Starting phenix.real_space_refine on Sun Jun 29 03:33:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ujz_8561/06_2025/5ujz_8561_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ujz_8561/06_2025/5ujz_8561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5ujz_8561/06_2025/5ujz_8561.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ujz_8561/06_2025/5ujz_8561.map" model { file = "/net/cci-nas-00/data/ceres_data/5ujz_8561/06_2025/5ujz_8561_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ujz_8561/06_2025/5ujz_8561_trim.cif" } resolution = 4.8 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 ------------------------------------------------------------------------------- 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= 0.071 sd= 0.427 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: 5 Type Number sf(0) Gaussians S 75 5.16 5 C 11004 2.51 5 N 2985 2.21 5 O 3483 1.98 5 H 16401 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33948 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 4973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4973 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "B" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2716 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "C" Number of atoms: 4973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4973 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "D" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2716 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "E" Number of atoms: 4973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4973 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "F" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2716 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "G" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3476 Classifications: {'peptide': 236} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "H" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3476 Classifications: {'peptide': 236} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "I" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3476 Classifications: {'peptide': 236} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.43, per 1000 atoms: 0.43 Number of scatterers: 33948 At special positions: 0 Unit cell: (141.04, 129.56, 182.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 O 3483 8.00 N 2985 7.00 C 11004 6.00 H 16401 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 637 " distance=2.08 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.04 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 648 " distance=2.02 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS D 637 " distance=2.05 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 278 " distance=2.04 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.04 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS D 644 " - pdb=" SG CYS D 648 " distance=2.02 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS F 637 " distance=1.96 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 278 " distance=2.04 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 71 " distance=2.03 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 139 " distance=2.04 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 306 " distance=2.03 Simple disulfide: pdb=" SG CYS F 644 " - pdb=" SG CYS F 648 " distance=2.02 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 89 " distance=2.03 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 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 406 " - " ASN A 129 " " NAG A 407 " - " ASN A 163 " " NAG A 408 " - " ASN A 15 " " NAG A 409 " - " ASN A 27 " " NAG A 410 " - " ASN A 290 " " NAG B 701 " - " ASN B 654 " " NAG C 406 " - " ASN C 129 " " NAG C 407 " - " ASN C 163 " " NAG C 408 " - " ASN C 15 " " NAG C 409 " - " ASN C 27 " " NAG C 410 " - " ASN C 290 " " NAG D 701 " - " ASN D 654 " " NAG E 406 " - " ASN E 129 " " NAG E 407 " - " ASN E 163 " " NAG E 408 " - " ASN E 15 " " NAG E 409 " - " ASN E 27 " " NAG E 410 " - " ASN E 290 " " NAG F 701 " - " ASN F 654 " " NAG J 1 " - " ASN A 91 " " NAG K 1 " - " ASN A 58 " " NAG L 1 " - " ASN C 91 " " NAG M 1 " - " ASN C 58 " " NAG N 1 " - " ASN E 91 " " NAG O 1 " - " ASN E 58 " Time building additional restraints: 9.43 Conformation dependent library (CDL) restraints added in 2.7 seconds 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 45 sheets defined 18.4% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 removed outlier: 3.977A pdb=" N GLY A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.217A pdb=" N TRP A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.980A