Starting phenix.real_space_refine on Fri Dec 8 11:45:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0j_20550/12_2023/6q0j_20550_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0j_20550/12_2023/6q0j_20550.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0j_20550/12_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_20550/12_2023/6q0j_20550_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0j_20550/12_2023/6q0j_20550_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0j_20550/12_2023/6q0j_20550.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0j_20550/12_2023/6q0j_20550.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0j_20550/12_2023/6q0j_20550_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0j_20550/12_2023/6q0j_20550_updated.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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-1.21rc1-5172/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: 8.44, per 1000 atoms: 1.03 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: 3.62 Conformation dependent library (CDL) restraints added in 3.9 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: 1.89 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: 2.78 Time building geometry restraints manager: 3.91 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: 4748 25.66 - 51.33: 24 51.33 - 76.99: 3 76.99 - 102.65: 2 102.65 - 128.32: 2 Dihedral angle restraints: 4779 sinusoidal: 54 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 4776 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: 1.420 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: 3.820 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 33.180 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.890 ------------------------------------------------------------------------------- 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 : 8.718 128.318 1691 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 % Allowed : 0.00 % Favored : 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 450 PHE 0.000 0.000 PHE A 498 TYR 0.000 0.000 TYR A 472 *********************** 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 : 0.949 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0763 time to fit residues: 8.9591 Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.932 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1891 ------------------------------------------------------------------------------- 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: 0.7042 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 8216 Z= 0.418 Angle : 0.849 16.075 11453 Z= 0.533 Chirality : 0.045 0.158 1556 Planarity : 0.006 0.027 1640 Dihedral : 8.818 114.706 1691 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.23 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.20), residues: 1618 helix: -0.56 (0.16), residues: 883 sheet: -1.09 (0.51), residues: 102 loop : -1.72 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 450 PHE 0.000 0.000 PHE A 498 TYR 0.000 0.000 TYR A 472 *********************** 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 : 0.973 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0752 time to fit residues: 8.9860 Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1656 ------------------------------------------------------------------------------- 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: 9.9990 chunk 45 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 145 optimal weight: 30.0000 chunk 157 optimal weight: 7.9990 chunk 129 optimal weight: 20.0000 chunk 144 optimal weight: 30.0000 chunk 49 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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: 0.7233 moved from start: 0.6805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 8216 Z= 0.345 Angle : 0.655 8.009 11453 Z= 0.423 Chirality : 0.042 0.146 1556 Planarity : 0.004 0.025 1640 Dihedral : 8.667 108.538 1691 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.09 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.20), residues: 1618 helix: -0.10 (0.17), residues: 873 sheet: -1.02 (0.52), residues: 109 loop : -1.63 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 450 PHE 0.000 0.000 PHE A 498 TYR 0.000 0.000 TYR A 472 *********************** 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 : 0.940 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0747 time to fit residues: 8.8984 Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1977 ------------------------------------------------------------------------------- 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: 5.9990 chunk 109 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 146 optimal weight: 30.0000 chunk 154 optimal weight: 50.0000 chunk 76 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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: 0.7237 moved from start: 0.7416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8216 Z= 0.229 Angle : 0.475 5.021 11453 Z= 0.311 Chirality : 0.041 0.134 1556 Planarity : 0.003 0.012 1640 Dihedral : 8.415 115.225 1691 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.72 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1618 helix: 0.89 (0.17), residues: 872 sheet: -0.91 (0.51), residues: 111 loop : -1.47 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 450 PHE 0.000 0.000 PHE A 498 TYR 0.000 0.000 TYR A 472 *********************** 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 : 0.971 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0804 time to fit residues: 9.3060 Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0999 ------------------------------------------------------------------------------- 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: 30.0000 chunk 2 optimal weight: 10.0000 chunk 115 optimal weight: 50.0000 chunk 63 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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: 0.7345 moved from start: 0.8837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 8216 Z= 0.341 Angle : 0.627 10.471 11453 Z= 0.406 Chirality : 0.042 0.144 1556 Planarity : 0.004 0.021 1640 Dihedral : 9.109 113.940 1691 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.21 % Favored : 90.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1618 helix: 0.31 (0.17), residues: 852 sheet: -0.80 (0.49), residues: 109 loop : -1.45 (0.26), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 450 PHE 0.000 0.000 PHE A 498 TYR 0.000 0.000 TYR A 472 *********************** 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 : 1.