Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 04:41:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe9_22145/04_2023/6xe9_22145.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe9_22145/04_2023/6xe9_22145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe9_22145/04_2023/6xe9_22145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe9_22145/04_2023/6xe9_22145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe9_22145/04_2023/6xe9_22145.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xe9_22145/04_2023/6xe9_22145.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.002 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: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 13855 2.51 5 N 3871 2.21 5 O 4241 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 697": "OD1" <-> "OD2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "A TYR 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 787": "OE1" <-> "OE2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 938": "OE1" <-> "OE2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 57": "OD1" <-> "OD2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "C PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 40": "OE1" <-> "OE2" Residue "M GLU 169": "OE1" <-> "OE2" Residue "M PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 308": "OE1" <-> "OE2" Residue "M GLU 334": "OE1" <-> "OE2" Residue "M GLU 370": "OE1" <-> "OE2" Residue "M PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 501": "OE1" <-> "OE2" Residue "M PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 603": "OD1" <-> "OD2" Residue "M PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 748": "OD1" <-> "OD2" Residue "M PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 900": "OE1" <-> "OE2" Residue "M ARG 916": "NH1" <-> "NH2" Residue "M GLU 941": "OE1" <-> "OE2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 57": "OD1" <-> "OD2" Residue "N PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 87": "OD1" <-> "OD2" Residue "N TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 132": "OE1" <-> "OE2" Residue "O PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 22081 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 8719 Classifications: {'peptide': 1183} Incomplete info: {'truncation_to_alanine': 253} Link IDs: {'PTRANS': 26, 'TRANS': 1156} Chain breaks: 3 Unresolved non-hydrogen bonds: 934 Unresolved non-hydrogen angles: 1143 Unresolved non-hydrogen dihedrals: 748 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 26, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 9, 'ASP:plan': 23, 'PHE:plan': 4, 'GLU:plan': 49, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 566 Chain: "B" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1159 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 3, 'TRANS': 144} Chain: "C" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1160 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain: "M" Number of atoms: 8724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1184, 8724 Classifications: {'peptide': 1184} Incomplete info: {'truncation_to_alanine': 254} Link IDs: {'PTRANS': 26, 'TRANS': 1157} Chain breaks: 3 Unresolved non-hydrogen bonds: 938 Unresolved non-hydrogen angles: 1148 Unresolved non-hydrogen dihedrals: 751 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 26, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 9, 'ASP:plan': 23, 'PHE:plan': 4, 'GLU:plan': 50, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 570 Chain: "N" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1159 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 3, 'TRANS': 144} Chain: "O" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1160 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Time building chain proxies: 11.45, per 1000 atoms: 0.52 Number of scatterers: 22081 At special positions: 0 Unit cell: (156.704, 130.144, 216.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4241 8.00 N 3871 7.00 C 13855 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: 10.71 Conformation dependent library (CDL) restraints added in 3.7 seconds 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5626 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 17 sheets defined 67.5% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 24 through 31 removed outlier: 4.073A pdb=" N ALA A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 84 Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 96 through 110 Processing helix chain 'A' and resid 134 through 142 Processing helix chain 'A' and resid 152 through 168 removed outlier: 3.587A pdb=" N ARG A 168 " --> pdb=" O MET A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 198 removed outlier: 3.571A pdb=" N LYS A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL A 196 " --> pdb=" O GLN A 192 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.994A pdb=" N ASN A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Proline residue: A 229 - end of helix Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 287 through 295 removed outlier: 4.294A pdb=" N TYR A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 295 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 327 through 343 removed outlier: 3.987A pdb=" N MET A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 362 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 381 through 392 Processing helix chain 'A' and resid 394 through 404 removed outlier: 3.609A