pdb=" N GLN A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 557 Processing helix chain 'B' and resid 574 through 626 removed outlier: 3.765A pdb=" N GLN B 625 " --> pdb=" O LYS B 621 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B 626 " --> pdb=" O VAL B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 654 Processing helix chain 'B' and resid 662 through 670 Processing helix chain 'C' and resid 60 through 67 removed outlier: 3.977A pdb=" N GLY C 67 " --> pdb=" O GLY C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 109 Processing helix chain 'C' and resid 122 through 127 removed outlier: 4.216A pdb=" N TRP C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.981A pdb=" N GLN C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 557 Processing helix chain 'D' and resid 574 through 626 removed outlier: 3.766A pdb=" N GLN D 625 " --> pdb=" O LYS D 621 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU D 626 " --> pdb=" O VAL D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 654 Processing helix chain 'D' and resid 662 through 670 Processing helix chain 'E' and resid 60 through 67 removed outlier: 3.977A pdb=" N GLY E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 109 Processing helix chain 'E' and resid 122 through 127 removed outlier: 4.216A pdb=" N TRP E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 195 removed outlier: 3.981A pdb=" N GLN E 191 " --> pdb=" O ASN E 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 557 Processing helix chain 'F' and resid 574 through 626 removed outlier: 3.765A pdb=" N GLN F 625 " --> pdb=" O LYS F 621 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU F 626 " --> pdb=" O VAL F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 645 through 654 Processing helix chain 'F' and resid 662 through 670 Processing helix chain 'G' and resid 80 through 84 Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'H' and resid 80 through 84 Processing helix chain 'H' and resid 211 through 215 Processing helix chain 'I' and resid 80 through 84 Processing helix chain 'I' and resid 211 through 215 Processing sheet with id=AA1, first strand: chain 'B' and resid 531 through 536 removed outlier: 4.062A pdb=" N CYS B 637 " --> pdb=" O ILE B 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 22 removed outlier: 6.223A pdb=" N THR A 22 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS A 26 " --> pdb=" O THR A 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 45 through 48 removed outlier: 5.886A pdb=" N LEU A 45 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N CYS A 278 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.768A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 115 through 118 removed outlier: 8.620A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 118 Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 140 removed outlier: 4.710A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB1, first strand: chain 'A' and resid 287 through 289 removed outlier: 3.956A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 531 through 536 removed outlier: 4.062A pdb=" N CYS D 637 " --> pdb=" O ILE D 633 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 19 through 22 removed outlier: 6.223A pdb=" N THR C 22 " --> pdb=" O LYS C 26 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS C 26 " --> pdb=" O THR C 22 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 48 removed outlier: 5.885A pdb=" N LEU C 45 " --> pdb=" O ASP C 276 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N CYS C 278 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.767A pdb=" N LEU C 54 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 115 through 118 removed outlier: 8.620A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 115 through 118 Processing sheet with id=AB9, first strand: chain 'C' and resid 136 through 140 removed outlier: 4.710A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC2, first strand: chain 'C' and resid 287 through 289 removed outlier: 3.956A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 531 through 536 removed outlier: 4.062A pdb=" N CYS F 637 " --> pdb=" O ILE F 633 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 19 through 22 removed outlier: 6.223A pdb=" N THR E 22 " --> pdb=" O LYS E 26 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 33 through 35 Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 48 removed outlier: 5.886A pdb=" N LEU E 45 " --> pdb=" O ASP E 276 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N CYS E 278 " --> pdb=" O LEU E 45 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.767A