Starting phenix.real_space_refine on Sat Jul 26 04:50:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6q0j_20550/07_2025/6q0j_20550.cif Found real_map, /net/cci-nas-00/data/ceres_data/6q0j_20550/07_2025/6q0j_20550.map 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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6q0j_20550/07_2025/6q0j_20550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6q0j_20550/07_2025/6q0j_20550.map" model { file = "/net/cci-nas-00/data/ceres_data/6q0j_20550/07_2025/6q0j_20550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6q0j_20550/07_2025/6q0j_20550.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 9.63, per 1000 atoms: 1.17 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 - 3.00 Amino acid : True - 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: 2.47 Conformation dependent library (CDL) restraints added in 2.9 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... Secondary structure from input PDB file: 79 helices and 10 sheets defined 59.6% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 491 through 506 Processing helix chain 'A' and resid 536 through 543 Processing helix chain 'A' and resid 549 through 570 Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'A' and resid 586 through 588 No H-bonds generated for 'chain 'A' and resid 586 through 588' Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 621 through 627 Processing helix chain 'A' and resid 634 through 652 removed outlier: 3.546A pdb=" N ASP A 638 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 671 Processing helix chain 'A' and resid 677 through 681 Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 700 through 704 Processing helix chain 'A' and resid 706 through 720 removed outlier: 3.792A pdb=" N LEU A 716 " --> pdb=" O ALA A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 506 Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 549 through 570 Processing helix chain 'B' and resid 578 through 580 No H-bonds generated for 'chain 'B' and resid 578 through 580' Processing helix chain 'B' and resid 586 through 588 No H-bonds generated for 'chain 'B' and resid 586 through 588' Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 621 through 627 Processing helix chain 'B' and resid 634 through 652 removed outlier: 3.546A pdb=" N ASP B 638 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 671 Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 686 through 697 Processing helix chain 'B' and resid 700 through 704 Processing helix chain 'B' and resid 706 through 717 Processing helix chain 'C' and resid 44 through 60 Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 117 through 121 Processing helix chain 'C' and resid 151 through 159 Processing helix chain 'C' and resid 162 through 185 removed outlier: 3.655A pdb=" N LYS C 168 " --> pdb=" O GLN C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 241 through 259 removed outlier: 3.945A pdb=" N ASP C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 274 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) removed outlier: 3.658A pdb=" N MET C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 331 through 342 Processing helix chain 'C' and resid 345 through 349 Processing helix chain 'C' and resid 351 through 357 removed outlier: 3.603A pdb=" N VAL C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 367 Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'D' and resid 44 through 60 Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 104 through 116 Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 151 through 159 Processing helix chain 'D' and resid 162 through 185 removed outlier: 3.655A pdb=" N LYS D 168 " --> pdb=" O GLN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 194 No H-bonds generated for 'chain 'D' and resid 192 through 194' Processing helix chain 'D' and resid 212 through 219 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 241 through 259 removed outlier: 3.946A pdb=" N ASP D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 274 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) removed outlier: 3.658A pdb=" N MET D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 331 through 342 Processing helix chain 'D' and resid 345 through 349 Processing helix chain 'D' and resid 351 through 357 removed outlier: 3.603A pdb=" N VAL D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 367 Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'X' and resid 3 through 16 Processing helix chain 'X' and resid 18 through 31 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) Processing helix chain 'X' and resid 38 through 67 removed outlier: 3.867A pdb=" N ASN X 42 " --> pdb=" O ASN X 38 " (cutoff:3.500A) 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 102 removed outlier: 4.216A pdb=" N VAL X 84 " --> pdb=" O LYS X 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 111 through 133 Processing helix chain 'X' and resid 137 through 160 removed outlier: 3.635A pdb=" N VAL X 141 " --> pdb=" O THR X 137 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE X 155 " --> pdb=" O ASP X 151 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET X 160 " --> pdb=" O SER X 156 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 181 Processing helix chain 'X' and resid 184 through 202 removed outlier: 3.625A pdb=" N ALA X 201 " --> pdb=" O ASP X 197 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU X 202 " --> pdb=" O ASP X 198 " (cutoff:3.500A) Processing helix chain 'X' and resid 210 through 230 Processing helix chain 'Y' and resid 3 through 16 Processing helix chain 'Y' and resid 20 through 31 Processing helix chain 'Y' and resid 38 through 65 removed outlier: 3.915A pdb=" N ASN Y 42 " --> pdb=" O ASN Y 38 " (cutoff:3.500A) 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 73 through 102 removed outlier: 3.572A pdb=" N LYS Y 85 " --> pdb=" O GLU Y 81 " (cutoff:3.500A) Processing helix chain 'Y' and resid 111 through 131 Processing helix chain 'Y' and resid 137 through 160 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) removed outlier: 3.508A pdb=" N MET Y 160 " --> pdb=" O SER Y 156 " (cutoff:3.500A) Processing helix chain 'Y' and resid 164 through 181 Processing helix chain 'Y' and resid 184 through 202 removed outlier: 3.830A pdb=" N ALA Y 201 " --> pdb=" O ASP Y 197 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU Y 202 " --> pdb=" O ASP Y 198 " (cutoff:3.500A) Processing helix chain 'Y' and resid 207 through 210 Processing helix chain 'Y' and resid 211 through 229 Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 464 removed outlier: 6.993A pdb=" N VAL A 471 " --> pdb=" O ILE A 463 " (cutoff:3.500A) 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=AA2, first strand: chain 'A' and resid 572 through 573 Processing sheet with id=AA3, first strand: chain 'A' and resid 582 through 585 Processing sheet with id=AA4, first strand: chain 'B' and resid 462 through 464 removed outlier: 6.993A pdb=" N VAL B 471 " --> pdb=" O ILE B 463 " (cutoff:3.500A) 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=AA5, first strand: chain 'B' and resid 572 through 573 Processing sheet with id=AA6, first strand: chain 'B' and resid 582 through 585 Processing sheet with id=AA7, first strand: chain 'C' and resid 68 through 76 removed outlier: 7.208A pdb=" N ILE C 71 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N SER C 86 " --> pdb=" O ILE C 71 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLU C 73 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS C 84 " --> pdb=" O GLU C 73 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU C 144 " --> pdb=" O PHE C 129 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N PHE C 129 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 149 through 150 Processing sheet with id=AA9, first strand: chain 'D' and resid 68 through 76 removed outlier: 7.208A pdb=" N ILE D 71 " --> pdb=" O SER D 86 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N SER D 86 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLU D 73 " --> pdb=" O LYS D 84 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS D 84 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLU D 144 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N PHE D 129 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 149 through 150 731 hydrogen bonds defined for protein. 2086 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: 2.76 Time building geometry restraints manager: 2.80 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: 0.00 - 2.16: 9877 2.16 - 4.32: 1390 4.32 - 6.47: 151 6.47 - 8.63: 29 8.63 - 10.79: 6 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: 4758 25.66 - 51.33: 24 51.33 - 76.99: 9 76.99 - 102.65: 2 102.65 - 128.32: 2 Dihedral angle restraints: 4795 sinusoidal: 70 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 4792 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: 1620 2.78 - 3.32: 8744 3.32 - 3.87: 12822 3.87 - 4.41: 12459 4.41 - 4.96: 20644 Nonbonded interactions: 56289 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 3.120 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 3.040 ... (remaining 56284 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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: 0.980 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 29.590 Find NCS groups from input model: 0.360 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.060 ------------------------------------------------------------------------------- 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= 0.907 Angle : 1.513 10.788 11453 Z= 1.136 Chirality : 0.090 0.570 1556 Planarity : 0.005 0.057 1640 Dihedral : 9.517 128.318 1707 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 Details of bonding type rmsd hydrogen bonds : bond 0.17959 ( 731) hydrogen bonds : angle 7.65975 ( 2086) covalent geometry : bond 0.01220 ( 8216) covalent geometry : angle 1.51324 (11453) *********************** 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 to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.925 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0783 time to fit residues: 9.1171 Evaluate side-chains 54 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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: 5.9990 chunk 121 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 30.0000 chunk 64 optimal weight: 20.0000 chunk 125 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.068404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.048998 restraints weight = 202483.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.050045 restraints weight = 149833.