Starting phenix.real_space_refine on Sat May 17 08:24:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w20_43736/05_2025/8w20_43736.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w20_43736/05_2025/8w20_43736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w20_43736/05_2025/8w20_43736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w20_43736/05_2025/8w20_43736.map" model { file = "/net/cci-nas-00/data/ceres_data/8w20_43736/05_2025/8w20_43736.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w20_43736/05_2025/8w20_43736.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.110 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 9462 2.51 5 N 3000 2.21 5 O 2900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15412 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 768 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 84 Chain: "C" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 2091 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 280} Link IDs: {'PTRANS': 17, 'TRANS': 387} Chain breaks: 12 Unresolved non-hydrogen bonds: 977 Unresolved non-hydrogen angles: 1275 Unresolved non-hydrogen dihedrals: 781 Unresolved non-hydrogen chiralities: 114 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 5, 'TYR:plan': 9, 'ASN:plan1': 19, 'TRP:plan': 7, 'ASP:plan': 37, 'PHE:plan': 8, 'GLU:plan': 7, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 547 Chain: "A" Number of atoms: 4279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 4279 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 329} Link IDs: {'PTRANS': 15, 'TRANS': 716} Chain breaks: 1 Unresolved non-hydrogen bonds: 1073 Unresolved non-hydrogen angles: 1358 Unresolved non-hydrogen dihedrals: 815 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 13, 'TRP:plan': 1, 'ASP:plan': 53, 'GLU:plan': 52, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 672 Chain: "D" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 756 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 69 Chain: "E" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1125 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 12, 'TRANS': 208} Unresolved non-hydrogen bonds: 497 Unresolved non-hydrogen angles: 649 Unresolved non-hydrogen dihedrals: 377 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 21, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 278 Chain: "F" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 696 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 98 Chain: "G" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1115 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 12, 'TRANS': 206} Unresolved non-hydrogen bonds: 491 Unresolved non-hydrogen angles: 641 Unresolved non-hydrogen dihedrals: 373 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 20, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 275 Chain: "H" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 728 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "I" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 2044 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 290} Link IDs: {'PTRANS': 17, 'TRANS': 387} Chain breaks: 12 Unresolved non-hydrogen bonds: 1029 Unresolved non-hydrogen angles: 1346 Unresolved non-hydrogen dihedrals: 829 Unresolved non-hydrogen chiralities: 119 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 5, 'TYR:plan': 11, 'ASN:plan1': 19, 'TRP:plan': 8, 'ASP:plan': 37, 'PHE:plan': 9, 'GLU:plan': 8, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 580 Chain: "J" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 698 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 8, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 99 Chain: "K" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1112 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PTRANS': 12, 'TRANS': 206} Unresolved non-hydrogen bonds: 494 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 375 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 20, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 275 Time building chain proxies: 9.47, per 1000 atoms: 0.61 Number of scatterers: 15412 At special positions: 0 Unit cell: (236.04, 239.412, 210.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2900 8.00 N 3000 7.00 C 9462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 71 " distance=2.11 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 222 " distance=2.03 Simple disulfide: pdb=" SG CYS D 78 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 71 " distance=2.10 Simple disulfide: pdb=" SG CYS E 192 " - pdb=" SG CYS E 222 " distance=2.03 Simple disulfide: pdb=" SG CYS F 78 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 71 " distance=2.09 Simple disulfide: pdb=" SG CYS G 192 " - pdb=" SG CYS G 222 " distance=2.03 Simple disulfide: pdb=" SG CYS H 78 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 71 " distance=2.08 Simple disulfide: pdb=" SG CYS I 192 " - pdb=" SG CYS I 222 " distance=2.03 Simple disulfide: pdb=" SG CYS J 78 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 71 " distance=2.07 Simple disulfide: pdb=" SG CYS K 192 " - pdb=" SG CYS K 222 " distance=2.02 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: 3.89 Conformation dependent library (CDL) restraints added in 2.5 seconds 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5112 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 31 sheets defined 30.5% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'B' and resid 54 through 62 removed outlier: 3.560A pdb=" N ALA B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 151 Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 67 through 80 Processing helix chain 'A' and resid 81 through 111 Proline residue: A 93 - end of helix removed outlier: 4.055A pdb=" N HIS A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 138 through 157 Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 172 through 182 Processing helix chain 'A' and resid 182 through 203 removed outlier: 3.571A pdb=" N THR A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 218 through 