pdb=" N LEU E 54 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 115 through 118 removed outlier: 8.620A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 115 through 118 Processing sheet with id=AD1, first strand: chain 'E' and resid 136 through 140 removed outlier: 4.711A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD3, first strand: chain 'E' and resid 287 through 289 removed outlier: 3.957A pdb=" N CYS E 282 " --> pdb=" O ILE E 289 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AD5, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.346A pdb=" N GLN G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AD7, first strand: chain 'G' and resid 129 through 132 removed outlier: 6.016A pdb=" N GLY G 141 " --> pdb=" O ASN G 209 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 136 through 137 removed outlier: 5.311A pdb=" N ASP G 158 " --> pdb=" O GLY G 223 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET G 159 " --> pdb=" O GLY G 175 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY G 175 " --> pdb=" O MET G 159 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N TRP G 161 " --> pdb=" O VAL G 173 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL G 173 " --> pdb=" O TRP G 161 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AE1, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.346A pdb=" N GLN H 38 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU H 47 " --> pdb=" O GLN H 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 13 Processing sheet with id=AE3, first strand: chain 'H' and resid 129 through 132 removed outlier: 6.015A pdb=" N GLY H 141 " --> pdb=" O ASN H 209 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 136 through 137 removed outlier: 5.312A pdb=" N ASP H 158 " --> pdb=" O GLY H 223 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N MET H 159 " --> pdb=" O GLY H 175 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY H 175 " --> pdb=" O MET H 159 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N TRP H 161 " --> pdb=" O VAL H 173 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL H 173 " --> pdb=" O TRP H 161 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 4 through 5 Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.346A pdb=" N GLN I 38 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU I 47 " --> pdb=" O GLN I 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AE8, first strand: chain 'I' and resid 129 through 132 removed outlier: 6.015A pdb=" N GLY I 141 " --> pdb=" O ASN I 209 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 136 through 137 removed outlier: 5.312A pdb=" N ASP I 158 " --> pdb=" O GLY I 223 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N MET I 159 " --> pdb=" O GLY I 175 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY I 175 " --> pdb=" O MET I 159 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TRP I 161 " --> pdb=" O VAL I 173 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL I 173 " --> pdb=" O TRP I 161 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 1935 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: 15.18 Time building geometry restraints manager: 11.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 16395 1.02 - 1.22: 19 1.22 - 1.42: 7734 1.42 - 1.62: 10094 1.62 - 1.82: 102 Bond restraints: 34344 Sorted by residual: bond pdb=" CA GLN G 90 " pdb=" CB GLN G 90 " ideal model delta sigma weight residual 1.530 1.490 0.041 1.50e-02 4.44e+03 7.40e+00 bond pdb=" CA GLN H 90 " pdb=" CB GLN H 90 " ideal model delta sigma weight residual 1.530 1.490 0.040 1.50e-02 4.44e+03 7.22e+00 bond pdb=" CA GLN I 90 " pdb=" CB GLN I 90 " ideal model delta sigma weight residual 1.530 1.490 0.040 1.50e-02 4.44e+03 7.19e+00 bond pdb=" CB GLN G 91 " pdb=" CG GLN G 91 " ideal model delta sigma weight residual 1.520 1.441 0.079 3.00e-02 1.11e+03 6.96e+00 bond pdb=" CB GLN I 91 " pdb=" CG GLN I 91 " ideal model delta sigma weight residual 1.520 1.441 0.079 3.00e-02 1.11e+03 6.96e+00 ... (remaining 34339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 57632 2.40 - 4.80: 3486 4.80 - 7.20: 388 7.20 - 9.60: 47 9.60 - 11.99: 4 Bond angle restraints: 61557 Sorted by residual: angle pdb=" N GLY H 31 " pdb=" CA GLY H 31 " pdb=" C GLY H 31 " ideal model delta sigma weight residual 115.08 127.07 -11.99 1.19e+00 7.06e-01 1.02e+02 angle pdb=" N GLY I 31 " pdb=" CA GLY I 31 " pdb=" C GLY I 31 " ideal model delta sigma weight residual 115.08 127.04 -11.96 1.19e+00 7.06e-01 1.01e+02 angle pdb=" N GLY G 31 " pdb=" CA GLY G 31 " pdb=" C GLY G 31 " ideal model delta sigma weight residual 115.08 