Starting phenix.real_space_refine on Fri Jun 13 21:59:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w20_43736/06_2025/8w20_43736.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w20_43736/06_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_43736/06_2025/8w20_43736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w20_43736/06_2025/8w20_43736.map" model { file = "/net/cci-nas-00/data/ceres_data/8w20_43736/06_2025/8w20_43736.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w20_43736/06_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-5710/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: 10.63, per 1000 atoms: 0.69 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: 4.34 Conformation dependent library (CDL) restraints added in 2.8 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: 2.55 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: 8.14 Time building geometry restraints manager: 5.08 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: 2.180 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: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 43.820 Find NCS groups from input model: 0.640 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: 0.020 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.860 ------------------------------------------------------------------------------- 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 : 1.384 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: 0.2512 time to fit residues: 63.9816 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 : 1.718 ------------------------------------------------------------------------------- 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 = 0.180489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.148306 restraints weight = 40052.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.139043 restraints weight = 57222.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.135014 restraints weight = 44601.840| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15609 Z= 0.180 Angle : 0.577 8.408 21574 Z= 0.325 Chirality : 0.043 0.195 2656 Planarity : 0.005 0.056 3056 Dihedral : 4.336 23.014 2839 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % 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: 1.77 (0.16), residues: 2742 helix: 2.84 (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 0.05575 ( 1082) hydrogen bonds : angle 4.62932 ( 3021) SS BOND : bond 0.01052 ( 15) SS BOND : angle 1.15442 ( 30) covalent geometry : bond 0.00358 (15594) covalent geometry : angle 0.57618 (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 : 1.710 Fit side-chains revert: symmetry clash REVERT: A 222 MET cc_start: 0.8271 (mtp) cc_final: 0.8038 (mtp) outliers start: 2 outliers final: 1 residues processed: 112 average time/residue: 0.1978 time to fit residues: 39.1680 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 : 1.565 ------------------------------------------------------------------------------- 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: 0.4980 chunk 234 optimal weight: 50.0000 chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 = 0.4280 r_free = 0.4280 target = 0.172431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.145486 restraints weight = 39462.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.138550 restraints weight = 59579.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.134021 restraints weight = 64584.093| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 15609 Z= 0.340 Angle : 0.745 10.950 21574 Z= 0.424 Chirality : 0.047 0.255 2656 Planarity : 0.006 0.084 3056 Dihedral : 5.029 32.062 2839 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.67 % Allowed : 7.57 % Favored : 91.76 % 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: 1.10 (0.16), residues: 2742 helix: 2.56 (0.17), residues: 786 sheet: 0.29 (0.20), residues: 725 loop : -0.15 (0.19), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP B 117 HIS 0.015 0.004 HIS B 72 PHE 0.075 0.005 PHE B 97 TYR 0.043 0.004 TYR D 105 ARG 0.008 0.001 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.07455 ( 1082) hydrogen bonds : angle 5.16021 ( 3021) SS BOND : bond 0.01329 ( 15) SS BOND : angle 1.29254 ( 30) covalent geometry : bond 0.00714 (15594) covalent geometry : angle 0.74421 (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 94 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 2.353 Fit side-chains REVERT: A 787 MET cc_start: 0.8337 (ttt) cc_final: 0.8084 (ttm) REVERT: D 75 MET cc_start: 0.7886 (ttt) cc_final: 0.7638 (ttt) REVERT: I 161 TRP cc_start: 0.9014 (t60) cc_final: 0.8640 (t60) REVERT: J 75 MET cc_start: 0.9056 (ttm) cc_final: 0.8750 (ttm) outliers start: 3 outliers final: 2 residues processed: 94 average time/residue: 0.1841 time to fit residues: 32.1851 Evaluate side-chains 78 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 1.795 ------------------------------------------------------------------------------- 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: 0.7980 chunk 259 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 26 optimal weight: 0.0870 chunk 126 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 225 optimal weight: 7.9990 overall best weight: 1.