Starting phenix.real_space_refine on Fri Oct 23 03:48:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6q0j_20550/10_2026/6q0j_20550.cif Found real_map, /net/cci-nas-00/data/ceres_data/6q0j_20550/10_2026/6q0j_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_20550/10_2026/6q0j_20550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6q0j_20550/10_2026/6q0j_20550.map" model { file = "/net/cci-nas-00/data/ceres_data/6q0j_20550/10_2026/6q0j_20550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6q0j_20550/10_2026/6q0j_20550.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6q0j_20550/10_2026/6q0j_20550.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6q0j_20550/10_2026/6q0j_20550.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/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: {'ASP:plan': 13, 'TRP:plan': 5, 'GLU:plan': 13, 'GLN:plan1': 16, 'ARG:plan': 15, 'TYR:plan': 9, 'HIS:plan': 10, 'ASN:plan1': 10, 'PHE:plan': 10} 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: {'ASP:plan': 13, 'TRP:plan': 5, 'GLU:plan': 13, 'GLN:plan1': 16, 'ARG:plan': 15, 'TYR:plan': 9, 'HIS:plan': 10, 'ASN:plan1': 10, 'PHE:plan': 10} 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: {'ASP:plan': 13, 'TRP:plan': 5, 'GLU:plan': 13, 'GLN:plan1': 16, 'ARG:plan': 15, 'TYR:plan': 9, 'HIS:plan': 10, 'ASN:plan1': 11, 'PHE:plan': 10} 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: {'ASP:plan': 13, 'TRP:plan': 5, 'GLU:plan': 13, 'GLN:plan1': 16, 'ARG:plan': 15, 'TYR:plan': 9, 'HIS:plan': 10, 'ASN:plan1': 11, 'PHE:plan': 10} 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: {'ASP:plan': 17, 'GLU:plan': 23, 'GLN:plan1': 13, 'ARG:plan': 14, 'PHE:plan': 13, 'ASN:plan1': 9, 'HIS:plan': 8, 'TYR:plan': 8, 'TRP:plan': 2} 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: {'ASP:plan': 17, 'GLU:plan': 23, 'GLN:plan1': 13, 'ARG:plan': 14, 'PHE:plan': 13, 'ASN:plan1': 9, 'HIS:plan': 8, 'TYR:plan': 8, 'TRP:plan': 2} 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: {'ASP:plan': 17, 'GLU:plan': 23, 'GLN:plan1': 13, 'ARG:plan': 14, 'PHE:plan': 13, 'ASN:plan1': 9, 'HIS:plan': 8, 'TYR:plan': 8, 'TRP:plan': 2} 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: {'ASP:plan': 17, 'GLU:plan': 23, 'GLN:plan1': 13, 'ARG:plan': 14, 'PHE:plan': 13, 'ASN:plan1': 9, 'HIS:plan': 8, 'TYR:plan': 8, 'TRP:plan': 2} 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: {'ASP:plan': 15, 'GLU:plan': 24, 'GLN:plan1': 11, 'ARG:plan': 13, 'TYR:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 5} 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: {'ASP:plan': 15, 'GLU:plan': 24, 'GLN:plan1': 11, 'ARG:plan': 13, 'TYR:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 5} 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: 3.69, per 1000 atoms: 0.45 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: 0.56 Conformation dependent library (CDL) restraints added in 564.5 milliseconds 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: 0.19 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: 1.09 Time building geometry restraints manager: 0.74 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: 4749 25.66 - 51.33: 11 51.33 - 76.99: 9 76.99 - 102.65: 2 102.65 - 128.32: 2 Dihedral angle restraints: 4773 sinusoidal: 48 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 4770 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 403)) selection = (chain 'D' and (resid 43 through 99 or resid 101 through 206 or resid 208 throug \ h 347 or resid 349 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: 1.200 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.900 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 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 : 9.031 128.318 1685 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 TYR 0.000 0.000 TYR A 472 PHE 0.000 0.000 PHE A 498 TRP 0.000 0.000 TRP A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.01220 / 0.91 ( 8216) covalent geometry : angle 1.51324 / 1.14 (11453) hydrogen bonds : bond 0.17959 / 13.59 ( 731) hydrogen bonds : angle 7.65975 / 5.66 ( 2086) *********************** 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 : 0.273 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0345 time to fit residues: 3.8961 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 : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.071834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.051614 restraints weight = 193091.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.052806 restraints weight = 145993.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.053450 restraints weight = 103696.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.053657 restraints weight = 100740.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.054095 restraints weight = 87115.432| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8216 Z= 0.251 Angle : 0.586 5.831 11453 Z= 0.371 Chirality : 0.043 0.141 1556 Planarity : 0.004 0.016 1640 Dihedral : 8.125 112.323 1685 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.50 % Allowed : 2.55 % Favored : 96.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.20), residues: 1618 helix: 0.78 (0.17), residues: 910 sheet: -0.78 (0.53), residues: 91 loop : -1.35 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 472 PHE 0.000 0.000 PHE A 498 TRP 0.000 0.000 TRP A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.25 ( 8216) covalent geometry : angle 0.58600 / 0.37 (11453) hydrogen bonds : bond 0.04321 / 3.32 ( 731) hydrogen bonds : angle 4.83725 / 3.54 ( 2086) *********************** 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 : 0.316 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0346 time to fit residues: 3.8932 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 : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [53, 56, 39, 71, 132, 122, 78, 114, 75, 49, 87] chunk 53 optimal weight: 0.0370 chunk 56 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 122 optimal weight: 0.0970 chunk 78 optimal weight: 8.9990 chunk 114 optimal weight: 30.0000 chunk 75 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 overall best weight: 4.