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.050402 restraints weight = 116136.372| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3653 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= 0.292 Angle : 0.669 8.205 11453 Z= 0.432 Chirality : 0.044 0.139 1556 Planarity : 0.004 0.019 1640 Dihedral : 8.680 117.970 1707 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.80 % Favored : 95.71 % 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: -0.88 (0.20), residues: 1618 helix: 0.20 (0.16), residues: 908 sheet: -0.81 (0.53), residues: 101 loop : -1.68 (0.24), residues: 609 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 Details of bonding type rmsd hydrogen bonds : bond 0.05051 ( 731) hydrogen bonds : angle 5.40757 ( 2086) covalent geometry : bond 0.00398 ( 8216) covalent geometry : angle 0.66948 (11453) *********************** 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 to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.841 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0796 time to fit residues: 9.3367 Evaluate side-chains 54 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 122 optimal weight: 7.9990 chunk 115 optimal weight: 50.0000 chunk 136 optimal weight: 40.0000 chunk 76 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 chunk 89 optimal weight: 40.0000 chunk 62 optimal weight: 20.0000 chunk 104 optimal weight: 20.0000 overall best weight: 9.5392 ------------------------------------------------------------------------------- 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 = 0.3171 r_free = 0.3171 target = 0.057430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.040462 restraints weight = 251056.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.041718 restraints weight = 185936.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.042262 restraints weight = 132944.644| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.7931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 8216 Z= 0.459 Angle : 0.863 9.008 11453 Z= 0.556 Chirality : 0.047 0.177 1556 Planarity : 0.006 0.035 1640 Dihedral : 10.160 108.527 1707 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.62 % Allowed : 6.97 % 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: -2.16 (0.19), residues: 1618 helix: -0.85 (0.15), residues: 899 sheet: -1.67 (0.48), residues: 100 loop : -2.14 (0.24), residues: 619 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 Details of bonding type rmsd hydrogen bonds : bond 0.07110 ( 731) hydrogen bonds : angle 7.39933 ( 2086) covalent geometry : bond 0.00646 ( 8216) covalent geometry : angle 0.86342 (11453) *********************** 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 to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.918 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0732 time to fit residues: 8.7057 Evaluate side-chains 54 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 51 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 60 optimal weight: 40.0000 chunk 137 optimal weight: 2.9990 chunk 64 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 = 0.3202 r_free = 0.3202 target = 0.058594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.041648 restraints weight = 212765.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.042179 restraints weight = 148840.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.042744 restraints weight = 114580.895| |-----------------------------------------------------------------------------| r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.7787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8216 Z= 0.180 Angle : 0.445 5.025 11453 Z= 0.289 Chirality : 0.041 0.131 1556 Planarity : 0.002 0.016 1640 Dihedral : 8.789 104.904 1707 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.17 % Favored : 95.40 % 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: -0.37 (0.21), residues: 1618 helix: 0.88 (0.17), residues: 916 sheet: -1.77 (0.44), residues: 118 loop : -1.71 (0.26), residues: 584 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 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 731) hydrogen bonds : angle 5.50544 ( 2086) covalent geometry : bond 0.00252 ( 8216) covalent geometry : angle 0.44525 (11453) *********************** 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 to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.837 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0710 time to fit residues: 8.3990 Evaluate side-chains 54 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 30.0000 chunk 126 optimal weight: 30.0000 chunk 149 optimal weight: 0.8980 chunk 144 optimal weight: 0.0000 chunk 91 optimal weight: 40.0000 chunk 98 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 43 optimal weight: 30.0000 chunk 68 optimal weight: 20.0000 chunk 60 optimal weight: 30.0000 overall best weight: 7.9792 ------------------------------------------------------------------------------- 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 = 0.3151 r_free = 0.3151 target = 0.056298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.039512 restraints weight = 235913.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.040032 restraints weight = 174759.