" OE1 GLU A 459 " model vdw 2.169 2.440 nonbonded pdb=" O PHE A 457 " pdb=" ND2 ASN A 460 " model vdw 2.198 2.520 nonbonded pdb=" O PHE B 457 " pdb=" ND2 ASN B 460 " model vdw 2.198 2.520 nonbonded pdb=" OG SER B 388 " pdb=" O SER B 412 " model vdw 2.199 2.440 nonbonded pdb=" OG SER A 388 " pdb=" O SER A 412 " model vdw 2.199 2.440 ... (remaining 231912 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 6.820 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 76.610 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 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 : 0.004 0.051 28332 Z= 0.228 Angle : 0.730 8.152 38434 Z= 0.405 Chirality : 0.045 0.371 4344 Planarity : 0.006 0.116 4922 Dihedral : 11.908 84.643 10548 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.20 % 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: -0.27 (0.14), residues: 3462 helix: 0.29 (0.15), residues: 1118 sheet: -0.65 (0.20), residues: 590 loop : -0.18 (0.16), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B1503 HIS 0.007 0.001 HIS B1956 PHE 0.027 0.002 PHE A1132 TYR 0.046 0.002 TYR A 869 ARG 0.022 0.001 ARG B1784 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.2637 time to fit residues: 138.2766 Evaluate side-chains 261 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.766 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 0.9990 chunk 263 optimal weight: 0.0270 chunk 146 optimal weight: 8.9990 chunk 90 optimal weight: 0.0980 chunk 177 optimal weight: 10.0000 chunk 140 optimal weight: 0.1980 chunk 272 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 203 optimal weight: 0.0060 chunk 316 optimal weight: 0.9990 overall best weight: 0.2454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 559 HIS B 868 GLN ** B1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1291 HIS ** B1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28332 Z= 0.173 Angle : 0.602 8.647 38434 Z= 0.307 Chirality : 0.044 0.242 4344 Planarity : 0.004 0.073 4922 Dihedral : 4.585 32.098 3790 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.13 % Allowed : 1.83 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -0.03 (0.15), residues: 3462 helix: 0.56 (0.15), residues: 1142 sheet: -0.66 (0.19), residues: 622 loop : -0.02 (0.16), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B1503 HIS 0.004 0.001 HIS B 176 PHE 0.020 0.002 PHE A1492 TYR 0.026 0.002 TYR A1376 ARG 0.008 0.000 ARG A1016 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 328 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 329 average time/residue: 0.2523 time to fit residues: 123.3752 Evaluate side-chains 248 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.781 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 263 optimal weight: 0.7980 chunk 215 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 316 optimal weight: 0.0270 chunk 342 optimal weight: 20.0000 chunk 281 optimal weight: 5.9990 chunk 313 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 253 optimal weight: 1.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN B 559 HIS B 710 ASN ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1349 ASN ** B1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1587 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28332 Z= 0.170 Angle : 0.576 9.277 38434 Z= 0.295 Chirality : 0.042 0.205 4344 Planarity : 0.004 0.062 4922 Dihedral : 4.381 19.437 3790 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -0.48 (0.14), residues: 3462 helix: 0.18 (0.15), residues: 1138 sheet: -0.96 (0.19), residues: 646 loop : -0.25 (0.16), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B1503 HIS 0.004 0.001 HIS B 176 PHE 0.039 0.002 PHE B1492 TYR 0.026 0.001 TYR A1376 ARG 0.002 0.000 ARG A 845 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.2396 time to fit residues: 106.7714 Evaluate side-chains 225 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.654 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 6.9990 chunk 238 optimal weight: 9.9990 chunk 164 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 317 optimal weight: 2.9990 chunk 336 optimal weight: 8.9990 chunk 165 optimal weight: 0.7980 chunk 301 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 710 ASN ** A 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1121 GLN A1291 HIS ** A1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1688 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28332 Z= 0.169 Angle : 0.566 9.077 38434 Z= 0.287 Chirality : 0.042 0.151 4344 Planarity : 0.004 0.052 4922 Dihedral : 4.313 20.082 