pdb=" N PHE A 398 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 448 Processing helix chain 'A' and resid 476 through 508 removed outlier: 4.875A pdb=" N LEU A 500 " --> pdb=" O THR A 496 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLU A 501 " --> pdb=" O MET A 497 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 506 " --> pdb=" O GLN A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 530 removed outlier: 5.066A pdb=" N ILE A 528 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU A 529 " --> pdb=" O ILE A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 546 Processing helix chain 'A' and resid 551 through 563 Processing helix chain 'A' and resid 575 through 578 Processing helix chain 'A' and resid 596 through 603 Processing helix chain 'A' and resid 606 through 615 Processing helix chain 'A' and resid 618 through 625 removed outlier: 3.528A pdb=" N ALA A 622 " --> pdb=" O ASP A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 676 removed outlier: 3.809A pdb=" N LEU A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 708 Processing helix chain 'A' and resid 709 through 720 removed outlier: 3.631A pdb=" N CYS A 717 " --> pdb=" O GLY A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 735 Processing helix chain 'A' and resid 748 through 761 Processing helix chain 'A' and resid 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'A' and resid 779 through 836 removed outlier: 3.867A pdb=" N LYS A 791 " --> pdb=" O GLU A 787 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 793 " --> pdb=" O ASP A 789 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ASP A 794 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N VAL A 795 " --> pdb=" O LYS A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 848 removed outlier: 3.866A pdb=" N LEU A 843 " --> pdb=" O GLN A 839 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 848 " --> pdb=" O PHE A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 953 Processing helix chain 'A' and resid 1398 through 1534 removed outlier: 3.917A pdb=" N LEU A1463 " --> pdb=" O PHE A1459 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU A1466 " --> pdb=" O MET A1462 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS A1534 " --> pdb=" O GLY A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1627 removed outlier: 3.961A pdb=" N SER A1539 " --> pdb=" O GLU A1535 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A1627 " --> pdb=" O ALA A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1643 Processing helix chain 'A' and resid 1644 through 1675 removed outlier: 3.802A pdb=" N GLU A1648 " --> pdb=" O LYS A1644 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET A1660 " --> pdb=" O LEU A1656 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS A1661 " --> pdb=" O GLN A1657 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP A1666 " --> pdb=" O ASP A1662 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU A1667 " --> pdb=" O TYR A1663 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU A1675 " --> pdb=" O ARG A1671 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 18 removed outlier: 3.551A pdb=" N PHE B 18 " --> pdb=" O ALA B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 38 Processing helix chain 'B' and resid 43 through 51 Processing helix chain 'B' and resid 55 through 62 Processing helix chain 'B' and resid 68 through 78 Processing helix chain 'B' and resid 84 through 96 Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 120 through 129 removed outlier: 3.670A pdb=" N VAL B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 150 removed outlier: 3.700A pdb=" N LEU B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 41 Processing helix chain 'C' and resid 49 through 61 removed outlier: 3.874A pdb=" N LEU C 53 " --> pdb=" O ASP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 73 Processing helix chain 'C' and resid 81 through 94 Processing helix chain 'C' and resid 98 through 110 removed outlier: 3.757A pdb=" N CYS C 108 " --> pdb=" O ASN C 104 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 110 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 134 through 144 removed outlier: 4.353A pdb=" N VAL C 138 " --> pdb=" O THR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 163 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 71 through 75 removed outlier: 3.676A pdb=" N ASP M 74 " --> pdb=" O SER M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 84 Processing helix chain 'M' and resid 88 through 92 removed outlier: 3.637A pdb=" N GLU M 91 " --> pdb=" O ASP M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 110 Processing helix chain 'M' and resid 134 through 141 Processing helix chain 'M' and resid 152 through 168 Processing helix chain 'M' and resid 184 through 198 Processing helix chain 'M' and resid 218 through 234 removed outlier: 3.622A pdb=" N LYS M 222 " --> pdb=" O GLY M 218 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) Proline residue: M 229 - end of helix Processing helix chain 'M' and resid 273 through 279 Processing helix chain 'M' and resid 287 through 296 removed outlier: 3.607A pdb=" N TYR M 291 " --> pdb=" O PHE M 287 " (cutoff:3.500A) Processing helix chain 'M' and resid 298 through 302 Processing helix chain 'M' and resid 330 through 342 Processing helix chain 'M' and resid 345 through 358 Processing helix chain 'M' and resid 359 through 365 Processing helix chain 'M' and resid 386 through 391 Processing helix chain 