Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 19:36:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0j_20550/04_2023/6q0j_20550_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0j_20550/04_2023/6q0j_20550.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0j_20550/04_2023/6q0j_20550_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0j_20550/04_2023/6q0j_20550_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0j_20550/04_2023/6q0j_20550_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0j_20550/04_2023/6q0j_20550.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0j_20550/04_2023/6q0j_20550.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0j_20550/04_2023/6q0j_20550_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0j_20550/04_2023/6q0j_20550_updated.pdb" } resolution = 4.9 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= 0.003 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: 8 Type Number sf(0) Gaussians I 2 10.91 5 P 8 5.49 5 Mg 2 5.21 5 S 2 5.16 5 C 4871 2.51 5 N 1653 2.21 5 O 1673 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8213 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1394 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 281, 1392 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 247} Link IDs: {'PTRANS': 13, 'TRANS': 267} Chain breaks: 1 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 916 Unresolved non-hydrogen angles: 1168 Unresolved non-hydrogen dihedrals: 779 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 10, 'TYR:plan': 9, 'ASN:plan1': 10, 'TRP:plan': 5, 'ASP:plan': 13, 'PHE:plan': 10, 'GLU:plan': 13, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 478 Conformer: "B" Number of residues, atoms: 281, 1392 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 247} Link IDs: {'PTRANS': 13, 'TRANS': 267} Chain breaks: 1 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 916 Unresolved non-hydrogen angles: 1168 Unresolved non-hydrogen dihedrals: 779 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 10, 'TYR:plan': 9, 'ASN:plan1': 10, 'TRP:plan': 5, 'ASP:plan': 13, 'PHE:plan': 10, 'GLU:plan': 13, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 478 bond proxies already assigned to first conformer: 1387 Chain: "B" Number of atoms: 1399 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 282, 1397 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 248} Link IDs: {'PTRANS': 13, 'TRANS': 268} Chain breaks: 1 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 919 Unresolved non-hydrogen angles: 1172 Unresolved non-hydrogen dihedrals: 781 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 10, 'TYR:plan': 9, 'ASN:plan1': 11, 'TRP:plan': 5, 'ASP:plan': 13, 'PHE:plan': 10, 'GLU:plan': 13, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 481 Conformer: "B" Number of residues, atoms: 282, 1397 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 248} Link IDs: {'PTRANS': 13, 'TRANS': 268} Chain breaks: 1 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 919 Unresolved non-hydrogen angles: 1172 Unresolved non-hydrogen dihedrals: 781 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 10, 'TYR:plan': 9, 'ASN:plan1': 11, 'TRP:plan': 5, 'ASP:plan': 13, 'PHE:plan': 10, 'GLU:plan': 13, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 481 bond proxies already assigned to first conformer: 1392 Chain: "C" Number of atoms: 1514 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 1507 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 265} Link IDs: {'PTRANS': 17, 'TRANS': 288} Chain breaks: 1 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 949 Unresolved non-hydrogen angles: 1199 Unresolved non-hydrogen dihedrals: 796 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 8, 'TYR:plan': 8, 'ASN:plan1': 9, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 13, 'GLU:plan': 23, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 484 Conformer: "B" Number of residues, atoms: 306, 1507 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 265} Link IDs: {'PTRANS': 17, 'TRANS': 288} Chain breaks: 1 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 949 Unresolved non-hydrogen angles: 1199 Unresolved non-hydrogen dihedrals: 796 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 8, 'TYR:plan': 8, 'ASN:plan1': 9, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 13, 'GLU:plan': 23, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 484 bond proxies already assigned to first conformer: 1496 Chain: "D" Number of atoms: 1516 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 1507 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 265} Link IDs: {'PTRANS': 17, 'TRANS': 288} Chain breaks: 1 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 949 Unresolved non-hydrogen angles: 1199 Unresolved non-hydrogen dihedrals: 796 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 8, 'TYR:plan': 8, 'ASN:plan1': 9, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 13, 'GLU:plan': 23, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 484 Conformer: "B" Number of residues, atoms: 306, 1507 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 265} Link IDs: {'PTRANS': 17, 'TRANS': 288} Chain breaks: 1 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 949 Unresolved non-hydrogen angles: 1199 Unresolved non-hydrogen dihedrals: 796 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 8, 'TYR:plan': 8, 'ASN:plan1': 9, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 13, 'GLU:plan': 23, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 484 bond proxies already assigned to first conformer: 1493 Chain: "X" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1138 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 5, 'TRANS': 223} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 736 Unresolved non-hydrogen angles: 931 Unresolved non-hydrogen dihedrals: 610 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 24, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 419 Chain: "Y" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1138 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 5, 'TRANS': 223} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 736 Unresolved non-hydrogen angles: 931 Unresolved non-hydrogen dihedrals: 610 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 24, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 419 Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' MG': 1, 'AGS': 1, 'LCJ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' MG': 1, 'AGS': 1, 'LCJ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AGLU C 348 " occ=0.48 ... (8 atoms not shown) pdb=" CB BGLU C 348 " occ=0.52 residue: pdb=" N AGLU D 348 " occ=0.48 ... (8 atoms not shown) pdb=" CB BGLU D 348 " occ=0.52 Time building chain proxies: 9.14, per 1000 atoms: 1.11 Number of scatterers: 8213 At special positions: 0 Unit cell: (87.69, 160.95, 102.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) I 2 52.95 S 2 16.00 P 8 15.00 Mg 2 11.99 F 2 9.00 O 1673 8.00 N 1653 7.00 C 4871 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: 4.06 Conformation dependent library (CDL) restraints added in 3.5 seconds 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3088 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 8 sheets defined 53.0% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 492 through 507 removed outlier: 3.927A pdb=" N LYS A 507 " --> pdb=" O GLY A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 550 through 570 Processing helix chain 'A' and resid 579 through 581 No H-bonds generated for 'chain 'A' and resid 579 through 581' Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 622 through 626 Processing helix chain 'A' and resid 635 through 651 Processing helix chain 'A' and resid 662 through 671 Processing helix chain 'A' and resid 678 through 680 No H-bonds generated for 'chain 'A' and resid 678 through 680' Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 701 through 703 No H-bonds generated for 'chain 'A' and resid 701 through 703' Processing helix chain 'A' and resid 707 through 719 removed outlier: 3.792A pdb=" N LEU A 716 " --> pdb=" O ALA A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 507 removed outlier: 3.930A pdb=" N LYS B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 550 through 570 Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 585 through 587 No H-bonds generated for 'chain 'B' and resid 585 through 587' Processing helix chain 'B' and resid 617 through 619 No H-bonds generated for 'chain 'B' and resid 617 through 619' Processing helix chain 'B' and resid 622 through 626 Processing helix chain 'B' and resid 635 through 651 Processing helix chain 'B' and resid 662 through 671 Processing helix chain 'B' and resid 678 through 680 No H-bonds generated for 'chain 'B' and resid 678 through 680' Processing helix chain 'B' and resid 687 through 696 Processing helix chain 'B' and resid 701 through 703 No H-bonds generated for 'chain 'B' and resid 