228 Processing helix chain 'A' and resid 228 through 335 Processing helix chain 'A' and resid 445 through 595 removed outlier: 3.716A pdb=" N THR A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ARG A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN A 514 " --> pdb=" O THR A 510 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 618 removed outlier: 3.817A pdb=" N LYS A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 631 Processing helix chain 'A' and resid 633 through 643 Processing helix chain 'A' and resid 643 through 664 removed outlier: 3.863A pdb=" N THR A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 677 Processing helix chain 'A' and resid 680 through 690 Processing helix chain 'A' and resid 690 through 696 Processing helix chain 'A' and resid 696 through 709 removed outlier: 3.505A pdb=" N VAL A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 726 Processing helix chain 'A' and resid 727 through 737 Processing helix chain 'A' and resid 737 through 758 removed outlier: 3.511A pdb=" N GLY A 741 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 772 Processing helix chain 'A' and resid 773 through 783 Processing helix chain 'A' and resid 783 through 889 Processing helix chain 'D' and resid 54 through 62 removed outlier: 3.551A pdb=" N ALA D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 151 Processing helix chain 'E' and resid 69 through 73 Processing helix chain 'E' and resid 238 through 247 Processing helix chain 'F' and resid 54 through 62 removed outlier: 3.533A pdb=" N ALA F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 151 Processing helix chain 'G' and resid 69 through 73 Processing helix chain 'G' and resid 238 through 247 Processing helix chain 'H' and resid 54 through 62 removed outlier: 3.538A pdb=" N ALA H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 151 Processing helix chain 'I' and resid 69 through 73 Processing helix chain 'I' and resid 238 through 247 Processing helix chain 'J' and resid 54 through 62 Processing helix chain 'J' and resid 148 through 151 Processing helix chain 'K' and resid 69 through 73 Processing helix chain 'K' and resid 238 through 247 Processing sheet with id=AA1, first strand: chain 'B' and resid 73 through 76 removed outlier: 3.781A pdb=" N CYS B 96 " --> pdb=" O THR B 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 104 through 106 removed outlier: 3.508A pdb=" N ALA B 104 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR B 126 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LEU B 162 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS B 124 " --> pdb=" O LEU B 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 48 removed outlier: 3.535A pdb=" N GLU C 112 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THR C 91 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 137 through 138 removed outlier: 7.310A pdb=" N ARG C 137 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N GLY C 212 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE C 233 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER C 217 " --> pdb=" O ASP C 231 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASP C 231 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N VAL C 176 " --> pdb=" O ALA C 180 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN C 182 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ASP C 203 " --> pdb=" O PRO C 148 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL C 152 " --> pdb=" O PRO C 199 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY C 212 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLN C 202 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU C 210 " --> pdb=" O GLN C 202 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LYS C 204 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU C 208 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 259 through 262 Processing sheet with id=AA6, first strand: chain 'C' and resid 333 through 334 Processing sheet with id=AA7, first strand: chain 'C' and resid 369 through 369 Processing sheet with id=AA8, first strand: chain 'C' and resid 409 through 413 removed outlier: 3.607A pdb=" N THR C 411 " --> pdb=" O THR C 425 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N THR C 425 " --> pdb=" O THR C 411 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 485 through 486 Processing sheet with id=AB1, first strand: chain 'D' and resid 73 through 76 removed outlier: 3.609A pdb=" N CYS D 96 " --> pdb=" O THR D 76 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 104 through 106 removed outlier: 6.755A pdb=" N THR D 126 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU D 162 " --> pdb=" O LYS D 124 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LYS D 124 " --> pdb=" O LEU D 162 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 43 through 48 removed outlier: 3.511A pdb=" N GLU E 112 " --> pdb=" O ARG E 125 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N THR E 91 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 137 through 138 removed outlier: 7.325A pdb=" N ARG E 137 " --> pdb=" O LEU E 210 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N GLY E 212 " --> pdb=" O ARG E 137 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE E 233 " --> pdb=" O ASN E 215 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N SER E 217 " --> pdb=" O ASP E 231 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASP E 231 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA E 180 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL E 176 " --> pdb=" O ALA E 180 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASN E 182 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ASP E 203 " --> pdb=" O PRO E 148 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL E 152 " --> pdb=" O PRO E 199 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY E 212 " --> pdb=" O LEU E 200 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLN E 202 " --> pdb=" O LEU E 210 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU E 210 " --> pdb=" O GLN E 202 