'M' and resid 394 through 404 Processing helix chain 'M' and resid 420 through 451 Processing helix chain 'M' and resid 476 through 508 removed outlier: 5.681A pdb=" N GLU M 501 " --> pdb=" O MET M 497 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN M 506 " --> pdb=" O GLN M 502 " (cutoff:3.500A) Processing helix chain 'M' and resid 521 through 530 removed outlier: 3.596A pdb=" N ILE M 525 " --> pdb=" O LEU M 521 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE M 528 " --> pdb=" O CYS M 524 " (cutoff:3.500A) Processing helix chain 'M' and resid 536 through 546 Processing helix chain 'M' and resid 551 through 564 removed outlier: 3.829A pdb=" N PHE M 555 " --> pdb=" O THR M 551 " (cutoff:3.500A) Processing helix chain 'M' and resid 596 through 603 Processing helix chain 'M' and resid 611 through 615 Processing helix chain 'M' and resid 619 through 625 removed outlier: 3.533A pdb=" N ASP M 623 " --> pdb=" O LYS M 619 " (cutoff:3.500A) Processing helix chain 'M' and resid 658 through 676 Processing helix chain 'M' and resid 697 through 709 Processing helix chain 'M' and resid 710 through 720 Processing helix chain 'M' and resid 727 through 735 removed outlier: 3.767A pdb=" N ARG M 731 " --> pdb=" O PHE M 727 " (cutoff:3.500A) Processing helix chain 'M' and resid 748 through 761 Processing helix chain 'M' and resid 763 through 765 No H-bonds generated for 'chain 'M' and resid 763 through 765' Processing helix chain 'M' and resid 781 through 822 removed outlier: 3.696A pdb=" N GLU M 787 " --> pdb=" O HIS M 783 " (cutoff:3.500A) Processing helix chain 'M' and resid 824 through 837 removed outlier: 3.508A pdb=" N ASN M 828 " --> pdb=" O VAL M 824 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN M 837 " --> pdb=" O LEU M 833 " (cutoff:3.500A) Processing helix chain 'M' and resid 838 through 852 Proline residue: M 849 - end of helix Processing helix chain 'M' and resid 852 through 890 removed outlier: 4.316A pdb=" N GLN M 856 " --> pdb=" O GLN M 852 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU M 880 " --> pdb=" O LYS M 876 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU M 883 " --> pdb=" O ALA M 879 " (cutoff:3.500A) Processing helix chain 'M' and resid 892 through 954 Processing helix chain 'M' and resid 1398 through 1531 removed outlier: 3.568A pdb=" N PHE M1459 " --> pdb=" O LYS M1455 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER M1470 " --> pdb=" O GLU M1466 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP M1475 " --> pdb=" O SER M1471 " (cutoff:3.500A) Processing helix chain 'M' and resid 1535 through 1611 removed outlier: 3.973A pdb=" N ARG M1541 " --> pdb=" O GLU M1537 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL M1547 " --> pdb=" O LEU M1543 " (cutoff:3.500A) Processing helix chain 'M' and resid 1619 through 1676 removed outlier: 3.833A pdb=" N VAL M1632 " --> pdb=" O LEU M1628 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS M1633 " --> pdb=" O GLU M1629 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU M1653 " --> pdb=" O ALA M1649 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG M1654 " --> pdb=" O ILE M1650 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 18 removed outlier: 3.551A pdb=" N PHE N 18 " --> pdb=" O ALA N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 38 Processing helix chain 'N' and resid 43 through 51 Processing helix chain 'N' and resid 55 through 62 Processing helix chain 'N' and resid 68 through 78 Processing helix chain 'N' and resid 84 through 96 Processing helix chain 'N' and resid 105 through 114 Processing helix chain 'N' and resid 120 through 129 removed outlier: 3.670A pdb=" N VAL N 124 " --> pdb=" O THR N 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 150 removed outlier: 3.700A pdb=" N LEU N 143 " --> pdb=" O ASN N 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 41 Processing helix chain 'O' and resid 49 through 61 removed outlier: 3.875A pdb=" N LEU O 53 " --> pdb=" O ASP O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 73 Processing helix chain 'O' and resid 81 through 94 Processing helix chain 'O' and resid 98 through 110 removed outlier: 3.757A pdb=" N CYS O 108 " --> pdb=" O ASN O 104 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE O 109 " --> pdb=" O ALA O 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP O 110 " --> pdb=" O PHE O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 119 through 127 Processing helix chain 'O' and resid 134 through 144 removed outlier: 4.353A pdb=" N VAL O 138 " --> pdb=" O THR O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 157 through 163 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 38 removed outlier: 5.022A pdb=" N ILE A 49 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU A 60 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLU A 51 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 117 removed outlier: 6.307A pdb=" N CYS A 121 " --> pdb=" O ARG A 683 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL A 682 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LEU A 174 " --> pdb=" O VAL A 682 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N CYS A 684 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN A 171 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LEU A 464 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE A 173 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY A 264 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 406 through 