701 through 703' Processing helix chain 'B' and resid 707 through 719 removed outlier: 4.086A pdb=" N ALA B 718 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG B 719 " --> pdb=" O GLU B 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 59 Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 105 through 120 removed outlier: 4.412A pdb=" N VAL C 117 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N HIS C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU C 120 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 158 Processing helix chain 'C' and resid 163 through 184 removed outlier: 3.655A pdb=" N LYS C 168 " --> pdb=" O GLN C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 213 through 219 Processing helix chain 'C' and resid 232 through 235 No H-bonds generated for 'chain 'C' and resid 232 through 235' Processing helix chain 'C' and resid 242 through 258 Processing helix chain 'C' and resid 268 through 273 removed outlier: 3.617A pdb=" N GLU C 272 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 273 " --> pdb=" O LYS C 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 268 through 273' Processing helix chain 'C' and resid 310 through 319 Processing helix chain 'C' and resid 332 through 341 Processing helix chain 'C' and resid 346 through 348 No H-bonds generated for 'chain 'C' and resid 346 through 348' Processing helix chain 'C' and resid 352 through 356 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 371 through 377 Processing helix chain 'D' and resid 44 through 59 Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'D' and resid 105 through 120 removed outlier: 4.411A pdb=" N VAL D 117 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N HIS D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU D 120 " --> pdb=" O GLN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 158 Processing helix chain 'D' and resid 163 through 184 removed outlier: 3.655A pdb=" N LYS D 168 " --> pdb=" O GLN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 213 through 219 Processing helix chain 'D' and resid 232 through 235 No H-bonds generated for 'chain 'D' and resid 232 through 235' Processing helix chain 'D' and resid 242 through 258 Processing helix chain 'D' and resid 268 through 273 removed outlier: 3.617A pdb=" N GLU D 272 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 268 through 273' Processing helix chain 'D' and resid 310 through 319 Processing helix chain 'D' and resid 332 through 341 Processing helix chain 'D' and resid 346 through 348 No H-bonds generated for 'chain 'D' and resid 346 through 348' Processing helix chain 'D' and resid 352 through 356 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 371 through 377 Processing helix chain 'X' and resid 3 through 15 Processing helix chain 'X' and resid 19 through 32 removed outlier: 4.193A pdb=" N ALA X 25 " --> pdb=" O ASP X 21 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET X 26 " --> pdb=" O MET X 22 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS X 27 " --> pdb=" O ALA X 23 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR X 32 " --> pdb=" O GLU X 28 " (cutoff:3.500A) Processing helix chain 'X' and resid 39 through 68 removed outlier: 3.886A pdb=" N LEU X 43 " --> pdb=" O GLU X 39 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU X 44 " --> pdb=" O GLU X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 80 through 101 removed outlier: 3.528A pdb=" N GLU X 87 " --> pdb=" O VAL X 84 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE X 93 " --> pdb=" O LEU X 90 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY X 99 " --> pdb=" O ASP X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 112 through 132 Processing helix chain 'X' and resid 138 through 159 removed outlier: 3.618A pdb=" N ILE X 155 " --> pdb=" O ASP X 151 " (cutoff:3.500A) Processing helix chain 'X' and resid 165 through 180 Processing helix chain 'X' and resid 185 through 201 removed outlier: 3.625A pdb=" N ALA X 201 " --> pdb=" O ASP X 197 " (cutoff:3.500A) Processing helix chain 'X' and resid 211 through 229 Processing helix chain 'Y' and resid 3 through 15 Processing helix chain 'Y' and resid 21 through 32 removed outlier: 3.794A pdb=" N THR Y 32 " --> pdb=" O GLU Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 64 removed outlier: 3.907A pdb=" N LEU Y 43 " --> pdb=" O GLU Y 39 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU Y 44 " --> pdb=" O GLU Y 40 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL Y 52 " --> pdb=" O TYR Y 48 " (cutoff:3.500A) Processing helix chain 'Y' and resid 74 through 101 removed outlier: 3.572A pdb=" N LYS Y 85 " --> pdb=" O GLU Y 81 " (cutoff:3.500A) Processing helix chain 'Y' and resid 112 through 130 Processing helix chain 'Y' and resid 136 through 159 removed outlier: 4.603A pdb=" N SER Y 140 " --> pdb=" O GLU Y 136 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL Y 141 " --> pdb=" O THR Y 137 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLU Y 154 " --> pdb=" O GLN Y 150 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE Y 155 " --> pdb=" O ASP Y 151 " (cutoff:3.500A) Processing helix chain 'Y' and resid 165 through 180 Processing helix chain 'Y' and resid 185 through 201 removed outlier: 3.830A pdb=" N ALA Y 201 " --> pdb=" O ASP Y 197 " (cutoff:3.500A) Processing helix chain 'Y' and resid 208 through 210 No H-bonds generated for 'chain 'Y' and resid 208 through 210' Processing helix chain 'Y' and resid 212 through 228 Processing sheet with id= A, first strand: chain 'A' and resid 470 through 475 removed outlier: 5.953A pdb=" N GLN A 530 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N PHE A 516 " --> pdb=" O GLN A 530 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 582 through 585 Processing sheet with id= C, first strand: chain 'B' and resid 470 through 475 removed outlier: 5.953A pdb=" N GLN B 530 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE B 516 " --> pdb=" O GLN B 530 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 582 through 585 Processing sheet with id= E, first strand: chain 'C' and resid 129 through 135 removed outlier: 6.667A pdb=" N CYS C 142 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA C 132 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER C 140 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N TYR C 134 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU C 138 " --> pdb=" O TYR C 134 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER C 86 " --> pdb=" O LYS C 70 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LYS C 70 " --> pdb=" O SER C 86 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 196 through 198 Processing sheet with id= G, first strand: chain 'D' and resid 129 through 135 removed outlier: 6.667A pdb=" N CYS D 142 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA D 132 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER D 140 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N TYR D 134 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU D 138 " --> pdb=" O TYR D 134 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER D 86 " --> pdb=" O LYS D 70 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS D 70 " --> pdb=" O SER D 86 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 196 through 198 605 hydrogen bonds defined for protein. 1747 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: 2.32 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 3295 1.37 - 1.56: 4853 1.56 - 1.74: 64 1.74 - 1.93: 0 1.93 - 2.11: 4 Bond restraints: 8216 Sorted by residual: bond pdb=" C3' AGS C 403 " pdb=" C4' AGS C 403 " ideal model delta sigma weight residual 1.526 1.278 0.248 1.10e-02 8.26e+03 5.10e+02 bond pdb=" C1' AGS C 403 " pdb=" C2' AGS C 403 " ideal model delta sigma weight residual 1.530 1.256 0.274 1.30e-02 5.92e+03 4.43e+02 bond pdb=" C1' AGS C 403 " pdb=" O4' AGS C 403 " ideal model delta sigma weight residual 1.415 1.568 -0.153 1.10e-02 8.26e+03 1.94e+02 bond pdb=" C6 AGS C 403 " pdb=" N6 AGS C 403 " ideal model delta sigma weight residual 1.335 1.450 -0.115 1.00e-02 1.00e+04 1.31e+02 bond pdb=" C2' AGS C 403 " pdb=" C3' AGS C 403 " ideal model delta sigma weight residual 1.530 1.663 -0.133 1.30e-02 5.92e+03 1.05e+02 ... (remaining 8211 not shown) Histogram of bond angle deviations from ideal: 97.72 - 105.40: 82 105.40 - 113.08: 4382 113.08 - 120.76: 3803 120.76 - 128.44: 3173 128.44 - 136.12: 13 Bond angle restraints: 11453 Sorted by residual: angle pdb=" C5 AGS D 403 " pdb=" C4 AGS D 403 " pdb=" N3 AGS D 403 " ideal model delta sigma weight residual 126.80 118.70 8.10 7.41e-01 1.82e+00 1.19e+02 angle pdb=" N1 AGS C 403 " pdb=" C2 AGS C 403 " pdb=" N3 AGS C 403 " ideal model delta sigma weight residual 128.80 120.04 8.76 8.41e-01 1.41e+00 1.08e+02 angle pdb=" C5 AGS C 403 " pdb=" N7 AGS C 403 " pdb=" C8 AGS C 403 " ideal model delta sigma weight residual 103.67 108.08 -4.41 4.26e-01 5.51e+00 1.07e+02 angle pdb=" N7 AGS C 403 " pdb=" C8 AGS C 403 " pdb=" N9 AGS