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.172771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.145074 restraints weight = 39539.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.138021 restraints weight = 65167.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.135141 restraints weight = 60664.370| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 15609 Z= 0.250 Angle : 0.622 7.540 21574 Z= 0.351 Chirality : 0.045 0.212 2656 Planarity : 0.005 0.072 3056 Dihedral : 4.588 26.867 2839 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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: 1.04 (0.17), residues: 2742 helix: 2.76 (0.17), residues: 790 sheet: 0.15 (0.20), residues: 697 loop : -0.30 (0.19), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP H 117 HIS 0.010 0.003 HIS B 72 PHE 0.042 0.003 PHE D 95 TYR 0.027 0.003 TYR B 114 ARG 0.006 0.001 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.06250 ( 1082) hydrogen bonds : angle 4.65633 ( 3021) SS BOND : bond 0.00502 ( 15) SS BOND : angle 1.26613 ( 30) covalent geometry : bond 0.00524 (15594) covalent geometry : angle 0.62098 (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 88 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 75 MET cc_start: 0.8217 (ttt) cc_final: 0.7774 (ttt) REVERT: H 100 MET cc_start: 0.7890 (mmp) cc_final: 0.7330 (mmm) REVERT: I 161 TRP cc_start: 0.9042 (t60) cc_final: 0.8612 (t60) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1823 time to fit residues: 29.3901 Evaluate side-chains 76 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.578 ------------------------------------------------------------------------------- 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: 1.9990 chunk 94 optimal weight: 9.9990 chunk 141 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 264 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4300 r_free = 0.4300 target = 0.174306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.147393 restraints weight = 39994.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.139995 restraints weight = 61133.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.136326 restraints weight = 64894.689| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15609 Z= 0.182 Angle : 0.530 7.478 21574 Z= 0.297 Chirality : 0.043 0.148 2656 Planarity : 0.005 0.067 3056 Dihedral : 4.174 24.004 2839 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.22 % Allowed : 2.00 % Favored : 97.77 % 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: 1.23 (0.17), residues: 2742 helix: 3.18 (0.17), residues: 791 sheet: 0.04 (0.20), residues: 697 loop : -0.25 (0.19), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 117 HIS 0.011 0.003 HIS B 72 PHE 0.031 0.002 PHE B 97 TYR 0.024 0.002 TYR D 114 ARG 0.004 0.001 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.05427 ( 1082) hydrogen bonds : angle 4.26809 ( 3021) SS BOND : bond 0.00247 ( 15) SS BOND : angle 0.97584 ( 30) covalent geometry : bond 0.00376 (15594) covalent geometry : angle 0.52883 (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 90 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 1.549 Fit side-chains revert: symmetry clash REVERT: C 42 PHE cc_start: 0.7772 (p90) cc_final: 0.7560 (p90) REVERT: A 787 MET cc_start: 0.7968 (ttt) cc_final: 0.7673 (ttm) REVERT: H 100 MET cc_start: 0.6862 (mmp) cc_final: 0.6312 (mmm) REVERT: I 161 TRP cc_start: 0.8997 (t60) cc_final: 0.8646 (t60) outliers start: 1 outliers final: 1 residues processed: 90 average time/residue: 0.1740 time to fit residues: 28.9543 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 : 1.553 ------------------------------------------------------------------------------- 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: 0.2980 chunk 107 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 276 optimal weight: 40.0000 chunk 269 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 151 optimal weight: 40.0000 chunk 264 optimal weight: 0.0170 chunk 235 optimal weight: 50.0000 chunk 179 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 overall best weight: 1.6624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.173154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.146266 restraints weight = 39288.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.139536 restraints weight = 59645.