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.063089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.045306 restraints weight = 259220.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.045675 restraints weight = 196347.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.046490 restraints weight = 140138.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.047168 restraints weight = 103277.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.047271 restraints weight = 88119.825| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (16 function evaluations) r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8216 Z= 0.233 Angle : 0.535 4.468 11453 Z= 0.344 Chirality : 0.042 0.137 1556 Planarity : 0.003 0.016 1640 Dihedral : 8.231 113.048 1685 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.23 % Favored : 95.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.21), residues: 1618 helix: 1.63 (0.17), residues: 912 sheet: -1.03 (0.45), residues: 119 loop : -1.20 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 472 PHE 0.000 0.000 PHE A 498 TRP 0.000 0.000 TRP A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.23 ( 8216) covalent geometry : angle 0.53496 / 0.34 (11453) hydrogen bonds : bond 0.04413 / 3.36 ( 731) hydrogen bonds : angle 5.08530 / 3.67 ( 2086) *********************** 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 : 0.319 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0350 time to fit residues: 4.0049 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 : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [98, 109, 79, 156, 90, 113, 129, 141, 58, 69, 93] chunk 98 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 156 optimal weight: 30.0000 chunk 90 optimal weight: 30.0000 chunk 113 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 141 optimal weight: 0.2980 chunk 58 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 overall best weight: 5.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.058903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.040818 restraints weight = 272982.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.041532 restraints weight = 185384.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.042764 restraints weight = 127824.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.042706 restraints weight = 109267.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.043002 restraints weight = 99029.338| |-----------------------------------------------------------------------------| r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.7522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 8216 Z= 0.304 Angle : 0.584 6.809 11453 Z= 0.378 Chirality : 0.042 0.140 1556 Planarity : 0.004 0.021 1640 Dihedral : 8.521 99.315 1685 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.10 % Favored : 94.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.21), residues: 1618 helix: 1.01 (0.16), residues: 912 sheet: -1.13 (0.46), residues: 118 loop : -1.51 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 472 PHE 0.000 0.000 PHE A 498 TRP 0.000 0.000 TRP A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.30 ( 8216) covalent geometry : angle 0.58440 / 0.38 (11453) hydrogen bonds : bond 0.05042 / 3.88 ( 731) hydrogen bonds : angle 5.65475 / 4.10 ( 2086) *********************** 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 : 0.289 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0329 time to fit residues: 3.7536 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 : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [110, 86, 127, 18, 1, 117, 21, 53, 145, 78, 63] chunk 110 optimal weight: 9.9990 chunk 86 optimal weight: 30.0000 chunk 127 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 78 optimal weight: 0.0040 chunk 63 optimal weight: 10.0000 overall best weight: 5.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.058110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.040096 restraints weight = 299500.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.040983 restraints weight = 206191.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.041812 restraints weight = 133786.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.042542 restraints weight = 96697.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.042771 restraints weight = 86729.722| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.8102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8216 Z= 0.234 Angle : 0.482 4.520 11453 Z= 0.314 Chirality : 0.041 0.135 1556 Planarity : 0.003 0.019 1640 Dihedral : 8.035 98.224 1685 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.21), residues: 1618 helix: 1.57 (0.17), residues: 906 sheet: -0.63 (0.49), residues: 103 loop : -1.42 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 472 PHE 0.000 0.000 PHE A 498 TRP 0.000 0.000 TRP A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.23 ( 8216) covalent geometry : angle 0.48160 / 0.31 (11453) hydrogen bonds : bond 0.04377 / 3.35 ( 731) hydrogen bonds : angle 5.28229 / 3.82 ( 2086) *********************** 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 : 0.220 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0318 time to fit residues: 3.5561 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 : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [50, 28, 51, 157, 151, 83, 93, 44, 129, 89, 148] chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 157 optimal weight: 8.9990 chunk 151 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 89 optimal weight: 40.0000 chunk 148 optimal weight: 40.