C 403 " ideal model delta sigma weight residual 114.03 107.60 6.43 6.99e-01 2.05e+00 8.45e+01 angle pdb=" C4 AGS D 403 " pdb=" C5 AGS D 403 " pdb=" N7 AGS D 403 " ideal model delta sigma weight residual 110.73 106.63 4.10 4.52e-01 4.89e+00 8.24e+01 ... (remaining 11448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.66: 4739 25.66 - 51.33: 11 51.33 - 76.99: 3 76.99 - 102.65: 2 102.65 - 128.32: 2 Dihedral angle restraints: 4757 sinusoidal: 32 harmonic: 4725 Sorted by residual: dihedral pdb=" N PRO C 264 " pdb=" C PRO C 264 " pdb=" CA PRO C 264 " pdb=" CB PRO C 264 " ideal model delta harmonic sigma weight residual 115.10 128.62 -13.52 0 2.50e+00 1.60e-01 2.92e+01 dihedral pdb=" C PHE A 707 " pdb=" N PHE A 707 " pdb=" CA PHE A 707 " pdb=" CB PHE A 707 " ideal model delta harmonic sigma weight residual -122.60 -135.38 12.78 0 2.50e+00 1.60e-01 2.61e+01 dihedral pdb=" N PHE A 707 " pdb=" C PHE A 707 " pdb=" CA PHE A 707 " pdb=" CB PHE A 707 " ideal model delta harmonic sigma weight residual 122.80 134.94 -12.14 0 2.50e+00 1.60e-01 2.36e+01 ... (remaining 4754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1276 0.114 - 0.228: 260 0.228 - 0.342: 16 0.342 - 0.456: 2 0.456 - 0.570: 2 Chirality restraints: 1556 Sorted by residual: chirality pdb=" CA PHE A 707 " pdb=" N PHE A 707 " pdb=" C PHE A 707 " pdb=" CB PHE A 707 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.12e+00 chirality pdb=" CA PRO C 264 " pdb=" N PRO C 264 " pdb=" C PRO C 264 " pdb=" CB PRO C 264 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CA LYS A 522 " pdb=" N LYS A 522 " pdb=" C LYS A 522 " pdb=" CB LYS A 522 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 1553 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 703 " -0.027 2.00e-02 2.50e+03 5.65e-02 3.20e+01 pdb=" C GLU B 703 " 0.098 2.00e-02 2.50e+03 pdb=" O GLU B 703 " -0.037 2.00e-02 2.50e+03 pdb=" N ARG B 704 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN X 76 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.31e+01 pdb=" C GLN X 76 " -0.063 2.00e-02 2.50e+03 pdb=" O GLN X 76 " 0.023 2.00e-02 2.50e+03 pdb=" N GLN X 77 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 75 " -0.018 2.00e-02 2.50e+03 3.61e-02 1.31e+01 pdb=" C GLY D 75 " 0.063 2.00e-02 2.50e+03 pdb=" O GLY D 75 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA D 76 " -0.021 2.00e-02 2.50e+03 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.78: 1631 2.78 - 3.32: 8850 3.32 - 3.87: 12973 3.87 - 4.41: 12682 4.41 - 4.96: 20657 Nonbonded interactions: 56793 Sorted by model distance: nonbonded pdb="MG MG D 401 " pdb=" O1A AGS D 403 " model vdw 2.229 2.170 nonbonded pdb="MG MG D 401 " pdb=" O1B AGS D 403 " model vdw 2.263 2.170 nonbonded pdb=" O ALA X 24 " pdb=" N LYS X 27 " model vdw 2.416 2.520 nonbonded pdb="MG MG C 401 " pdb=" O3B AGS C 403 " model vdw 2.421 2.170 nonbonded pdb=" O2B AGS D 403 " pdb=" O2G AGS D 403 " model vdw 2.421 2.440 ... (remaining 56788 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' and (resid 449 through 557 or resid 559 through 733)) selection = (chain 'B' and (resid 449 through 557 or resid 559 through 733)) } ncs_group { reference = (chain 'C' and (resid 43 through 99 or resid 101 through 206 or resid 208 throug \ h 347 or resid 349 through 379 or resid 401 through 403)) selection = (chain 'D' and (resid 43 through 99 or resid 101 through 206 or resid 208 throug \ h 347 or resid 349 through 379 or resid 401 through 403)) } ncs_group { reference = chain 'X' selection = chain 'Y' } 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=0.43 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: 1.250 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: 0.010 Extract box with map and model: 4.160 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 33.280 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6269 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 : 0.012 0.274 8216 Z= 0.857 Angle : 1.527 10.788 11453 Z= 1.138 Chirality : 0.090 0.570 1556 Planarity : 0.005 0.057 1640 Dihedral : 8.168 128.318 1669 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 1.31 % Allowed : 5.41 % Favored : 93.