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.135744 restraints weight = 64181.880| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 15609 Z= 0.219 Angle : 0.580 7.839 21574 Z= 0.326 Chirality : 0.044 0.241 2656 Planarity : 0.005 0.071 3056 Dihedral : 4.403 27.019 2839 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % 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: 1.09 (0.17), residues: 2742 helix: 3.18 (0.17), residues: 786 sheet: -0.16 (0.20), residues: 720 loop : -0.31 (0.19), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 117 HIS 0.011 0.003 HIS B 72 PHE 0.037 0.003 PHE D 95 TYR 0.029 0.003 TYR D 105 ARG 0.003 0.001 ARG A 608 Details of bonding type rmsd hydrogen bonds : bond 0.05885 ( 1082) hydrogen bonds : angle 4.44909 ( 3021) SS BOND : bond 0.00333 ( 15) SS BOND : angle 1.02391 ( 30) covalent geometry : bond 0.00464 (15594) covalent geometry : angle 0.57913 (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 88 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 75 MET cc_start: 0.8120 (ttt) cc_final: 0.7731 (ttt) REVERT: H 100 MET cc_start: 0.6799 (mmp) cc_final: 0.6222 (mmm) REVERT: I 161 TRP cc_start: 0.9032 (t60) cc_final: 0.8663 (t60) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2063 time to fit residues: 32.7630 Evaluate side-chains 77 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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: 0.5980 chunk 77 optimal weight: 8.9990 chunk 163 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 245 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 176 optimal weight: 20.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.167129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.141084 restraints weight = 40474.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.136376 restraints weight = 60461.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.132537 restraints weight = 58057.949| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.5511 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= 0.270 Angle : 0.635 8.661 21574 Z= 0.358 Chirality : 0.045 0.174 2656 Planarity : 0.005 0.070 3056 Dihedral : 4.664 25.820 2839 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % 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: 0.82 (0.17), residues: 2742 helix: 2.93 (0.17), residues: 785 sheet: -0.43 (0.19), residues: 733 loop : -0.36 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.003 TRP H 117 HIS 0.015 0.004 HIS B 72 PHE 0.037 0.004 PHE B 97 TYR 0.048 0.003 TYR H 114 ARG 0.008 0.001 ARG H 89 Details of bonding type rmsd hydrogen bonds : bond 0.06330 ( 1082) hydrogen bonds : angle 4.64424 ( 3021) SS BOND : bond 0.00311 ( 15) SS BOND : angle 1.22375 ( 30) covalent geometry : bond 0.00570 (15594) covalent geometry : angle 0.63428 (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 : 1.715 Fit side-chains revert: symmetry clash REVERT: B 75 MET cc_start: 0.8260 (ttt) cc_final: 0.8057 (ttt) REVERT: H 100 MET cc_start: 0.7039 (mmp) cc_final: 0.6548 (mmm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1763 time to fit residues: 26.0384 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 : 1.677 ------------------------------------------------------------------------------- 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: 8.9990 chunk 267 optimal weight: 40.0000 chunk 147 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 164 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 overall best weight: 1.6982 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.167866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.141255 restraints weight = 40178.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.134579 restraints weight = 61083.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.131637 restraints weight = 61099.768| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 15609 Z= 0.224 Angle : 0.577 7.827 21574 Z= 0.324 Chirality : 0.044 0.229 2656 Planarity : 0.005 0.065 3056 Dihedral : 4.458 30.523 2839 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: 0.90 (0.17), residues: 2742 helix: 3.06 (0.17), residues: 787 sheet: -0.36 (0.20), residues: 707 loop : -0.40 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 117 HIS 0.015 0.003 HIS B 72 PHE 0.035 0.003 PHE D 95 TYR 0.031 0.003 TYR H 114 ARG 0.004 0.001 ARG H 89 Details of bonding type rmsd hydrogen bonds : bond 0.05782 ( 1082) hydrogen bonds : angle 4.49327 ( 3021) SS BOND : bond 0.00391 ( 15) SS BOND : angle 1.14328 ( 30) covalent geometry : bond 0.00476 (15594) covalent geometry : angle 0.57548 (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 84 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 75 MET cc_start: 0.7954 (ttt) cc_final: 0.7707 (ttt) REVERT: A 787 MET cc_start: 0.8049 (ttt) cc_final: 0.7756 (ttm) REVERT: H 100 MET cc_start: 0.7041 (mmp) cc_final: 0.6610 (mmm) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1773 time to fit residues: 27.9765 Evaluate side-chains 76 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 2.020 ------------------------------------------------------------------------------- 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: 10.0000 chunk 250 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 195 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 210 optimal weight: 9.9990 chunk 59 optimal weight: 0.4980 chunk 240 optimal weight: 50.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 HIS D 72 HIS H 72 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.165645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.139295 restraints weight = 40253.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.129432 restraints weight = 55739.