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.040729 restraints weight = 124262.554| |-----------------------------------------------------------------------------| r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.8823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8216 Z= 0.364 Angle : 0.629 6.072 11453 Z= 0.410 Chirality : 0.042 0.145 1556 Planarity : 0.004 0.019 1640 Dihedral : 9.355 108.343 1707 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.52 % Favored : 89.98 % 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: -1.01 (0.21), residues: 1618 helix: 0.29 (0.17), residues: 870 sheet: -1.72 (0.44), residues: 113 loop : -1.79 (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 Details of bonding type rmsd hydrogen bonds : bond 0.05676 ( 731) hydrogen bonds : angle 6.50015 ( 2086) covalent geometry : bond 0.00501 ( 8216) covalent geometry : angle 0.62932 (11453) *********************** 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 to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.966 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0753 time to fit residues: 8.8758 Evaluate side-chains 54 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 57 optimal weight: 30.0000 chunk 32 optimal weight: 8.9990 chunk 115 optimal weight: 50.0000 chunk 143 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 109 optimal weight: 0.0970 chunk 127 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- 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 = 0.3200 r_free = 0.3200 target = 0.058216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.041425 restraints weight = 219963.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.042241 restraints weight = 150202.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.042363 restraints weight = 118489.072| |-----------------------------------------------------------------------------| r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.8591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8216 Z= 0.110 Angle : 0.385 3.052 11453 Z= 0.247 Chirality : 0.040 0.141 1556 Planarity : 0.002 0.017 1640 Dihedral : 8.478 109.745 1707 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.04 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.22), residues: 1618 helix: 1.74 (0.17), residues: 917 sheet: -1.58 (0.45), residues: 113 loop : -1.67 (0.27), residues: 588 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 Details of bonding type rmsd hydrogen bonds : bond 0.03491 ( 731) hydrogen bonds : angle 4.94574 ( 2086) covalent geometry : bond 0.00151 ( 8216) covalent geometry : angle 0.38460 (11453) *********************** 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 to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.861 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0746 time to fit residues: 8.8090 Evaluate side-chains 54 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 121 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 56 optimal weight: 30.0000 chunk 157 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 143 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 59 optimal weight: 50.0000 chunk 67 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3166 r_free = 0.3166 target = 0.056851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.040065 restraints weight = 283349.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.040846 restraints weight = 189575.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.041393 restraints weight = 130665.428| |-----------------------------------------------------------------------------| r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.9053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8216 Z= 0.235 Angle : 0.481 4.623 11453 Z= 0.312 Chirality : 0.041 0.138 1556 Planarity : 0.003 0.016 1640 Dihedral : 8.574 113.064 1707 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.46 % Favored : 91.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1618 helix: 1.63 (0.17), residues: 908 sheet: -1.60 (0.45), residues: 113 loop : -1.64 (0.27), residues: 597 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 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 731) hydrogen bonds : angle 5.33985 ( 2086) covalent geometry : bond 0.00323 ( 8216) covalent geometry : angle 0.48100 (11453) *********************** 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 to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.918 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0739 time to fit residues: 8.8052 Evaluate side-chains 54 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 94 optimal weight: 30.0000 chunk 92 optimal weight: 10.0000 chunk 41 optimal weight: 0.5980 chunk 114 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- 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 = 0.3152 r_free = 0.3152 target = 0.056361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.039999 restraints weight = 199018.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.041691 restraints weight = 146881.