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.18), residues: 1618 helix: -1.71 (0.15), residues: 865 sheet: -1.16 (0.49), residues: 93 loop : -2.05 (0.22), residues: 660 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.931 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0763 time to fit residues: 8.9337 Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.016 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 30.0000 chunk 64 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 145 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.093 8216 Z= 0.407 Angle : 0.834 15.872 11453 Z= 0.529 Chirality : 0.045 0.163 1556 Planarity : 0.005 0.024 1640 Dihedral : 8.523 114.122 1669 Min Nonbonded Distance : 1.663 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.48 % Favored : 93.96 % 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: -1.62 (0.20), residues: 1618 helix: -0.55 (0.16), residues: 883 sheet: -1.06 (0.52), residues: 102 loop : -1.70 (0.24), residues: 633 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.967 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0772 time to fit residues: 9.0949 Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.984 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 145 optimal weight: 30.0000 chunk 157 optimal weight: 8.9990 chunk 129 optimal weight: 20.0000 chunk 144 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.6258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 8216 Z= 0.272 Angle : 0.542 5.360 11453 Z= 0.351 Chirality : 0.042 0.139 1556 Planarity : 0.004 0.019 1640 Dihedral : 8.047 113.280 1669 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.23 % Favored : 94.28 % 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: -0.45 (0.21), residues: 1618 helix: 0.61 (0.17), residues: 881 sheet: -1.04 (0.49), residues: 114 loop : -1.42 (0.26), residues: 623 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.991 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0740 time to fit residues: 8.8429 Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.009 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 146 optimal weight: 6.9990 chunk 154 optimal weight: 50.0000 chunk 76 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.7387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 8216 Z= 0.259 Angle : 0.517 8.647 11453 Z= 0.336 Chirality : 0.041 0.142 1556 Planarity : 0.003 0.017 1640 Dihedral : 8.149 109.321 1669 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.85 % Favored : 93.59 % 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: -0.01 (0.21), residues: 1618 helix: 1.06 (0.17), residues: 877 sheet: -0.84 (0.51), residues: 111 loop : -1.36 (0.26), residues: 630 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0789 time to fit residues: 9.3013 Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.870 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 10.0000 chunk 87 optimal weight: 40.0000 chunk 2 optimal weight: 7.9990 chunk 115 optimal weight: 30.0000 chunk 63 optimal weight: 10.0000 chunk 131 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 0.2980 chunk 138 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 overall best weight: 3.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.7712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 8216 Z= 0.163 Angle : 0.401 3.342 11453 Z= 0.263 Chirality : 0.040 0.131 1556 Planarity : 0.002 0.011 1640 Dihedral : 7.972 112.787 1669 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.73 % Favored : 94.84 % 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: 0.71 (0.22), residues: 1618 helix: 1.76 (0.18), residues: 885 sheet: -0.73 (0.51), residues: 110 loop : -1.22 (0.27), residues: 623 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.968 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0765 time to fit residues: 9.1666 Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 90 optimal weight: 50.0000 chunk 38 optimal weight: 7.9990 chunk 154 optimal weight: 0.5980 chunk 128 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 0.1980 chunk 81 optimal weight: 30.0000 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.8691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 8216 Z= 0.209 Angle : 0.469 6.627 11453 Z= 0.303 Chirality : 0.041 0.142 1556 Planarity : 0.003 0.015 1640 Dihedral : 8.296 114.823 1669 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.85 % Favored : 92.66 % 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: 0.57 (0.22), residues: 1618 helix: 1.63 (0.18), residues: 874 sheet: -0.30 (0.50), residues: 99 loop : -1.29 (0.26), residues: 645 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0777 time to fit residues: 9.2409 Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 88 optimal weight: 30.0000 chunk 113 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 130 optimal weight: 40.0000 chunk 86 optimal weight: 10.0000 chunk 154 optimal weight: 0.4980 chunk 96 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 overall best weight: 6.