Starting phenix.real_space_refine on Tue Mar 3 19:38:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6q0j_20550/03_2026/6q0j_20550.cif Found real_map, /net/cci-nas-00/data/ceres_data/6q0j_20550/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6q0j_20550/03_2026/6q0j_20550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6q0j_20550/03_2026/6q0j_20550.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6q0j_20550/03_2026/6q0j_20550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6q0j_20550/03_2026/6q0j_20550.map" } 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-dev-5986/lib/python3.9/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: 4.05, per 1000 atoms: 0.49 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: 0.75 Conformation dependent library (CDL) restraints added in 989.5 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: 0.27 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: 1.22 Time building geometry restraints manager: 0.92 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 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: 1.130 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.240 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.970 ------------------------------------------------------------------------------- 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 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 covalent geometry : bond 0.01220 ( 8216) covalent geometry : angle 1.51324 (11453) hydrogen bonds : bond 0.17959 ( 731) hydrogen bonds : angle 7.65975 ( 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 : 0.219 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0341 time to fit residues: 3.7889 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: 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.070631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.050249 restraints weight = 194958.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.051368 restraints weight = 146206.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.052694 restraints weight = 100125.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.052817 restraints weight = 88421.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.053292 restraints weight = 74582.123| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8216 Z= 0.253 Angle : 0.599 6.433 11453 Z= 0.377 Chirality : 0.043 0.146 1556 Planarity : 0.004 0.017 1640 Dihedral : 8.480 116.176 1707 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.24 % Favored : 96.27 % 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: -0.26 (0.20), residues: 1618 helix: 0.76 (0.17), residues: 906 sheet: -0.66 (0.52), residues: 101 loop : -1.47 (0.24), residues: 611 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 covalent geometry : bond 0.00357 ( 8216) covalent geometry : angle 0.59907 (11453) hydrogen bonds : bond 0.04481 ( 731) hydrogen bonds : angle 4.88816 ( 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 : 0.286 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0365 time to fit residues: 4.0542 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 : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 53 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 122 optimal weight: 0.0270 chunk 78 optimal weight: 10.0000 chunk 114 optimal weight: 30.0000 chunk 75 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- 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 = 0.3320 r_free = 0.3320 target = 0.064371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.045732 restraints weight = 262495.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.046548 restraints weight = 175990.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.047140 restraints weight = 131761.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.047715 restraints weight = 100876.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.048326 restraints weight = 88513.395| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8216 Z= 0.194 Angle : 0.488 4.238 11453 Z= 0.314 Chirality : 0.041 0.134 1556 Planarity : 0.003 0.015 1640 Dihedral : 8.197 114.444 1707 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.61 % Favored : 95.89 % 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: 1.04 (0.21), residues: 1618 helix: 2.02 (0.17), residues: 916 sheet: -1.04 (0.46), residues: 119 loop : -1.14 (0.26), residues: 583 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 covalent geometry : bond 0.00277 ( 8216) covalent geometry : angle 0.48816 (11453) hydrogen bonds : bond 0.04158 ( 731) hydrogen bonds : angle 4.67804 ( 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 : 0.292 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0345 time to fit residues: 3.8667 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 : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 chunk 79 optimal weight: 30.0000 chunk 156 optimal weight: 30.0000 chunk 90 optimal weight: 30.0000 chunk 113 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 141 optimal weight: 0.6980 chunk 58 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 overall best weight: 6.7390 ------------------------------------------------------------------------------- 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 = 0.3197 r_free = 0.3197 target = 0.058475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.040455 restraints weight = 274216.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.041421 restraints weight = 178533.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.042238 restraints weight = 129016.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.042459 restraints weight = 109421.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.042604 restraints weight = 103530.570| |-----------------------------------------------------------------------------| r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 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 = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.7547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 8216 Z= 0.362 Angle : 0.658 7.759 11453 Z= 0.429 Chirality : 0.043 0.140 1556 Planarity : 0.004 0.025 1640 Dihedral : 9.307 102.674 1707 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.16 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.27 (0.21), residues: 1618 helix: 0.82 (0.17), residues: 893 sheet: -1.17 (0.45), residues: 118 loop : -1.46 (0.26), residues: 607 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 covalent geometry : bond 0.00506 ( 8216) covalent geometry : angle 0.65784 (11453) hydrogen bonds : bond 0.05553 ( 731) hydrogen bonds : angle 6.03445 ( 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 : 0.296 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0354 time to fit residues: 3.9564 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 110 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 = 0.058446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.040661 restraints weight = 293589.