409 Processing sheet with id=AA4, first strand: chain 'A' and resid 569 through 570 removed outlier: 3.531A pdb=" N GLN A 570 " --> pdb=" O CYS A 582 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS A 582 " --> pdb=" O GLN A 570 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 725 through 726 Processing sheet with id=AA6, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AA7, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AA8, first strand: chain 'C' and resid 116 through 118 Processing sheet with id=AA9, first strand: chain 'M' and resid 35 through 36 Processing sheet with id=AB1, first strand: chain 'M' and resid 52 through 53 Processing sheet with id=AB2, first strand: chain 'M' and resid 121 through 123 removed outlier: 8.219A pdb=" N VAL M 682 " --> pdb=" O SER M 172 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU M 174 " --> pdb=" O VAL M 682 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N CYS M 684 " --> pdb=" O LEU M 174 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR M 176 " --> pdb=" O CYS M 684 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE M 173 " --> pdb=" O LEU M 464 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY M 264 " --> pdb=" O ASN M 255 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 236 through 237 Processing sheet with id=AB4, first strand: chain 'M' and resid 569 through 570 removed outlier: 3.648A pdb=" N GLN M 570 " --> pdb=" O CYS M 582 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS M 582 " --> pdb=" O GLN M 570 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 723 through 726 Processing sheet with id=AB6, first strand: chain 'N' and resid 26 through 27 Processing sheet with id=AB7, first strand: chain 'N' and resid 103 through 104 Processing sheet with id=AB8, first strand: chain 'O' and resid 116 through 118 1554 hydrogen bonds defined for protein. 4545 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: 8.97 Time building geometry restraints manager: 11.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7619 1.34 - 1.46: 4305 1.46 - 1.58: 10299 1.58 - 1.69: 0 1.69 - 1.81: 190 Bond restraints: 22413 Sorted by residual: bond pdb=" CB ASN N 100 " pdb=" CG ASN N 100 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.28e+00 bond pdb=" CB ASN B 100 " pdb=" CG ASN B 100 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.20e+00 bond pdb=" CA GLY M 462 " pdb=" C GLY M 462 " ideal model delta sigma weight residual 1.520 1.513 0.007 7.30e-03 1.88e+04 8.22e-01 bond pdb=" CA ASN B 100 " pdb=" CB ASN B 100 " ideal model delta sigma weight residual 1.525 1.538 -0.013 1.43e-02 4.89e+03 7.74e-01 bond pdb=" CD GLN B 126 " pdb=" NE2 GLN B 126 " ideal model delta sigma weight residual 1.328 1.346 -0.018 2.10e-02 2.27e+03 7.17e-01 ... (remaining 22408 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.88: 406 106.88 - 113.66: 12446 113.66 - 120.44: 8782 120.44 - 127.22: 8517 127.22 - 134.01: 140 Bond angle restraints: 30291 Sorted by residual: angle pdb=" N VAL M 824 " pdb=" CA VAL M 824 " pdb=" C VAL M 824 " ideal model delta sigma weight residual 113.42 107.86 5.56 1.17e+00 7.31e-01 2.26e+01 angle pdb=" CA VAL M 824 " pdb=" C VAL M 824 " pdb=" N ILE M 825 " ideal model delta sigma weight residual 118.90 116.22 2.68 9.40e-01 1.13e+00 8.13e+00 angle pdb=" CA VAL M 824 " pdb=" C VAL M 824 " pdb=" O VAL M 824 " ideal model delta sigma weight residual 118.90 121.00 -2.10 8.80e-01 1.29e+00 5.68e+00 angle pdb=" C LYS A 578 " pdb=" N THR A 579 " pdb=" CA THR A 579 " ideal model delta sigma weight residual 121.54 126.01 -4.47 1.91e+00 2.74e-01 5.48e+00 angle pdb=" C LYS M 282 " pdb=" N ASP M 283 " pdb=" CA ASP M 283 " ideal model delta sigma weight residual 121.54 125.89 -4.35 1.91e+00 2.74e-01 5.19e+00 ... (remaining 30286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 12289 17.96 - 35.91: 1136 35.91 - 53.86: 190 53.86 - 71.82: 53 71.82 - 89.77: 25 Dihedral angle restraints: 13693 sinusoidal: 5068 harmonic: 8625 Sorted by residual: dihedral pdb=" CA LEU M1543 " pdb=" C LEU M1543 " pdb=" N GLU M1544 " pdb=" CA GLU M1544 " ideal model delta harmonic sigma weight residual 180.00 151.63 28.37 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA PRO M 534 " pdb=" C PRO M 534 " pdb=" N PRO M 535 " pdb=" CA PRO M 535 " ideal model delta harmonic sigma weight residual 180.00 157.92 22.08 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA LEU A 34 " pdb=" C LEU A 34 " pdb=" N VAL A 35 " pdb=" CA VAL A 35 " ideal model delta harmonic sigma weight residual -180.00 -160.10 -19.90 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 13690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2083 0.026 - 0.052: 846 0.052 - 0.078: 324 0.078 - 0.104: 126 0.104 - 0.130: 40 Chirality restraints: 3419 Sorted by residual: chirality pdb=" CA ILE A 471 " pdb=" N ILE A 471 " pdb=" C ILE A 471 " pdb=" CB ILE A 471 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ILE M 49 " pdb=" N ILE M 49 " pdb=" C ILE M 49 " pdb=" CB ILE M 49 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE M 774 " pdb=" N ILE M 774 " pdb=" C ILE M 774 " pdb=" CB ILE M 774 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 3416 not shown) Planarity restraints: 4025 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN N 100 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C ASN N 100 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN N 100 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY N 101 