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LYS E 204 " --> pdb=" O LEU E 208 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU E 208 " --> pdb=" O LYS E 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 73 through 76 removed outlier: 3.718A pdb=" N CYS F 96 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN F 85 " --> pdb=" O ILE F 116 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE F 116 " --> pdb=" O GLN F 85 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET F 87 " --> pdb=" O TYR F 114 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 104 through 106 removed outlier: 6.717A pdb=" N THR F 126 " --> pdb=" O ILE F 160 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU F 162 " --> pdb=" O LYS F 124 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS F 124 " --> pdb=" O LEU F 162 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 43 through 48 removed outlier: 3.517A pdb=" N GLU G 112 " --> pdb=" O ARG G 125 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR G 91 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 137 through 138 removed outlier: 7.317A pdb=" N ARG G 137 " --> pdb=" O LEU G 210 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N GLY G 212 " --> pdb=" O ARG G 137 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE G 233 " --> pdb=" O ASN G 215 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER G 217 " --> pdb=" O ASP G 231 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASP G 231 " --> pdb=" O SER G 217 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA G 180 " --> pdb=" O VAL G 176 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL G 176 " --> pdb=" O ALA G 180 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN G 182 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ASP G 203 " --> pdb=" O PRO G 148 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL G 152 " --> pdb=" O PRO G 199 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU G 200 " --> pdb=" O VAL G 211 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 73 through 76 removed outlier: 3.664A pdb=" N CYS H 96 " --> pdb=" O THR H 76 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 104 through 106 removed outlier: 3.525A pdb=" N ALA H 104 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR H 126 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU H 162 " --> pdb=" O LYS H 124 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LYS H 124 " --> pdb=" O LEU H 162 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 33 through 34 removed outlier: 3.789A pdb=" N ASP I 33 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ASP I 203 " --> pdb=" O PRO I 148 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL I 152 " --> pdb=" O PRO I 199 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU I 200 " --> pdb=" O VAL I 211 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ARG I 137 " --> pdb=" O LEU I 210 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N GLY I 212 " --> pdb=" O ARG I 137 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 33 through 34 removed outlier: 3.789A pdb=" N ASP I 33 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN I 182 " --> pdb=" O THR I 174 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL I 176 " --> pdb=" O ALA I 180 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA I 180 " --> pdb=" O VAL I 176 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ASP I 231 " --> pdb=" O SER I 217 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N SER I 217 " --> pdb=" O ASP I 231 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE I 233 " --> pdb=" O ASN I 215 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ARG I 137 " --> pdb=" O LEU I 210 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N GLY I 212 " --> pdb=" O ARG I 137 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 43 through 48 removed outlier: 3.515A pdb=" N GLU I 112 " --> pdb=" O ARG I 125 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N THR I 91 " --> pdb=" O VAL I 110 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 259 through 262 Processing sheet with id=AC6, first strand: chain 'I' and resid 333 through 334 Processing sheet with id=AC7, first strand: chain 'I' and resid 369 through 369 Processing sheet with id=AC8, first strand: chain 'I' and resid 409 through 413 removed outlier: 3.590A pdb=" N THR I 411 " --> pdb=" O THR I 425 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N THR I 425 " --> pdb=" O THR I 411 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 485 through 486 Processing sheet with id=AD1, first strand: chain 'J' and resid 73 through 76 removed outlier: 3.608A pdb=" N CYS J 96 " --> pdb=" O THR J 76 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 104 through 106 removed outlier: 6.721A pdb=" N THR J 126 " --> pdb=" O ILE J 160 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU J 162 " --> pdb=" O LYS J 124 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS J 124 " --> pdb=" O LEU J 162 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 43 through 48 removed outlier: 3.532A pdb=" N GLU K 112 " --> pdb=" O ARG K 125 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N THR K 91 " --> pdb=" O VAL K 110 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 137 through 138 removed outlier: 7.333A pdb=" N ARG K 137 " --> pdb=" O LEU K 210 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N GLY K 212 " --> pdb=" O ARG K 137 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE K 233 " --> pdb=" O ASN K 215 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N SER K 217 " --> pdb=" O ASP K 231 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ASP K 231 " --> pdb=" O SER K 217 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA K 180 " --> pdb=" O VAL K 176 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N VAL K 176 " --> pdb=" O ALA K 180 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASN K 182 " --> pdb=" O THR K 174 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASP K 203 " --> pdb=" O PRO K 148 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL K 152 " --> pdb=" O PRO K 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU K 200 " --> pdb=" O VAL K 211 " (cutoff:3.500A) 1083 hydrogen bonds defined for protein. 