3790 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.07 % Allowed : 2.03 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -0.69 (0.14), residues: 3462 helix: 0.10 (0.15), residues: 1144 sheet: -1.11 (0.19), residues: 666 loop : -0.42 (0.16), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1595 HIS 0.004 0.001 HIS A 176 PHE 0.028 0.002 PHE B1492 TYR 0.023 0.002 TYR A1376 ARG 0.004 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 274 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 0.2331 time to fit residues: 98.4449 Evaluate side-chains 216 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.794 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 250 optimal weight: 0.8980 chunk 138 optimal weight: 9.9990 chunk 287 optimal weight: 0.0020 chunk 232 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 171 optimal weight: 8.9990 chunk 301 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 overall best weight: 2.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 ASN A 918 ASN A1364 GLN ** A1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28332 Z= 0.192 Angle : 0.575 8.364 38434 Z= 0.294 Chirality : 0.042 0.164 4344 Planarity : 0.004 0.060 4922 Dihedral : 4.378 27.195 3790 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -0.83 (0.14), residues: 3462 helix: 0.05 (0.15), residues: 1144 sheet: -1.23 (0.19), residues: 660 loop : -0.55 (0.16), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP B1503 HIS 0.010 0.001 HIS A1136 PHE 0.035 0.002 PHE B1132 TYR 0.020 0.001 TYR B1376 ARG 0.005 0.000 ARG B1030 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2433 time to fit residues: 99.3917 Evaluate side-chains 206 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.810 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 5.9990 chunk 302 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 197 optimal weight: 0.0060 chunk 83 optimal weight: 0.8980 chunk 336 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 111 optimal weight: 0.0060 chunk 176 optimal weight: 4.9990 overall best weight: 0.4412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 ASN A1291 HIS ** A1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 28332 Z= 0.145 Angle : 0.572 9.126 38434 Z= 0.287 Chirality : 0.043 0.156 4344 Planarity : 0.004 0.054 4922 Dihedral : 4.223 28.935 3790 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.07 % Allowed : 0.98 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -0.88 (0.14), residues: 3462 helix: -0.03 (0.15), residues: 1144 sheet: -1.16 (0.19), residues: 650 loop : -0.59 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A1503 HIS 0.007 0.001 HIS B1312 PHE 0.040 0.002 PHE A1492 TYR 0.023 0.001 TYR A1376 ARG 0.004 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 279 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 279 average time/residue: 0.2332 time to fit residues: 99.5423 Evaluate side-chains 217 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.750 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 0.0000 chunk 37 optimal weight: 0.0970 chunk 191 optimal weight: 7.9990 chunk 245 optimal weight: 0.0070 chunk 190 optimal weight: 0.0020 chunk 283 optimal weight: 0.0060 chunk 188 optimal weight: 0.7980 chunk 335 optimal weight: 0.0970 chunk 209 optimal weight: 0.0870 chunk 204 optimal weight: 0.0370 chunk 154 optimal weight: 0.7980 overall best weight: 0.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28332 Z= 0.141 Angle : 0.579 9.780 38434 Z= 0.290 Chirality : 0.043 0.207 4344 Planarity : 0.004 0.053 4922 Dihedral : 4.216 27.462 3790 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -0.96 (0.14), residues: 3462 helix: -0.12 (0.15), residues: 1144 sheet: -1.24 (0.19), residues: 664 loop : -0.61 (0.16), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A1503 HIS 0.004 0.001 HIS B1312 PHE 0.030 0.002 PHE B1132 TYR 0.024 0.001 TYR B 62 ARG 0.011 0.000 ARG A1261 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.2323 time to fit residues: 99.2269 Evaluate side-chains 219 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.809 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 0.6980 chunk 133 optimal weight: 6.9990 chunk 200 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 213 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 165 optimal weight: 0.2980 chunk 31 optimal weight: 0.1980 chunk 263 optimal weight: 0.0030 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1291 HIS ** A1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28332 Z= 0.143 Angle : 0.572 8.025 38434 