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 100 " -0.011 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" C ASN B 100 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN B 100 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY B 101 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO M 534 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO M 535 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO M 535 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO M 535 " 0.029 5.00e-02 4.00e+02 ... (remaining 4022 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 521 2.66 - 3.22: 24145 3.22 - 3.78: 39430 3.78 - 4.34: 49329 4.34 - 4.90: 74626 Nonbonded interactions: 188051 Sorted by model distance: nonbonded pdb=" NE2 GLN M 802 " pdb=" OH TYR N 88 " model vdw 2.096 2.520 nonbonded pdb=" OG SER A 39 " pdb=" OE1 GLU A 45 " model vdw 2.128 2.440 nonbonded pdb=" O ALA M 798 " pdb=" NE2 GLN M 802 " model vdw 2.175 2.520 nonbonded pdb=" OG1 THR A 485 " pdb=" OH TYR A 663 " model vdw 2.176 2.440 nonbonded pdb=" O ASP M 170 " pdb=" OG1 THR M 677 " model vdw 2.178 2.440 ... (remaining 188046 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 'M' and resid 24 through 1675) } ncs_group { reference = chain 'B' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'O' } 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: 1.490 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: 7.580 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 61.690 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.130 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 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 0.035 22413 Z= 0.166 Angle : 0.501 5.869 30291 Z= 0.291 Chirality : 0.036 0.130 3419 Planarity : 0.003 0.051 4025 Dihedral : 14.921 89.775 8067 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 0.77 % 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 (0.14), residues: 2925 helix: -0.16 (0.11), residues: 1828 sheet: -3.15 (0.34), residues: 183 loop : -2.73 (0.19), residues: 914 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 258 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 3 residues processed: 268 average time/residue: 0.4027 time to fit residues: 163.1222 Evaluate side-chains 189 residues out of total 2591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 186 time to evaluate : 3.036 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1995 time to fit residues: 5.0441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 246 optimal weight: 5.9990 chunk 221 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 118 optimal weight: 0.1980 chunk 228 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 139 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 265 optimal weight: 8.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 166 GLN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN A 364 ASN A 375 GLN A 381 ASN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 ASN ** A 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN A 689 HIS ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 GLN A 828 ASN A 839 GLN A 861 GLN A 948 GLN ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** M 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 ASN ** M 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 228 ASN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 244 ASN M 288 HIS M 318 ASN ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 483 ASN ** M 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 689 HIS ** M 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 856 GLN M 875 GLN M 886 GLN N 16 GLN N 40 GLN ** N 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 110 HIS N 131 HIS ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 94 ASN O 104 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 22413 Z= 0.188 Angle : 0.545 11.388 30291 Z= 0.288 Chirality : 0.038 0.258 3419 Planarity : 0.004 0.056 4025 Dihedral : 4.250 30.081 3119 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.41 (0.16), residues: 2925 helix: 0.96 (0.12), residues: 1847 sheet: -2.78 (0.37), residues: 177 loop : -2.34 (0.20), residues: 901 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 230 time to evaluate : 3.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 235 average time/residue: 0.3994 time to fit residues: 143.5505 Evaluate side-chains 174 residues out of total 2591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.771 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 147 optimal weight: 0.0470 chunk 82 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 180 optimal weight: 0.0170 chunk 73 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 286 optimal weight: 0.3980 chunk 236 optimal weight: 7.9990 chunk 263 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 overall best weight: 1.4920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 ASN A 615 GLN A 719 GLN A 723 ASN ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 ASN ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 689 HIS ** M 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 828 ASN ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 22413 Z= 0.182 Angle : 0.537 12.941 30291 Z= 0.283 Chirality : 0.038 0.161 3419 Planarity : 0.003 0.054 4025 Dihedral : 4.242 29.866 3119 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 0.05 % 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: 0.07 (0.16), residues: 2925 helix: 1.39 (0.12), residues: 1852 sheet: -2.75 (0.36), residues: 178 loop : -2.27 (0.20), residues: 895 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.3820 time to fit residues: 131.2073 Evaluate side-chains 171 residues out of total 2591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 2.919 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 262 optimal weight: 20.0000 chunk 199 optimal weight: 0.2980 chunk 137 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 266 optimal weight: 8.9990 chunk 282 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 ASN ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 689 HIS ** M 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 ASN ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 22413 Z= 0.204 Angle : 0.543 12.274 30291 Z= 0.290 Chirality : 0.038 0.148 3419 Planarity : 0.004 0.071 4025 Dihedral : 4.316 29.660 3119 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.16), residues: 2925 helix: 1.59 (0.12), residues: 1843 sheet: -2.67 (0.36), residues: 178 loop : -2.23 (0.20), residues: 904 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 3.034 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: 1 outliers final: 0 residues processed: 217 average time/residue: 0.3769 time to fit residues: 127.4257 Evaluate side-chains 165 residues out of total 2591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.884 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 235 optimal weight: 5.9990 chunk 160 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 116 optimal weight: 40.0000 chunk 240 optimal weight: 8.9990 chunk 195 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 144 optimal weight: 0.0070 chunk 253 optimal weight: 20.0000 chunk 71 optimal weight: 0.0000 overall best weight: 1.7206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 ASN ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 ASN M 102 HIS M 192 GLN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 689 HIS ** M 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 GLN O 29 GLN ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 22413 Z= 0.192 Angle : 0.532 10.823 30291 Z= 0.283 Chirality : 0.038 0.155 3419 Planarity : 0.004 0.055 4025 Dihedral : 4.327 29.636 3119 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer Outliers : 0.10 % 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: 0.40 (0.16), residues: 2925 helix: 1.68 (0.12), residues: 1837 sheet: -2.58 (0.37), residues: 177 loop : -2.18 (0.20), residues: 911 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 215 time to evaluate : 2.839 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 outliers start: 2 outliers final: 1 residues processed: 217 average time/residue: 0.3802 time to fit residues: 128.5950 Evaluate side-chains 173 residues out of total 2591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 2.701 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2372 time to fit residues: 4.1101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 94 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 282 optimal weight: 0.8980 chunk 234 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 148 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 ASN ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN M 64 ASN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 689 HIS ** M 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 GLN ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 22413 Z= 0.166 Angle : 0.544 13.500 30291 Z= 0.287 Chirality : 0.038 0.142 3419 Planarity : 0.003 0.056 4025 Dihedral : 4.307 29.706 3119 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer Outliers : 0.05 % 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: 0.47 (0.16), residues: 2925 helix: 1.68 (0.12), residues: 1860 sheet: -2.52 (0.38), residues: 174 loop : -2.11 (0.20), residues: 891 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 2.852 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: 221 average time/residue: 0.3722 time to fit residues: 129.0682 Evaluate side-chains 177 residues out of total 2591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 2.635 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 272 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 206 optimal weight: 0.5980 chunk 159 optimal weight: 2.9990 chunk 237 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 281 optimal weight: 0.0870 chunk 176 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 ASN ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 GLN ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 22413 Z= 0.170 Angle : 0.550 11.024 30291 Z= 0.287 Chirality : 0.038 0.171 3419 Planarity : 0.003 0.055 4025 Dihedral : 4.314 29.643 3119 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 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: 0.53 (0.16), residues: 2925 helix: 1.73 (0.12), residues: 1864 sheet: -2.50 (0.38), residues: 178 loop : -2.10 (0.20), residues: 883 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 3.