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.041652 restraints weight = 187262.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.042326 restraints weight = 133480.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.042755 restraints weight = 103686.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.042851 restraints weight = 89901.609| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 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 = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.7879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8216 Z= 0.220 Angle : 0.462 4.832 11453 Z= 0.302 Chirality : 0.041 0.129 1556 Planarity : 0.003 0.017 1640 Dihedral : 8.338 104.633 1707 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.92 % Favored : 94.71 % 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 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: 0.38 (0.21), residues: 1618 helix: 1.47 (0.17), residues: 920 sheet: -1.19 (0.45), residues: 114 loop : -1.44 (0.27), residues: 584 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 covalent geometry : bond 0.00303 ( 8216) covalent geometry : angle 0.46243 (11453) hydrogen bonds : bond 0.04178 ( 731) hydrogen bonds : angle 5.27295 ( 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 : 0.264 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0335 time to fit residues: 3.7188 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 : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 89 optimal weight: 50.0000 chunk 148 optimal weight: 50.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3183 r_free = 0.3183 target = 0.057461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.039234 restraints weight = 300157.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.040425 restraints weight = 196954.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.040990 restraints weight = 136149.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.041440 restraints weight = 105956.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.041869 restraints weight = 94110.298| |-----------------------------------------------------------------------------| r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 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 = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.8799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8216 Z= 0.227 Angle : 0.471 4.649 11453 Z= 0.308 Chirality : 0.041 0.132 1556 Planarity : 0.003 0.016 1640 Dihedral : 8.396 112.178 1707 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.72 % Favored : 92.91 % 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: 1.93 (0.17), residues: 905 sheet: -0.91 (0.46), residues: 105 loop : -1.36 (0.27), residues: 608 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 covalent geometry : bond 0.00319 ( 8216) covalent geometry : angle 0.47106 (11453) hydrogen bonds : bond 0.04205 ( 731) hydrogen bonds : angle 5.07096 ( 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 : 0.284 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0357 time to fit residues: 4.0290 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 : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 126 optimal weight: 30.0000 chunk 147 optimal weight: 9.9990 chunk 60 optimal weight: 40.0000 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3195 r_free = 0.3195 target = 0.057920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.040275 restraints weight = 253481.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.041767 restraints weight = 181102.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.042468 restraints weight = 117634.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.042612 restraints weight = 90409.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.043097 restraints weight = 81918.276| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 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 = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.8853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8216 Z= 0.149 Angle : 0.388 3.825 11453 Z= 0.251 Chirality : 0.040 0.128 1556 Planarity : 0.002 0.016 1640 Dihedral : 8.080 109.537 1707 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.23 % 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: 1.27 (0.22), residues: 1618 helix: 2.43 (0.17), residues: 909 sheet: -1.48 (0.44), residues: 121 loop : -1.27 (0.28), 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 covalent geometry : bond 0.00205 ( 8216) covalent geometry : angle 0.38794 (11453) hydrogen bonds : bond 0.03518 ( 731) hydrogen bonds : angle 4.65824 ( 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 : 0.184 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0392 time to fit residues: 4.0657 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 : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 119 optimal weight: 30.0000 chunk 92 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 156 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 151 optimal weight: 30.0000 chunk 111 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 56 optimal weight: 30.0000 overall best weight: 9.7990 ------------------------------------------------------------------------------- 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 = 0.3130 r_free = 0.3130 target = 0.055386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.039424 restraints weight = 219343.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.039450 restraints weight = 157935.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.039858 restraints weight = 130872.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.040097 restraints weight = 106704.