3021 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: 6.39 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 2867 1.26 - 1.40: 3476 1.40 - 1.55: 9101 1.55 - 1.69: 80 1.69 - 1.83: 70 Bond restraints: 15594 Sorted by residual: bond pdb=" C LYS B 102 " pdb=" O LYS B 102 " ideal model delta sigma weight residual 1.235 1.121 0.114 1.30e-02 5.92e+03 7.73e+01 bond pdb=" CA ARG A 234 " pdb=" C ARG A 234 " ideal model delta sigma weight residual 1.524 1.431 0.093 1.26e-02 6.30e+03 5.41e+01 bond pdb=" C LYS D 124 " pdb=" O LYS D 124 " ideal model delta sigma weight residual 1.236 1.169 0.066 1.21e-02 6.83e+03 3.01e+01 bond pdb=" N ASP A 599 " pdb=" CA ASP A 599 " ideal model delta sigma weight residual 1.457 1.491 -0.035 6.40e-03 2.44e+04 2.94e+01 bond pdb=" CA LEU A 638 " pdb=" C LEU A 638 " ideal model delta sigma weight residual 1.524 1.592 -0.068 1.28e-02 6.10e+03 2.78e+01 ... (remaining 15589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 20691 2.75 - 5.51: 605 5.51 - 8.26: 234 8.26 - 11.01: 11 11.01 - 13.76: 3 Bond angle restraints: 21544 Sorted by residual: angle pdb=" N TRP A 645 " pdb=" CA TRP A 645 " pdb=" C TRP A 645 " ideal model delta sigma weight residual 111.07 100.55 10.52 1.07e+00 8.73e-01 9.66e+01 angle pdb=" N ASP A 639 " pdb=" CA ASP A 639 " pdb=" C ASP A 639 " ideal model delta sigma weight residual 111.33 122.89 -11.56 1.21e+00 6.83e-01 9.13e+01 angle pdb=" N VAL A 637 " pdb=" CA VAL A 637 " pdb=" C VAL A 637 " ideal model delta sigma weight residual 111.00 101.46 9.54 1.09e+00 8.42e-01 7.66e+01 angle pdb=" C GLY A 619 " pdb=" N PRO A 620 " pdb=" CA PRO A 620 " ideal model delta sigma weight residual 119.32 128.78 -9.46 1.14e+00 7.69e-01 6.89e+01 angle pdb=" N ALA A 257 " pdb=" CA ALA A 257 " pdb=" C ALA A 257 " ideal model delta sigma weight residual 111.36 102.36 9.00 1.09e+00 8.42e-01 6.81e+01 ... (remaining 21539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 8989 16.01 - 32.02: 71 32.02 - 48.02: 33 48.02 - 64.03: 16 64.03 - 80.04: 2 Dihedral angle restraints: 9111 sinusoidal: 1193 harmonic: 7918 Sorted by residual: dihedral pdb=" C TYR J 105 " pdb=" N TYR J 105 " pdb=" CA TYR J 105 " pdb=" CB TYR J 105 " ideal model delta harmonic sigma weight residual -122.60 -103.38 -19.22 0 2.50e+00 1.60e-01 5.91e+01 dihedral pdb=" CB CYS K 192 " pdb=" SG CYS K 192 " pdb=" SG CYS K 222 " pdb=" CB CYS K 222 " ideal model delta sinusoidal sigma weight residual 93.00 152.47 -59.47 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CB CYS C 192 " pdb=" SG CYS C 192 " pdb=" SG CYS C 222 " pdb=" CB CYS C 222 " ideal model delta sinusoidal sigma weight residual 93.00 152.19 -59.19 1 1.00e+01 1.00e-02 4.68e+01 ... (remaining 9108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2321 0.084 - 0.168: 305 0.168 - 0.253: 22 0.253 - 0.337: 4 0.337 - 0.421: 4 Chirality restraints: 2656 Sorted by residual: chirality pdb=" CA THR A 643 " pdb=" N THR A 643 " pdb=" C THR A 643 " pdb=" CB THR A 643 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CA LEU A 805 " pdb=" N LEU A 805 " pdb=" C LEU A 805 " pdb=" CB LEU A 805 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CG LEU A 806 " pdb=" CB LEU A 806 " pdb=" CD1 LEU A 806 " pdb=" CD2 LEU A 806 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 2653 not shown) Planarity restraints: 3056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 762 " -0.017 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C VAL A 762 " 0.063 2.00e-02 2.50e+03 pdb=" O VAL A 762 " -0.025 2.00e-02 2.50e+03 pdb=" N GLN A 763 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 638 " 0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C LEU A 638 " -0.057 2.00e-02 2.50e+03 pdb=" O LEU A 638 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP A 639 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 233 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C ALA A 233 " -0.056 2.00e-02 2.50e+03 pdb=" O ALA A 233 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG A 234 " 0.019 2.00e-02 2.50e+03 ... (remaining 3053 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4786 2.80 - 3.33: 12849 3.33 - 3.85: 23389 3.85 - 4.38: 22958 4.38 - 4.90: 41184 Nonbonded interactions: 105166 Sorted by model distance: nonbonded pdb=" O VAL A 600 " pdb=" N ALA A 602 " model vdw 2.278 3.120 nonbonded pdb=" CB GLU H 82 " pdb=" OE1 GLN H 85 " model vdw 2.404 3.440 nonbonded pdb=" O TYR F 147 " pdb=" C GLY F 148 " model vdw 2.492 3.270 nonbonded pdb=" O TYR H 147 " pdb=" C GLY H 148 " model vdw 2.501 3.270 nonbonded pdb=" O TYR D 147 " pdb=" C GLY D 148 " model vdw 2.506 3.270 ... (remaining 105161 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 'B' and ((resid 45 through 51 and (name N or name CA or name C or name O \ or name CB )) or resid 52 through 56 or (resid 57 through 62 and (name N or name \ CA or name C or name O or name CB )) or (resid 63 through 68 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 69 through 77 and (name N or na \ me CA or name C or name O or name CB )) or resid 78 through 83 or (resid 84 thro \ ugh 86 and (name N or name CA or name C or name O or name CB )) or resid 87 thro \ ugh 98 or (resid 99 through 102 and (name N or name CA or name C or name O or na \ me CB )) or resid 103 through 104 or (resid 105 through 110 and (name N or name \ CA or name C or name O or name CB )) or resid 111 through 115 or (resid 116 and \ (name N or name CA or name C or name O or name CB )) or resid 117 through 146 or \ (resid 147 and (name N or name CA or name C or name O or name CB )) or resid 14 \ 8 through 161 or (resid 162 through 165 and (name N or name CA or name C or name \ O or name CB )))) selection = (chain 'D' and ((resid 45 through 51 and (name N or name CA or name C or name O \ or name CB )) or resid 52 through 65 or (resid 66 through 68 and (name N or name \ CA or name C or name O or name CB )) or (resid 69 through 77 and (name N or nam \ e CA or name C or name O or name CB )) or resid 78 through 83 or (resid 84 throu \ gh 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throu \ gh 99 or (resid 100 through 102 and (name N or name CA or name C or name O or na \ me CB )) or resid 103 through 104 or (resid 105 through 110 and (name N or name \ CA or name C or name O or name CB )) or resid 111 or (resid 112 through 113 and \ (name N or name CA or name C or name O or name CB )) or resid 114 through 115 or \ (resid 116 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 7 through 123 or (resid 124 through 131 and (name N or name CA or name C or name \ O or name CB )) or (resid 132 through 139 and (name N or name CA or name C or n \ ame O or name CB )) or resid 140 through 146 or (resid 147 and (name N or name C \ A or name C or name O or name CB )) or resid 148 or (resid 149 through 150 and ( \ name N or name CA or name C or name O or name CB )) or resid 151 through 161 or \ (resid 162 through 165 and (name N or name CA or name C or name O or name CB ))) \ ) selection = (chain 'F' and ((resid 45 through 51 and (name N or name CA or name C or name O \ or name CB )) or resid 52 through 57 or (resid 58 through 62 and (name N or name \ CA or name C or name O or name CB )) or resid 63 through 83 or (resid 84 throug \ h 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throug \ h 91 or (resid 92 through 94 and (name N or name CA or name C or name O or name \ CB )) or resid 95 through 115 or (resid 116 and (name N or name CA or name C or \ name O or name CB )) or resid 117 through 136 or (resid 137 through 139 and (nam \ e N or name CA or name C or name O or name CB )) or resid 140 through 146 or (re \ sid 147 and (name N or name CA or name C or name O or name CB )) or resid 148 th \ rough 161 or (resid 162 through 165 and (name N or name CA or name C or name O o \ r name CB )))) selection = (chain 'H' and (resid 45 through 65 or (resid 66 through 68 and (name N or name \ CA or name C or name O or name CB )) or (resid 69 through 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 83 or (resid 84 throug \ h 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throug \ h 99 or (resid 100 through 102 and (name N or name CA or name C or name O or nam \ e CB )) or resid 103 through 104 or (resid 105 through 110 and (name N or name C \ A or name C or name O or name CB )) or resid 111 through 136 or (resid 137 throu \ gh 139 and (name N or name CA or name C or name O or name CB )) or resid 140 thr \ ough 148 or (resid 149 through 150 and (name N or name CA or name C or name O or \ name CB )) or resid 151 through 161 or (resid 162 through 165 and (name N or na \ me CA or name C or name O or name CB )))) selection = (chain 'J' and ((resid 45 through 51 and (name N or name CA or name C or name O \ or name CB )) or resid 52 through 64 or (resid 65 through 68 and (name N or name \ CA or name C or name O or name CB )) or (resid 69 through 77 and (name N or nam \ e CA or name C or name O or name CB )) or resid 78 through 104 or (resid 105 thr \ ough 110 and (name N or name CA or name C or name O or name CB )) or resid 111 t \ hrough 146 or (resid 147 and (name N or name CA or name C or name O or name CB ) \ ) or resid 148 through 165)) } ncs_group { reference = (chain 'C' and (resid 30 through 41 or (resid 42 through 48 and (name N or name \ CA or name C or name O or name CB )) or (resid 49 through 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 through 63 or (resid 64 throug \ h 70 and (name N or name CA or name C or name O or name CB )) or resid 71 throug \ h 117 or (resid 118 through 130 and (name N or name CA or name C or name O or na \ me CB )) or resid 131 through 190 or (resid 191 and (name N or name CA or name C \ or name O or name CB )) or resid 192 through 222 or (resid 223 and (name N or n \ ame CA or name C or name O or name CB )) or resid 224 through 504)) selection = (chain 'I' and (resid 30 through 165 or (resid 166 through 168 and (name N or na \ me CA or name C or name O or name CB )) or resid 169 through 504)) } ncs_group { reference = (chain 'E' and (resid 30 through 163 or (resid 164 through 168 and (name N or na \ me CA or name C or name O or name CB )) or resid 169 through 248)) selection = (chain 'G' and (resid 30 through 163 or (resid 164 through 168 and (name N or na \ me CA or name C or name O or name CB )) or resid 169 through 248)) selection = chain 'K' } 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=1.00 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 37.660 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 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 : 0.008 0.114 15609 Z= 0.498 Angle : 1.342 13.764 21574 Z= 0.946 Chirality : 0.057 0.421 2656 Planarity : 0.005 0.037 3056 Dihedral : 6.792 80.040 3954 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.59 % Favored : 97.16 % Rotamer: Outliers : 0.45 % Allowed : 0.89 % Favored : 98.66 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.16), residues: 2742 helix: 1.64 (0.16), residues: 771 sheet: 1.37 (0.21), residues: 661 loop : 0.09 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP C 64 HIS 0.003 0.001 HIS A 622 PHE 0.013 0.003 PHE F 97 TYR 0.037 0.004 TYR A 640 ARG 0.010 0.001 ARG A 753 Details of bonding type rmsd hydrogen bonds : bond 0.18848 ( 1082) hydrogen bonds : angle 6.99278 ( 3021) SS BOND : bond 0.03561 ( 15) SS BOND : angle 2.50375 ( 30) covalent geometry : bond 0.00754 (15594) covalent geometry : angle 1.33926 (21544) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.7865 (mt0) cc_final: 0.7579 (tm-30) REVERT: A 753 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8396 (mmm-85) REVERT: A 756 GLU cc_start: 0.8829 (tt0) cc_final: 0.7871 (tm-30) REVERT: D 66 LEU cc_start: 0.8618 (mp) cc_final: 0.8396 (mt) REVERT: J 105 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7223 (m-10) outliers start: 2 outliers final: 0 residues processed: 164 average time/residue: 0.2405 time to fit residues: 61.9045 Evaluate side-chains 108 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 233 optimal weight: 8.9990 chunk 209 optimal weight: 0.3980 chunk 116 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 251 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 622 HIS A 650 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.180511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.147846 restraints weight = 40081.