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.041946 restraints weight = 104140.008| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.9733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8216 Z= 0.241 Angle : 0.469 3.921 11453 Z= 0.311 Chirality : 0.041 0.134 1556 Planarity : 0.003 0.019 1640 Dihedral : 8.817 115.639 1707 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.91 % Favored : 92.72 % 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: 0.33 (0.22), residues: 1618 helix: 1.65 (0.17), residues: 901 sheet: -1.67 (0.45), residues: 115 loop : -1.66 (0.27), residues: 602 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 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 731) hydrogen bonds : angle 5.44464 ( 2086) covalent geometry : bond 0.00331 ( 8216) covalent geometry : angle 0.46882 (11453) *********************** 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 to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.856 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0736 time to fit residues: 8.5993 Evaluate side-chains 54 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 154 optimal weight: 0.6980 chunk 120 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 56 optimal weight: 30.0000 chunk 25 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 131 optimal weight: 0.4980 chunk 67 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 overall best weight: 4.4386 ------------------------------------------------------------------------------- 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 = 0.3150 r_free = 0.3150 target = 0.056305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.039475 restraints weight = 222500.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.040010 restraints weight = 165016.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.040869 restraints weight = 124762.675| |-----------------------------------------------------------------------------| r_work (final): 0.2686 ------------------------------------------------------------------------------- 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 = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.9940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8216 Z= 0.209 Angle : 0.443 3.955 11453 Z= 0.291 Chirality : 0.040 0.140 1556 Planarity : 0.002 0.017 1640 Dihedral : 8.537 120.098 1707 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.40 % Favored : 91.23 % 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: 0.63 (0.22), residues: 1618 helix: 1.93 (0.17), residues: 906 sheet: -1.59 (0.46), residues: 115 loop : -1.60 (0.27), residues: 597 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 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 731) hydrogen bonds : angle 5.21277 ( 2086) covalent geometry : bond 0.00287 ( 8216) covalent geometry : angle 0.44297 (11453) *********************** 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 to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.954 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1018 time to fit residues: 12.2634 Evaluate side-chains 54 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 26 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 137 optimal weight: 30.0000 chunk 88 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 144 optimal weight: 30.0000 chunk 53 optimal weight: 5.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 = 0.3149 r_free = 0.3149 target = 0.056180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.038889 restraints weight = 290308.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.040361 restraints weight = 203098.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.041139 restraints weight = 129163.574| |-----------------------------------------------------------------------------| r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 1.0248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8216 Z= 0.228 Angle : 0.456 4.263 11453 Z= 0.301 Chirality : 0.041 0.131 1556 Planarity : 0.002 0.016 1640 Dihedral : 8.478 121.408 1707 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.34 % Favored : 92.28 % 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: 0.56 (0.22), residues: 1618 helix: 1.92 (0.17), residues: 904 sheet: -1.65 (0.46), residues: 115 loop : -1.70 (0.27), residues: 599 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 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 731) hydrogen bonds : angle 5.24491 ( 2086) covalent geometry : bond 0.00313 ( 8216) covalent geometry : angle 0.45598 (11453) ********************** 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 to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 1.732 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1929 time to fit residues: 22.9519 Evaluate side-chains 54 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 94 optimal weight: 30.0000 chunk 39 optimal weight: 0.9990 chunk 138 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3165 r_free = 0.3165 target = 0.056799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.039483 restraints weight = 320497.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.040676 restraints weight = 216402.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.041522 restraints weight = 135499.368| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 1.0263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8216 Z= 0.149 Angle : 0.383 4.593 11453 Z= 0.249 Chirality : 0.040 0.131 1556 Planarity : 0.002 0.017 1640 Dihedral : 8.228 121.099 1707 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.10 % Favored : 93.53 % 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: 1.11 (0.23), residues: 1618 helix: 2.49 (0.17), residues: 904 sheet: -2.01 (0.44), residues: 129 loop : -1.53 (0.28), residues: 585 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 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 731) hydrogen bonds : angle 4.72919 ( 2086) covalent geometry : bond 0.00204 ( 8216) covalent geometry : angle 0.38337 (11453) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3173.53 seconds wall clock time: 57 minutes 16.50 seconds (3436.50 seconds total)