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.9652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 8216 Z= 0.320 Angle : 0.585 8.094 11453 Z= 0.385 Chirality : 0.042 0.139 1556 Planarity : 0.004 0.018 1640 Dihedral : 8.972 121.710 1669 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.59 % Favored : 92.03 % 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: -0.40 (0.21), residues: 1618 helix: 0.68 (0.17), residues: 862 sheet: -0.74 (0.47), residues: 99 loop : -1.44 (0.26), residues: 657 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.051 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0792 time to fit residues: 9.4680 Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 30.0000 chunk 61 optimal weight: 50.0000 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 1.0123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 8216 Z= 0.297 Angle : 0.535 6.811 11453 Z= 0.353 Chirality : 0.041 0.137 1556 Planarity : 0.003 0.016 1640 Dihedral : 8.918 126.275 1669 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.09 % Favored : 90.35 % 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: -0.50 (0.21), residues: 1618 helix: 0.66 (0.17), residues: 857 sheet: -0.90 (0.47), residues: 101 loop : -1.54 (0.26), residues: 660 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.067 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0814 time to fit residues: 9.7438 Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.038 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 143 optimal weight: 20.0000 chunk 86 optimal weight: 30.0000 chunk 62 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 94 optimal weight: 30.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 1.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.072 8216 Z= 0.425 Angle : 0.710 10.062 11453 Z= 0.463 Chirality : 0.043 0.162 1556 Planarity : 0.005 0.034 1640 Dihedral : 9.890 135.913 1669 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.50 % Allowed : 12.38 % Favored : 87.12 % 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: -1.77 (0.20), residues: 1618 helix: -0.51 (0.17), residues: 831 sheet: -1.34 (0.46), residues: 92 loop : -1.92 (0.24), residues: 695 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.057 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0753 time to fit residues: 9.0476 Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.047 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 146 optimal weight: 30.0000 chunk 126 optimal weight: 40.0000 chunk 13 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 1.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 8216 Z= 0.330 Angle : 0.578 7.356 11453 Z= 0.382 Chirality : 0.042 0.138 1556 Planarity : 0.004 0.028 1640 Dihedral : 9.398 133.698 1669 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.82 % Favored : 87.80 % 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: -1.41 (0.21), residues: 1618 helix: -0.15 (0.17), residues: 859 sheet: -1.38 (0.46), residues: 101 loop : -1.86 (0.26), residues: 658 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0795 time to fit residues: 9.5646 Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 130 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 111 optimal weight: 0.0040 overall best weight: 2.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.056222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.039655 restraints weight = 231583.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.040151 restraints weight = 181658.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.040936 restraints weight = 133583.446| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 1.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 8216 Z= 0.137 Angle : 0.387 3.156 11453 Z= 0.252 Chirality : 0.040 0.131 1556 Planarity : 0.002 0.010 1640 Dihedral : 8.629 130.076 1669 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.03 % Favored : 92.59 % 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: -0.12 (0.22), residues: 1618 helix: 1.21 (0.18), residues: 868 sheet: -1.30 (0.48), residues: 101 loop : -1.70 (0.26), residues: 649 =============================================================================== Job complete usr+sys time: 1211.08 seconds wall clock time: 22 minutes 36.88 seconds (1356.88 seconds total)