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.138253 restraints weight = 59462.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.136461 restraints weight = 43612.079| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15609 Z= 0.181 Angle : 0.576 8.457 21574 Z= 0.324 Chirality : 0.044 0.196 2656 Planarity : 0.005 0.054 3056 Dihedral : 4.339 22.762 2839 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.45 % Allowed : 2.67 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.16), residues: 2742 helix: 2.85 (0.16), residues: 802 sheet: 1.03 (0.20), residues: 744 loop : 0.17 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 645 HIS 0.008 0.002 HIS B 72 PHE 0.022 0.002 PHE F 95 TYR 0.022 0.002 TYR H 114 ARG 0.010 0.001 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.05578 ( 1082) hydrogen bonds : angle 4.63442 ( 3021) SS BOND : bond 0.01298 ( 15) SS BOND : angle 1.06307 ( 30) covalent geometry : bond 0.00356 (15594) covalent geometry : angle 0.57530 (21544) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 1.630 Fit side-chains REVERT: A 222 MET cc_start: 0.8229 (mtp) cc_final: 0.7978 (mtp) outliers start: 2 outliers final: 1 residues processed: 112 average time/residue: 0.1939 time to fit residues: 38.0709 Evaluate side-chains 89 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 167 optimal weight: 10.0000 chunk 152 optimal weight: 30.0000 chunk 75 optimal weight: 4.9990 chunk 221 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 171 optimal weight: 20.0000 chunk 241 optimal weight: 0.8980 chunk 234 optimal weight: 50.0000 chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 622 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.172664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.145398 restraints weight = 39526.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.138372 restraints weight = 59752.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.134045 restraints weight = 61566.276| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 15609 Z= 0.350 Angle : 0.749 10.477 21574 Z= 0.427 Chirality : 0.048 0.240 2656 Planarity : 0.006 0.081 3056 Dihedral : 4.976 30.468 2839 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.67 % Allowed : 6.24 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.16), residues: 2742 helix: 2.64 (0.17), residues: 786 sheet: 0.43 (0.20), residues: 717 loop : -0.18 (0.19), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.005 TRP I 161 HIS 0.017 0.004 HIS B 72 PHE 0.067 0.005 PHE B 97 TYR 0.046 0.004 TYR D 105 ARG 0.009 0.001 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.07309 ( 1082) hydrogen bonds : angle 5.12710 ( 3021) SS BOND : bond 0.01256 ( 15) SS BOND : angle 1.17443 ( 30) covalent geometry : bond 0.00729 (15594) covalent geometry : angle 0.74857 (21544) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 2.078 Fit side-chains revert: symmetry clash REVERT: C 52 TYR cc_start: 0.8174 (t80) cc_final: 0.7941 (t80) REVERT: D 75 MET cc_start: 0.7831 (ttt) cc_final: 0.7499 (ttt) REVERT: H 105 TYR cc_start: 0.8196 (p90) cc_final: 0.7994 (p90) REVERT: J 75 MET cc_start: 0.9102 (ttm) cc_final: 0.8840 (ttm) outliers start: 3 outliers final: 2 residues processed: 93 average time/residue: 0.1828 time to fit residues: 31.2644 Evaluate side-chains 79 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 9 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 109 optimal weight: 0.5980 chunk 259 optimal weight: 20.0000 chunk 212 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 HIS H 72 HIS H 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.170652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.140952 restraints weight = 39254.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.135878 restraints weight = 69275.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.134198 restraints weight = 54524.774| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 15609 Z= 0.333 Angle : 0.724 9.496 21574 Z= 0.408 Chirality : 0.047 0.237 2656 Planarity : 0.006 0.078 3056 Dihedral : 5.016 27.957 2839 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.22 % Allowed : 7.13 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.16), residues: 2742 helix: 2.25 (0.17), residues: 786 sheet: 0.06 (0.20), residues: 688 loop : -0.47 (0.18), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP H 117 HIS 0.014 0.004 HIS B 72 PHE 0.044 0.004 PHE D 95 TYR 0.042 0.004 TYR B 114 ARG 0.006 0.001 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.07179 ( 1082) hydrogen bonds : angle 5.06120 ( 3021) SS BOND : bond 0.01276 ( 15) SS BOND : angle 1.86616 ( 30) covalent geometry : bond 0.00700 (15594) covalent geometry : angle 0.72126 (21544) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 1.739 Fit side-chains REVERT: B 75 MET cc_start: 0.7891 (ttt) cc_final: 0.7451 (ttt) REVERT: A 63 TRP cc_start: 0.8896 (t-100) cc_final: 0.8669 (t-100) REVERT: H 100 MET cc_start: 0.6776 (mmp) cc_final: 0.6232 (mmm) outliers start: 1 outliers final: 1 residues processed: 86 average time/residue: 0.1829 time to fit residues: 28.4065 Evaluate side-chains 77 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 9 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 141 optimal weight: 0.0070 chunk 109 optimal weight: 0.5980 chunk 84 optimal weight: 7.9990 chunk 264 optimal weight: 20.0000 chunk 127 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 160 optimal weight: 0.6980 chunk 176 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- 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 = 0.4309 r_free = 0.4309 target = 0.175546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.146821 restraints weight = 39591.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.141744 restraints weight = 64149.