126.97 -11.89 1.19e+00 7.06e-01 9.99e+01 angle pdb=" C GLU H 1 " pdb=" N ILE H 2 " pdb=" CA ILE H 2 " ideal model delta sigma weight residual 120.35 129.12 -8.77 1.39e+00 5.18e-01 3.98e+01 angle pdb=" C GLU G 1 " pdb=" N ILE G 2 " pdb=" CA ILE G 2 " ideal model delta sigma weight residual 120.35 129.11 -8.76 1.39e+00 5.18e-01 3.98e+01 ... (remaining 61552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.37: 15534 19.37 - 38.73: 943 38.73 - 58.10: 269 58.10 - 77.46: 45 77.46 - 96.83: 15 Dihedral angle restraints: 16806 sinusoidal: 9345 harmonic: 7461 Sorted by residual: dihedral pdb=" CA GLY H 223 " pdb=" C GLY H 223 " pdb=" N VAL H 224 " pdb=" CA VAL H 224 " ideal model delta harmonic sigma weight residual -180.00 -147.21 -32.79 0 5.00e+00 4.00e-02 4.30e+01 dihedral pdb=" CA GLY G 223 " pdb=" C GLY G 223 " pdb=" N VAL G 224 " pdb=" CA VAL G 224 " ideal model delta harmonic sigma weight residual 180.00 -147.26 -32.74 0 5.00e+00 4.00e-02 4.29e+01 dihedral pdb=" CA GLY I 223 " pdb=" C GLY I 223 " pdb=" N VAL I 224 " pdb=" CA VAL I 224 " ideal model delta harmonic sigma weight residual -180.00 -147.27 -32.73 0 5.00e+00 4.00e-02 4.28e+01 ... (remaining 16803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1990 0.062 - 0.125: 540 0.125 - 0.187: 130 0.187 - 0.249: 22 0.249 - 0.311: 12 Chirality restraints: 2694 Sorted by residual: chirality pdb=" C1 BMA L 3 " pdb=" O4 NAG L 2 " pdb=" C2 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.80e+01 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.38e+01 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.26e+01 ... (remaining 2691 not shown) Planarity restraints: 5244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 550 " -0.135 2.00e-02 2.50e+03 1.42e-01 3.04e+02 pdb=" CG ASN B 550 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN B 550 " 0.115 2.00e-02 2.50e+03 pdb=" ND2 ASN B 550 " -0.004 2.00e-02 2.50e+03 pdb="HD21 ASN B 550 " 0.217 2.00e-02 2.50e+03 pdb="HD22 ASN B 550 " -0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 550 " 0.131 2.00e-02 2.50e+03 1.42e-01 3.03e+02 pdb=" CG ASN D 550 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN D 550 " -0.118 2.00e-02 2.50e+03 pdb=" ND2 ASN D 550 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN D 550 " -0.209 2.00e-02 2.50e+03 pdb="HD22 ASN D 550 " 0.215 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 248 " -0.114 2.00e-02 2.50e+03 1.33e-01 2.67e+02 pdb=" CG ASN E 248 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN E 248 " 0.126 2.00e-02 2.50e+03 pdb=" ND2 ASN E 248 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN E 248 " 0.199 2.00e-02 2.50e+03 pdb="HD22 ASN E 248 " -0.195 2.00e-02 2.50e+03 ... (remaining 5241 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.32: 8096 2.32 - 2.89: 76978 2.89 - 3.46: 84880 3.46 - 4.03: 117495 4.03 - 4.60: 176327 Nonbonded interactions: 463776 Sorted by model distance: nonbonded pdb=" H ALA C 13 " pdb=" O TRP D 514 " model vdw 1.744 2.450 nonbonded pdb=" H GLY H 140 " pdb=" O LEU H 210 " model vdw 1.746 2.450 nonbonded pdb=" HE2 HIS A 130 " pdb=" O PRO A 162 " model vdw 1.746 2.450 nonbonded pdb=" HE2 HIS C 130 " pdb=" O PRO C 162 " model vdw 1.746 2.450 nonbonded pdb=" HE2 HIS E 130 " pdb=" O PRO E 162 " model vdw 1.746 2.450 ... (remaining 463771 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: 0.14 Found NCS groups: ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } Set up NCS constraints Number of NCS constrained groups: 5 pdb_interpretation.ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } Set refine NCS operators NCS operators will be refined. 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: 0.060 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: 0.620 Extract box with map and model: 1.350 Check model and map are aligned: 0.260 Set scattering table: 0.330 Process input model: 71.270 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 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 : 0.010 0.081 17997 Z= 0.446 Angle : 1.302 11.995 24459 Z= 0.756 Chirality : 0.064 0.311 2694 Planarity : 0.009 0.080 3132 Dihedral : 12.099 96.831 7023 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.60 % Favored : 92.27 % Rotamer: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.72 % 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: -3.77 (0.14), residues: 2172 helix: -1.08 (0.23), residues: 336 sheet: -3.00 (0.18), residues: 510 loop : -2.79 (0.14), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.005 TRP E 153 HIS 0.018 0.004 HIS D 611 PHE 0.048 0.005 PHE A 147 TYR 0.028 0.005 TYR C 95 ARG 0.025 0.002 ARG H 222 Details of bonding