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.124587 restraints weight = 60645.994| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.6042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 15609 Z= 0.306 Angle : 0.672 9.256 21574 Z= 0.380 Chirality : 0.046 0.233 2656 Planarity : 0.006 0.072 3056 Dihedral : 4.881 32.569 2839 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: 0.53 (0.17), residues: 2742 helix: 2.70 (0.17), residues: 784 sheet: -0.57 (0.20), residues: 703 loop : -0.58 (0.19), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP H 117 HIS 0.016 0.004 HIS B 72 PHE 0.040 0.004 PHE B 97 TYR 0.042 0.004 TYR H 114 ARG 0.008 0.001 ARG H 89 Details of bonding type rmsd hydrogen bonds : bond 0.06658 ( 1082) hydrogen bonds : angle 4.90790 ( 3021) SS BOND : bond 0.00383 ( 15) SS BOND : angle 1.54138 ( 30) covalent geometry : bond 0.00653 (15594) covalent geometry : angle 0.67038 (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 79 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 75 MET cc_start: 0.7358 (ttt) cc_final: 0.7036 (ttt) REVERT: C 42 PHE cc_start: 0.7933 (p90) cc_final: 0.7531 (p90) REVERT: A 787 MET cc_start: 0.8315 (ttt) cc_final: 0.7741 (ttm) REVERT: H 100 MET cc_start: 0.6999 (mmp) cc_final: 0.6566 (mmm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1817 time to fit residues: 27.2685 Evaluate side-chains 76 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.635 ------------------------------------------------------------------------------- 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: 0.9990 chunk 11 optimal weight: 0.5980 chunk 217 optimal weight: 0.0870 chunk 245 optimal weight: 0.0770 chunk 203 optimal weight: 0.0980 chunk 66 optimal weight: 0.6980 chunk 234 optimal weight: 50.0000 chunk 122 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 162 optimal weight: 0.6980 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.172863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.145251 restraints weight = 40224.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.137975 restraints weight = 61122.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.133611 restraints weight = 59658.165| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.5911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15609 Z= 0.101 Angle : 0.456 5.411 21574 Z= 0.252 Chirality : 0.042 0.148 2656 Planarity : 0.004 0.051 3056 Dihedral : 3.831 23.065 2839 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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 : 0.00 % 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: 3.59 (0.16), residues: 787 sheet: -0.24 (0.20), residues: 712 loop : -0.22 (0.20), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 117 HIS 0.004 0.001 HIS B 72 PHE 0.021 0.002 PHE J 144 TYR 0.015 0.001 TYR A 640 ARG 0.003 0.001 ARG A 743 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 1082) hydrogen bonds : angle 4.03886 ( 3021) SS BOND : bond 0.00244 ( 15) SS BOND : angle 0.77874 ( 30) covalent geometry : bond 0.00193 (15594) covalent geometry : angle 0.45538 (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 96 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 TRP cc_start: 0.8395 (m100) cc_final: 0.7238 (m-10) REVERT: C 42 PHE cc_start: 0.7589 (p90) cc_final: 0.7306 (p90) REVERT: A 787 MET cc_start: 0.7758 (ttt) cc_final: 0.7491 (ttm) REVERT: H 100 MET cc_start: 0.7816 (mmp) cc_final: 0.7338 (mmm) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1908 time to fit residues: 32.3914 Evaluate side-chains 82 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.656 ------------------------------------------------------------------------------- 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: 0.0000 chunk 24 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 239 optimal weight: 40.0000 chunk 255 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 226 optimal weight: 50.0000 chunk 214 optimal weight: 2.9990 chunk 38 optimal weight: 30.0000 overall best weight: 3.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 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 = 0.4175 r_free = 0.4175 target = 0.162483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.137155 restraints weight = 40321.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.130166 restraints weight = 64674.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.128135 restraints weight = 67472.104| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.6407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.137 15609 Z= 0.433 Angle : 0.809 11.382 21574 Z= 0.459 Chirality : 0.049 0.237 2656 Planarity : 0.007 0.094 3056 Dihedral : 5.263 33.286 2839 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.27 (0.17), residues: 2742 helix: 2.39 (0.17), residues: 786 sheet: -0.73 (0.20), residues: 720 loop : -0.65 (0.19), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.005 TRP B 117 HIS 0.016 0.004 HIS B 72 PHE 0.060 0.006 PHE B 97 TYR 0.056 0.005 TYR H 114 ARG 0.011 0.001 ARG H 89 Details of bonding type rmsd hydrogen bonds : bond 0.07601 ( 1082) hydrogen bonds : angle 5.31233 ( 3021) SS BOND : bond 0.00530 ( 15) SS BOND : angle 2.01315 ( 30) covalent geometry : bond 0.00928 (15594) covalent geometry : angle 0.80626 (21544) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5460.71 seconds wall clock time: 95 minutes 10.89 seconds (5710.89 seconds total)