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.057656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.039613 restraints weight = 297335.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.041096 restraints weight = 203916.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.041686 restraints weight = 127698.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.041936 restraints weight = 100790.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.042576 restraints weight = 88067.511| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.8570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8216 Z= 0.219 Angle : 0.453 4.338 11453 Z= 0.298 Chirality : 0.041 0.133 1556 Planarity : 0.003 0.016 1640 Dihedral : 8.138 103.322 1685 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.72 % Favored : 93.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.22), residues: 1618 helix: 1.91 (0.17), residues: 907 sheet: -1.02 (0.46), residues: 115 loop : -1.30 (0.28), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 472 PHE 0.000 0.000 PHE A 498 TRP 0.000 0.000 TRP A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.22 ( 8216) covalent geometry : angle 0.45329 / 0.30 (11453) hydrogen bonds : bond 0.04140 / 3.18 ( 731) hydrogen bonds : angle 5.08191 / 3.68 ( 2086) *********************** 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 : 0.325 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0349 time to fit residues: 3.9066 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 : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [112, 47, 10, 126, 147, 60, 11, 22, 113, 114, 70] chunk 112 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 126 optimal weight: 30.0000 chunk 147 optimal weight: 10.0000 chunk 60 optimal weight: 40.0000 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 113 optimal weight: 7.9990 chunk 114 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 overall best weight: 3.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.057907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.040006 restraints weight = 258932.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.041292 restraints weight = 179308.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.042013 restraints weight = 121274.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.042049 restraints weight = 99829.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.042311 restraints weight = 97180.067| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 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 = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.8804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8216 Z= 0.167 Angle : 0.398 3.842 11453 Z= 0.261 Chirality : 0.040 0.129 1556 Planarity : 0.002 0.017 1640 Dihedral : 7.876 107.096 1685 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.16 % Favored : 94.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.22), residues: 1618 helix: 2.46 (0.17), residues: 911 sheet: -1.30 (0.45), residues: 121 loop : -1.29 (0.28), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 472 PHE 0.000 0.000 PHE A 498 TRP 0.000 0.000 TRP A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.17 ( 8216) covalent geometry : angle 0.39822 / 0.26 (11453) hydrogen bonds : bond 0.03574 / 2.74 ( 731) hydrogen bonds : angle 4.64032 / 3.36 ( 2086) *********************** 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 : 0.232 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0300 time to fit residues: 3.2890 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 : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [119, 92, 74, 156, 147, 151, 111, 70, 6, 134, 56] chunk 119 optimal weight: 30.0000 chunk 92 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 70 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 56 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.055735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.038950 restraints weight = 234973.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.039854 restraints weight = 171791.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.040286 restraints weight = 125671.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.040577 restraints weight = 97558.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.040913 restraints weight = 87671.660| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 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 = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.9746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8216 Z= 0.349 Angle : 0.600 5.537 11453 Z= 0.397 Chirality : 0.042 0.142 1556 Planarity : 0.004 0.018 1640 Dihedral : 8.838 113.143 1685 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 5.22 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.21), residues: 1618 helix: 1.01 (0.17), residues: 913 sheet: -1.32 (0.45), residues: 115 loop : -1.69 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 472 PHE 0.000 0.000 PHE A 498 TRP 0.000 0.000 TRP A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.35 ( 8216) covalent geometry : angle 0.60048 / 0.40 (11453) hydrogen bonds : bond 0.05417 / 4.14 ( 731) hydrogen bonds : angle 6.19450 / 4.48 ( 2086) *********************** 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 : 0.319 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0347 time to fit residues: 3.8889 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 : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [127, 21, 35, 83, 144, 45, 147, 36, 70, 123, 34] chunk 127 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.056528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.039221 restraints weight = 315512.