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.040727 restraints weight = 92372.391| |-----------------------------------------------------------------------------| r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 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 = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.9989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 8216 Z= 0.446 Angle : 0.698 6.279 11453 Z= 0.461 Chirality : 0.043 0.143 1556 Planarity : 0.005 0.026 1640 Dihedral : 9.426 117.482 1707 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.02 % Favored : 89.55 % 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: -0.95 (0.20), residues: 1618 helix: 0.32 (0.16), residues: 890 sheet: -1.27 (0.45), residues: 105 loop : -1.88 (0.26), residues: 623 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 covalent geometry : bond 0.00612 ( 8216) covalent geometry : angle 0.69809 (11453) hydrogen bonds : bond 0.06212 ( 731) hydrogen bonds : angle 6.80020 ( 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 : 0.203 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0315 time to fit residues: 3.4124 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 : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 127 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 144 optimal weight: 0.0050 chunk 45 optimal weight: 7.9990 chunk 147 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 overall best weight: 3.4000 ------------------------------------------------------------------------------- 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 = 0.3159 r_free = 0.3159 target = 0.056598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.039293 restraints weight = 309709.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.040461 restraints weight = 219758.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.041367 restraints weight = 136844.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.041502 restraints weight = 107401.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.041720 restraints weight = 105960.007| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 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 = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.9857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8216 Z= 0.176 Angle : 0.433 4.287 11453 Z= 0.284 Chirality : 0.040 0.132 1556 Planarity : 0.002 0.019 1640 Dihedral : 8.479 117.986 1707 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.78 % Favored : 92.84 % 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: 0.29 (0.22), residues: 1618 helix: 1.60 (0.17), residues: 901 sheet: -1.82 (0.43), residues: 121 loop : -1.60 (0.27), 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 covalent geometry : bond 0.00244 ( 8216) covalent geometry : angle 0.43337 (11453) hydrogen bonds : bond 0.04175 ( 731) hydrogen bonds : angle 5.40363 ( 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 : 0.275 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0323 time to fit residues: 3.6117 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 82 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 94 optimal weight: 30.0000 chunk 90 optimal weight: 50.0000 chunk 5 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.3135 r_free = 0.3135 target = 0.055570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.038504 restraints weight = 267107.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.039650 restraints weight = 200395.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.039968 restraints weight = 139627.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.040874 restraints weight = 101275.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.040947 restraints weight = 91167.952| |-----------------------------------------------------------------------------| 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: 16 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 1.0357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8216 Z= 0.301 Angle : 0.540 5.328 11453 Z= 0.357 Chirality : 0.041 0.140 1556 Planarity : 0.003 0.016 1640 Dihedral : 8.721 122.287 1707 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.02 % Favored : 89.61 % 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: -0.17 (0.21), residues: 1618 helix: 1.11 (0.17), residues: 911 sheet: -1.08 (0.48), residues: 101 loop : -1.87 (0.27), residues: 606 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 covalent geometry : bond 0.00414 ( 8216) covalent geometry : angle 0.53973 (11453) hydrogen bonds : bond 0.04901 ( 731) hydrogen bonds : angle 5.95036 ( 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 : 0.218 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0310 time to fit residues: 3.4028 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 : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 93 optimal weight: 9.9990 chunk 25 optimal weight: 0.0050 chunk 106 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 15 optimal weight: 40.0000 chunk 130 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- 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 = 0.057000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.039555 restraints weight = 259573.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.041258 restraints weight = 175345.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.041934 restraints weight = 120022.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.041998 restraints weight = 95647.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.042110 restraints weight = 84730.611| |-----------------------------------------------------------------------------| r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 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 = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 1.0235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8216 Z= 0.140 Angle : 0.386 4.629 11453 Z= 0.252 Chirality : 0.040 0.134 1556 Planarity : 0.002 0.018 1640 Dihedral : 8.058 119.725 1707 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.92 % Favored : 94.71 % 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 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: 0.93 (0.22), residues: 1618 helix: 2.25 (0.17), residues: 906 sheet: -1.88 (0.44), residues: 121 loop : -1.49 (0.28), residues: 591 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 covalent geometry : bond 0.00190 ( 8216) covalent geometry : angle 0.38591 (11453) hydrogen bonds : bond 0.03574 ( 731) hydrogen bonds : angle 4.84912 ( 2086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1271.99 seconds wall clock time: 22 minutes 15.34 seconds (1335.34 seconds total)