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0782 time to fit residues: 9.2957 Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1958 ------------------------------------------------------------------------------- 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: 2.9990 chunk 139 optimal weight: 0.0070 chunk 30 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 154 optimal weight: 0.0570 chunk 128 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 51 optimal weight: 0.0570 chunk 81 optimal weight: 0.0050 overall best weight: 0.6250 ------------------------------------------------------------------------------- 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: 0.7216 moved from start: 0.8534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.015 8216 Z= 0.087 Angle : 0.355 2.816 11453 Z= 0.229 Chirality : 0.040 0.128 1556 Planarity : 0.002 0.010 1640 Dihedral : 8.359 117.726 1691 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.44 % Allowed : 3.05 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.22), residues: 1618 helix: 1.90 (0.17), residues: 883 sheet: -0.96 (0.47), residues: 109 loop : -1.32 (0.27), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 450 PHE 0.000 0.000 PHE A 498 TYR 0.000 0.000 TYR A 472 *********************** 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 : 0.932 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0750 time to fit residues: 8.9341 Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1486 ------------------------------------------------------------------------------- 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: 4.9990 chunk 17 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 chunk 113 optimal weight: 0.3980 chunk 87 optimal weight: 40.0000 chunk 130 optimal weight: 30.0000 chunk 86 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 94 optimal weight: 30.0000 chunk 71 optimal weight: 20.0000 overall best weight: 4.0788 ------------------------------------------------------------------------------- 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: 0.7286 moved from start: 0.8836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8216 Z= 0.200 Angle : 0.428 6.188 11453 Z= 0.279 Chirality : 0.040 0.131 1556 Planarity : 0.002 0.012 1640 Dihedral : 8.185 114.112 1691 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.97 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.22), residues: 1618 helix: 2.00 (0.18), residues: 881 sheet: -0.98 (0.46), residues: 109 loop : -1.36 (0.27), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 450 PHE 0.000 0.000 PHE A 498 TYR 0.000 0.000 TYR A 472 *********************** 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 : 0.858 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0731 time to fit residues: 8.6326 Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0832 ------------------------------------------------------------------------------- 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: 20.0000 chunk 61 optimal weight: 30.0000 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- 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: 0.7346 moved from start: 0.9574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8216 Z= 0.275 Angle : 0.515 7.621 11453 Z= 0.339 Chirality : 0.041 0.141 1556 Planarity : 0.003 0.015 1640 Dihedral : 8.670 114.800 1691 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.84 % Favored : 90.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.22), residues: 1618 helix: 1.33 (0.18), residues: 871 sheet: -1.21 (0.45), residues: 109 loop : -1.40 (0.27), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 450 PHE 0.000 0.000 PHE A 498 TYR 0.000 0.000 TYR A 472 *********************** 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 : 0.916 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0750 time to fit residues: 8.8892 Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.921 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1415 ------------------------------------------------------------------------------- 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: 30.0000 chunk 134 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 135 optimal weight: 9.9990 chunk 94 optimal weight: 30.0000 overall best weight: 11.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 1.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 8216 Z= 0.526 Angle : 0.818 12.845 11453 Z= 0.535 Chirality : 0.044 0.181 1556 Planarity : 0.006 0.039 1640 Dihedral : 10.086 121.437 1691 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.57 % Favored : 86.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.20), residues: 1618 helix: -0.86 (0.16), residues: 833 sheet: -1.67 (0.44), residues: 102 loop : -1.93 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 450 PHE 0.000 0.000 PHE A 498 TYR 0.000 0.000 TYR A 472 *********************** 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 : 1.175 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0834 time to fit residues: 9.7387 Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.973 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2401 ------------------------------------------------------------------------------- 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: 8.9990 chunk 92 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 chunk 146 optimal weight: 30.0000 chunk 126 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- 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: 0.7411 moved from start: 1.0731 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= 0.299 Angle : 0.551 6.898 11453 Z= 0.362 Chirality : 0.041 0.134 1556 Planarity : 0.003 0.018 1640 Dihedral : 9.311 119.029 1691 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.95 % Favored : 88.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.21), residues: 1618 helix: 0.01 (0.17), residues: 843 sheet: -1.73 (0.44), residues: 111 loop : -1.90 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 450 PHE 0.000 0.000 PHE A 498 TYR 0.000 0.000 TYR A 472 ********************** 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 : 0.969 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0798 time to fit residues: 9.4539 Evaluate side-chains 54 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2182 ------------------------------------------------------------------------------- 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: 10.0000 chunk 38 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 127 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 130 optimal weight: 50.0000 chunk 16 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 111 optimal weight: 0.0470 overall best weight: 1.6882 ------------------------------------------------------------------------------- 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 = 0.3160 r_free = 0.3160 target = 0.056847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.040091 restraints weight = 233466.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.040814 restraints weight = 175866.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.041629 restraints weight = 126526.950| |-----------------------------------------------------------------------------| r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 1.0513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8216 Z= 0.110 Angle : 0.372 2.781 11453 Z= 0.241 Chirality : 0.040 0.138 1556 Planarity : 0.002 0.008 1640 Dihedral : 8.511 115.535 1691 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.22 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.22), residues: 1618 helix: 1.41 (0.18), residues: 876 sheet: -1.65 (0.46), residues: 111 loop : -1.56 (0.27), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 450 PHE 0.000 0.000 PHE A 498 TYR 0.000 0.000 TYR A 472 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1287.75 seconds wall clock time: 24 minutes 3.44 seconds (1443.44 seconds total)