Z= 0.288 Chirality : 0.043 0.194 4344 Planarity : 0.004 0.050 4922 Dihedral : 4.171 26.726 3790 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.07 % Allowed : 0.78 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -0.99 (0.14), residues: 3462 helix: -0.08 (0.15), residues: 1144 sheet: -1.23 (0.19), residues: 656 loop : -0.68 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.002 TRP B1503 HIS 0.007 0.001 HIS A1467 PHE 0.027 0.002 PHE B1132 TYR 0.020 0.001 TYR A1376 ARG 0.010 0.000 ARG B1261 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 271 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 271 average time/residue: 0.2312 time to fit residues: 95.9467 Evaluate side-chains 221 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.625 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 2.9990 chunk 321 optimal weight: 10.0000 chunk 293 optimal weight: 0.0050 chunk 312 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 282 optimal weight: 1.9990 chunk 295 optimal weight: 0.5980 chunk 311 optimal weight: 4.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN A1263 GLN ** A1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28332 Z= 0.155 Angle : 0.577 9.715 38434 Z= 0.291 Chirality : 0.043 0.170 4344 Planarity : 0.004 0.061 4922 Dihedral : 4.273 26.454 3790 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -1.02 (0.14), residues: 3462 helix: -0.00 (0.15), residues: 1146 sheet: -1.32 (0.18), residues: 682 loop : -0.74 (0.16), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A1503 HIS 0.004 0.001 HIS A 176 PHE 0.024 0.002 PHE B1132 TYR 0.014 0.001 TYR B 869 ARG 0.006 0.000 ARG A1030 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.2327 time to fit residues: 94.3246 Evaluate side-chains 206 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.857 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 7.9990 chunk 330 optimal weight: 0.1980 chunk 201 optimal weight: 0.0170 chunk 156 optimal weight: 0.1980 chunk 229 optimal weight: 0.8980 chunk 346 optimal weight: 0.2980 chunk 319 optimal weight: 0.1980 chunk 276 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 213 optimal weight: 0.0040 chunk 169 optimal weight: 5.9990 overall best weight: 0.1230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN ** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1291 HIS ** A1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28332 Z= 0.141 Angle : 0.592 12.129 38434 Z= 0.291 Chirality : 0.043 0.173 4344 Planarity : 0.004 0.055 4922 Dihedral : 4.195 31.805 3790 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.07 % Allowed : 0.07 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.14), residues: 3462 helix: -0.09 (0.15), residues: 1144 sheet: -1.22 (0.18), residues: 672 loop : -0.75 (0.16), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B1503 HIS 0.004 0.001 HIS B 176 PHE 0.026 0.002 PHE A1132 TYR 0.020 0.001 TYR B 869 ARG 0.002 0.000 ARG B 186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 275 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 275 average time/residue: 0.2424 time to fit residues: 102.8225 Evaluate side-chains 215 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.702 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 0.9980 chunk 294 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 254 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 276 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 283 optimal weight: 10.0000 chunk 35 optimal weight: 0.0040 chunk 50 optimal weight: 1.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.089739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.068351 restraints weight = 62190.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.070816 restraints weight = 39795.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.072627 restraints weight = 28852.942| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 28332 Z= 0.145 Angle : 0.585 11.583 38434 Z= 0.289 Chirality : 0.042 0.172 4344 Planarity : 0.004 0.062 4922 Dihedral : 4.193 27.764 3790 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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 (0.14), residues: 3462 helix: -0.10 (0.15), residues: 1154 sheet: -1.15 (0.19), residues: 668 loop : -0.78 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP B1503 HIS 0.004 0.001 HIS B1312 PHE 0.024 0.002 PHE B1132 TYR 0.014 0.001 TYR B1063 ARG 0.004 0.000 ARG B1030 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4291.74 seconds wall clock time: 80 minutes 31.60 seconds (4831.60 seconds total)