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.4355 time to fit residues: 150.7204 Evaluate side-chains 177 residues out of total 2591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 2.677 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 174 optimal weight: 8.9990 chunk 112 optimal weight: 40.0000 chunk 168 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 221 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 ASN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 GLN ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 HIS ** M 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 494 ASN ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 689 HIS ** M 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 719 GLN ** M 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 22413 Z= 0.355 Angle : 0.676 8.475 30291 Z= 0.366 Chirality : 0.041 0.169 3419 Planarity : 0.005 0.059 4025 Dihedral : 4.690 28.931 3119 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 32.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer Outliers : 0.05 % 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: 0.25 (0.16), residues: 2925 helix: 1.51 (0.12), residues: 1850 sheet: -2.70 (0.36), residues: 177 loop : -2.15 (0.20), residues: 898 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 202 time to evaluate : 2.493 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 outliers start: 1 outliers final: 0 residues processed: 203 average time/residue: 0.3733 time to fit residues: 120.4658 Evaluate side-chains 159 residues out of total 2591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.606 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 256 optimal weight: 20.0000 chunk 269 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 262 optimal weight: 20.0000 chunk 157 optimal weight: 0.9980 chunk 114 optimal weight: 40.0000 chunk 205 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 261 optimal weight: 20.0000 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 GLN ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 211 GLN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 689 HIS ** M 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 22413 Z= 0.351 Angle : 0.668 8.230 30291 Z= 0.363 Chirality : 0.041 0.162 3419 Planarity : 0.004 0.058 4025 Dihedral : 4.842 29.257 3119 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 33.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer Outliers : 0.10 % 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: 0.20 (0.16), residues: 2925 helix: 1.51 (0.12), residues: 1821 sheet: -2.92 (0.34), residues: 183 loop : -2.06 (0.20), residues: 921 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 3.089 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 outliers start: 2 outliers final: 0 residues processed: 204 average time/residue: 0.3890 time to fit residues: 125.1128 Evaluate side-chains 160 residues out of total 2591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 2.605 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 172 optimal weight: 0.8980 chunk 277 optimal weight: 0.7980 chunk 169 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 192 optimal weight: 0.7980 chunk 290 optimal weight: 0.5980 chunk 267 optimal weight: 0.6980 chunk 231 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 HIS ** A 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 GLN ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN C 154 ASN M 211 GLN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 689 HIS ** M 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 GLN ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 22413 Z= 0.178 Angle : 0.610 11.207 30291 Z= 0.318 Chirality : 0.041 0.220 3419 Planarity : 0.004 0.057 4025 Dihedral : 4.644 29.592 3119 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 23.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 0.14 % 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: 0.44 (0.16), residues: 2925 helix: 1.67 (0.12), residues: 1843 sheet: -2.73 (0.36), residues: 185 loop : -1.99 (0.21), residues: 897 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 218 time to evaluate : 2.843 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 outliers start: 3 outliers final: 0 residues processed: 220 average time/residue: 0.3873 time to fit residues: 132.9475 Evaluate side-chains 171 residues out of total 2591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 2.941 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 184 optimal weight: 1.9990 chunk 246 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 213 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 238 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 42 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 GLN ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN B 135 ASN C 154 ASN M 211 GLN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 689 HIS ** M 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.048931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.036036 restraints weight = 234207.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.036958 restraints weight = 158233.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.037595 restraints weight = 119598.185| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 22413 Z= 0.193 Angle : 0.581 10.390 30291 Z= 0.307 Chirality : 0.040 0.198 3419 Planarity : 0.004 0.057 4025 Dihedral : 4.534 29.479 3119 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 24.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer Outliers : 0.14 % 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: 0.47 (0.16), residues: 2925 helix: 1.68 (0.12), residues: 1857 sheet: -2.74 (0.35), residues: 185 loop : -2.03 (0.21), residues: 883 =============================================================================== Job complete usr+sys time: 3847.74 seconds wall clock time: 72 minutes 6.66 seconds (4326.66 seconds total)