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.040519 restraints weight = 220719.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.041170 restraints weight = 144308.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.041187 restraints weight = 117220.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.041363 restraints weight = 116521.360| |-----------------------------------------------------------------------------| r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 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 = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.9769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8216 Z= 0.202 Angle : 0.437 4.081 11453 Z= 0.288 Chirality : 0.041 0.134 1556 Planarity : 0.002 0.019 1640 Dihedral : 8.285 115.011 1685 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.03 % Favored : 92.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.22), residues: 1618 helix: 1.81 (0.17), residues: 903 sheet: -1.83 (0.44), residues: 129 loop : -1.47 (0.28), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 472 PHE 0.000 0.000 PHE A 498 TRP 0.000 0.000 TRP A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.20 ( 8216) covalent geometry : angle 0.43661 / 0.29 (11453) hydrogen bonds : bond 0.04158 / 3.19 ( 731) hydrogen bonds : angle 5.31079 / 3.84 ( 2086) *********************** 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 : 0.210 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0306 time to fit residues: 3.5071 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 : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [82, 156, 9, 21, 94, 90, 5, 34, 48, 89, 50] chunk 82 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 90 optimal weight: 50.0000 chunk 5 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.055974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.038801 restraints weight = 259535.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.040093 restraints weight = 183526.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.040381 restraints weight = 133176.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.040830 restraints weight = 101862.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.041251 restraints weight = 89144.385| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 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 = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 1.0200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8216 Z= 0.269 Angle : 0.503 4.755 11453 Z= 0.332 Chirality : 0.041 0.138 1556 Planarity : 0.003 0.017 1640 Dihedral : 8.464 120.791 1685 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.02 % Favored : 90.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.22), residues: 1618 helix: 1.49 (0.17), residues: 915 sheet: -0.98 (0.49), residues: 101 loop : -1.76 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 472 PHE 0.000 0.000 PHE A 498 TRP 0.000 0.000 TRP A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.27 ( 8216) covalent geometry : angle 0.50332 / 0.33 (11453) hydrogen bonds : bond 0.04644 / 3.56 ( 731) hydrogen bonds : angle 5.65110 / 4.08 ( 2086) ********************** 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 : 0.312 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0351 time to fit residues: 3.9495 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 : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [93, 25, 106, 34, 127, 15, 130, 48, 129, 121, 137] chunk 93 optimal weight: 6.9990 chunk 25 optimal weight: 0.0050 chunk 106 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 15 optimal weight: 40.0000 chunk 130 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 overall best weight: 4.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.056377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.039403 restraints weight = 258545.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.040188 restraints weight = 185760.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.041057 restraints weight = 130273.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.041202 restraints weight = 99814.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.041525 restraints weight = 97881.760| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 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 = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 1.0302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8216 Z= 0.204 Angle : 0.433 4.189 11453 Z= 0.286 Chirality : 0.041 0.134 1556 Planarity : 0.002 0.018 1640 Dihedral : 8.210 121.507 1685 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.28 % Favored : 92.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.22), residues: 1618 helix: 1.94 (0.17), residues: 907 sheet: -1.84 (0.44), residues: 125 loop : -1.54 (0.28), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 472 PHE 0.000 0.000 PHE A 498 TRP 0.000 0.000 TRP A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.20 ( 8216) covalent geometry : angle 0.43313 / 0.29 (11453) hydrogen bonds : bond 0.04086 / 3.14 ( 731) hydrogen bonds : angle 5.20648 / 3.76 ( 2086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1253.66 seconds wall clock time: 21 minutes 59.98 seconds (1319.98 seconds total)