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.138653 restraints weight = 47934.175| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15609 Z= 0.153 Angle : 0.507 5.810 21574 Z= 0.284 Chirality : 0.043 0.147 2656 Planarity : 0.004 0.064 3056 Dihedral : 4.146 22.157 2839 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.17), residues: 2742 helix: 3.17 (0.17), residues: 789 sheet: 0.03 (0.20), residues: 697 loop : -0.27 (0.19), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 117 HIS 0.012 0.002 HIS B 72 PHE 0.022 0.002 PHE B 97 TYR 0.028 0.002 TYR J 147 ARG 0.005 0.000 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.05187 ( 1082) hydrogen bonds : angle 4.28756 ( 3021) SS BOND : bond 0.00353 ( 15) SS BOND : angle 1.06997 ( 30) covalent geometry : bond 0.00315 (15594) covalent geometry : angle 0.50610 (21544) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.744 Fit side-chains revert: symmetry clash REVERT: A 787 MET cc_start: 0.7985 (ttt) cc_final: 0.7663 (ttm) REVERT: H 87 MET cc_start: 0.7619 (mtp) cc_final: 0.7283 (mtm) REVERT: H 100 MET cc_start: 0.6835 (mmp) cc_final: 0.6262 (mmm) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2170 time to fit residues: 36.4809 Evaluate side-chains 81 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 164 optimal weight: 0.0670 chunk 107 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 276 optimal weight: 40.0000 chunk 269 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 151 optimal weight: 40.0000 chunk 264 optimal weight: 3.9990 chunk 235 optimal weight: 50.0000 chunk 179 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.174529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.147608 restraints weight = 39272.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.139810 restraints weight = 59069.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.136512 restraints weight = 59882.486| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15609 Z= 0.171 Angle : 0.523 6.048 21574 Z= 0.293 Chirality : 0.043 0.157 2656 Planarity : 0.004 0.065 3056 Dihedral : 4.082 22.947 2839 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.17), residues: 2742 helix: 3.36 (0.17), residues: 789 sheet: -0.06 (0.20), residues: 725 loop : -0.19 (0.19), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 117 HIS 0.011 0.002 HIS B 72 PHE 0.028 0.002 PHE D 95 TYR 0.021 0.002 TYR D 105 ARG 0.006 0.001 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.05303 ( 1082) hydrogen bonds : angle 4.20499 ( 3021) SS BOND : bond 0.00335 ( 15) SS BOND : angle 1.07013 ( 30) covalent geometry : bond 0.00358 (15594) covalent geometry : angle 0.52176 (21544) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.469 Fit side-chains REVERT: B 75 MET cc_start: 0.8175 (ttt) cc_final: 0.7942 (ttt) REVERT: A 787 MET cc_start: 0.8007 (ttt) cc_final: 0.7662 (ttm) REVERT: H 87 MET cc_start: 0.7047 (mtp) cc_final: 0.6839 (mtm) REVERT: H 100 MET cc_start: 0.6760 (mmp) cc_final: 0.6191 (mmm) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1715 time to fit residues: 28.6985 Evaluate side-chains 78 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 219 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 191 optimal weight: 30.0000 chunk 29 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 245 optimal weight: 0.2980 chunk 133 optimal weight: 7.9990 chunk 189 optimal weight: 7.9990 chunk 176 optimal weight: 20.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.166507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.139070 restraints weight = 39799.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.131842 restraints weight = 57624.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.127788 restraints weight = 59077.380| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 15609 Z= 0.350 Angle : 0.733 9.193 21574 Z= 0.415 Chirality : 0.047 0.202 2656 Planarity : 0.006 0.077 3056 Dihedral : 5.012 33.414 2839 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.17), residues: 2742 helix: 2.53 (0.17), residues: 783 sheet: -0.46 (0.20), residues: 733 loop : -0.42 (0.19), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.004 TRP H 117 HIS 0.018 0.004 HIS B 72 PHE 0.044 0.004 PHE B 97 TYR 0.059 0.004 TYR H 114 ARG 0.007 0.001 ARG H 89 Details of bonding type rmsd hydrogen bonds : bond 0.07102 ( 1082) hydrogen bonds : angle 5.01537 ( 3021) SS BOND : bond 0.00451 ( 15) SS BOND : angle 1.45154 ( 30) covalent geometry : bond 0.00745 (15594) covalent geometry : angle 0.73174 (21544) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 75 MET cc_start: 0.8111 (ttt) cc_final: 0.7786 (ttt) REVERT: A 787 MET cc_start: 0.8435 (ttt) cc_final: 0.8103 (mtp) REVERT: H 100 MET cc_start: 0.7125 (mmp) cc_final: 0.6608 (mmm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1694 time to fit residues: 24.9071 Evaluate side-chains 73 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 131 optimal weight: 0.8980 chunk 26 optimal weight: 20.0000 chunk 171 optimal weight: 20.0000 chunk 209 optimal weight: 6.9990 chunk 267 optimal weight: 50.0000 chunk 147 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 164 optimal weight: 0.3980 chunk 12 optimal weight: 10.0000 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.169235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.142021 restraints weight = 39786.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.135305 restraints weight = 61733.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.132123 restraints weight = 61401.467| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15609 Z= 0.193 Angle : 0.554 7.309 21574 Z= 0.310 Chirality : 0.044 0.218 2656 Planarity : 0.005 0.063 3056 Dihedral : 4.405 27.920 2839 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.17), residues: 2742 helix: 3.09 (0.17), residues: 786 sheet: -0.35 (0.20), residues: 707 loop : -0.38 (0.19), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP H 117 HIS 0.015 0.003 HIS B 72 PHE 0.034 0.003 PHE D 95 TYR 0.025 0.002 TYR B 114 ARG 0.004 0.001 ARG H 89 Details of bonding type rmsd hydrogen bonds : bond 0.05584 ( 1082) hydrogen bonds : angle 4.44800 ( 3021) SS BOND : bond 0.00316 ( 15) SS BOND : angle 1.04880 ( 30) covalent geometry : bond 0.00410 (15594) covalent geometry : angle 0.55325 (21544) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.494 Fit side-chains revert: symmetry clash REVERT: A 787 MET cc_start: 0.8199 (ttt) cc_final: 0.7934 (mtp) REVERT: H 100 MET cc_start: 0.7011 (mmp) cc_final: 0.6515 (mmm) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1699 time to fit residues: 27.2625 Evaluate side-chains 78 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 148 optimal weight: 30.0000 chunk 194 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 250 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 195 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 210 optimal weight: 9.9990 chunk 59 optimal weight: 0.1980 chunk 240 optimal weight: 50.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.167691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.141095 restraints weight = 39491.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.133250 restraints weight = 60329.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.130360 restraints weight = 63867.727| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.5933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 15609 Z= 0.259 Angle : 0.635 8.455 21574 Z= 0.357 Chirality : 0.045 0.215 2656 Planarity : 0.005 0.069 3056 Dihedral : 4.721 31.485 2839 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.17), residues: 2742 helix: 2.88 (0.17), residues: 785 sheet: -0.62 (0.19), residues: 730 loop : -0.42 (0.19), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP H 117 HIS 0.015 0.003 HIS B 72 PHE 0.036 0.003 PHE B 95 TYR 0.034 0.003 TYR H 114 ARG 0.007 0.001 ARG H 89 Details of bonding type rmsd hydrogen bonds : bond 0.06341 ( 1082) hydrogen bonds : angle 4.74314 ( 3021) SS BOND : bond 0.00385 ( 15) SS BOND : angle 1.27534 ( 30) covalent geometry : bond 0.00552 (15594) covalent geometry : angle 0.63409 (21544) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 75 MET cc_start: 0.7637 (ttt) cc_final: 0.7266 (ttt) REVERT: C 42 PHE cc_start: 0.7793 (p90) cc_final: 0.7464 (p90) REVERT: A 787 MET cc_start: 0.8245 (ttt) cc_final: 0.8002 (mtp) REVERT: H 100 MET cc_start: 0.7020 (mmp) cc_final: 0.6527 (mmm) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1804 time to fit residues: 26.9443 Evaluate side-chains 75 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 0.0470 chunk 217 optimal weight: 0.0010 chunk 245 optimal weight: 0.0070 chunk 203 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 234 optimal weight: 50.0000 chunk 122 optimal weight: 7.9990 chunk 164 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 162 optimal weight: 0.6980 overall best weight: 0.2902 ------------------------------------------------------------------------------- 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 = 0.4294 r_free = 0.4294 target = 0.176387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.145737 restraints weight = 40438.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.141672 restraints weight = 61586.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.139383 restraints weight = 55710.768| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15609 Z= 0.102 Angle : 0.451 5.309 21574 Z= 0.249 Chirality : 0.042 0.144 2656 Planarity : 0.004 0.053 3056 Dihedral : 3.718 22.200 2839 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.17), residues: 2742 helix: 3.68 (0.17), residues: 787 sheet: -0.22 (0.20), residues: 711 loop : -0.19 (0.20), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 117 HIS 0.005 0.001 HIS B 72 PHE 0.017 0.002 PHE J 144 TYR 0.014 0.001 TYR A 640 ARG 0.003 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 1082) hydrogen bonds : angle 3.96861 ( 3021) SS BOND : bond 0.00167 ( 15) SS BOND : angle 0.78169 ( 30) covalent geometry : bond 0.00201 (15594) covalent geometry : angle 0.45073 (21544) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 42 PHE cc_start: 0.7512 (p90) cc_final: 0.7212 (p90) REVERT: A 787 MET cc_start: 0.7890 (ttt) cc_final: 0.7662 (mtp) REVERT: H 100 MET cc_start: 0.7546 (mmp) cc_final: 0.7117 (mmm) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1773 time to fit residues: 30.0658 Evaluate side-chains 83 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 23 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 190 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 239 optimal weight: 50.0000 chunk 255 optimal weight: 0.5980 chunk 167 optimal weight: 10.0000 chunk 179 optimal weight: 9.9990 chunk 226 optimal weight: 50.0000 chunk 214 optimal weight: 5.9990 chunk 38 optimal weight: 30.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 HIS ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.161572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.135234 restraints weight = 40355.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.125822 restraints weight = 64519.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.123516 restraints weight = 66957.412| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.6468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.154 15609 Z= 0.477 Angle : 0.875 12.166 21574 Z= 0.495 Chirality : 0.051 0.252 2656 Planarity : 0.007 0.074 3056 Dihedral : 5.550 34.605 2839 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.56 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2742 helix: 2.02 (0.18), residues: 784 sheet: -0.72 (0.20), residues: 686 loop : -0.81 (0.19), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.005 TRP H 117 HIS 0.017 0.004 HIS B 72 PHE 0.069 0.006 PHE B 97 TYR 0.061 0.006 TYR H 114 ARG 0.008 0.001 ARG J 89 Details of bonding type rmsd hydrogen bonds : bond 0.08170 ( 1082) hydrogen bonds : angle 5.64142 ( 3021) SS BOND : bond 0.00658 ( 15) SS BOND : angle 1.93598 ( 30) covalent geometry : bond 0.01021 (15594) covalent geometry : angle 0.87268 (21544) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4945.55 seconds wall clock time: 87 minutes 6.88 seconds (5226.88 seconds total)