type rmsd link_NAG-ASN : bond 0.01466 ( 24) link_NAG-ASN : angle 3.81832 ( 72) link_BETA1-4 : bond 0.01087 ( 9) link_BETA1-4 : angle 3.95737 ( 27) hydrogen bonds : bond 0.10044 ( 675) hydrogen bonds : angle 10.75468 ( 1935) SS BOND : bond 0.01979 ( 21) SS BOND : angle 2.12651 ( 42) covalent geometry : bond 0.00981 (17943) covalent geometry : angle 1.27931 (24318) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0021 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 73 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 GLN cc_start: 0.8977 (tp40) cc_final: 0.8722 (tm-30) REVERT: B 549 THR cc_start: 0.9055 (m) cc_final: 0.8855 (p) REVERT: B 551 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7718 (mmtm) REVERT: B 574 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8104 (tt0) REVERT: B 575 ARG cc_start: 0.8379 (mmm-85) cc_final: 0.7902 (ptt180) REVERT: B 603 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8651 (tp30) REVERT: B 610 PHE cc_start: 0.8874 (t80) cc_final: 0.8426 (t80) REVERT: B 638 PHE cc_start: 0.7872 (m-80) cc_final: 0.7409 (m-10) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3210 time to fit residues: 25.5633 Evaluate side-chains 44 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.201 Evaluate side-chains 104 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.9304 (m-30) cc_final: 0.8599 (p0) REVERT: A 40 SER cc_start: 0.8704 (t) cc_final: 0.8387 (p) REVERT: A 88 ASN cc_start: 0.9107 (m-40) cc_final: 0.8703 (t0) REVERT: A 130 HIS cc_start: 0.7470 (m90) cc_final: 0.7081 (m90) REVERT: A 142 ASN cc_start: 0.8817 (m110) cc_final: 0.8321 (m110) REVERT: A 149 LYS cc_start: 0.8744 (mmmt) cc_final: 0.8443 (mmtm) REVERT: A 178 VAL cc_start: 0.8810 (t) cc_final: 0.8556 (p) REVERT: A 237 LEU cc_start: 0.9320 (tp) cc_final: 0.9017 (tt) REVERT: A 299 HIS cc_start: 0.7966 (t-90) cc_final: 0.7092 (t70) outliers start: 1 outliers final: 1 residues processed: 104 average time/residue: 0.3037 time to fit residues: 36.8388 Evaluate side-chains 67 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.400 Evaluate side-chains 56 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 13 LEU cc_start: 0.6042 (mt) cc_final: 0.5814 (mt) REVERT: G 208 ASN cc_start: 0.7766 (m-40) cc_final: 0.7409 (p0) REVERT: G 235 PHE cc_start: 0.8683 (p90) cc_final: 0.8331 (p90) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.4650 time to fit residues: 28.2207 Evaluate side-chains 30 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.264 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0028 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 9.9990 chunk 163 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 55 optimal weight: 0.0980 chunk 110 optimal weight: 0.4980 chunk 87 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 102 optimal weight: 0.3980 chunk 126 optimal weight: 0.0470 chunk 196 optimal weight: 0.0030 overall best weight: 0.2088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 635 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 198 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.066543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.066481 restraints weight = 259.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.066541 restraints weight = 20.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.066543 restraints weight = 3.247 | |-----------------------------------------------------------------------------| r_work (final): 0.2651 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.104311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.089589 restraints weight = 14175.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.093609 restraints weight = 6878.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.096067 restraints weight = 3831.038| |-----------------------------------------------------------------------------| r_work (final): 0.3654 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.101928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.087187 restraints weight = 22619.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.091924 restraints weight = 10190.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.095050 restraints weight = 5539.272| |-----------------------------------------------------------------------------| r_work (final): 0.3509 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.076870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.066889 restraints weight = 28774.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.069952 restraints weight = 14181.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.072052 restraints weight = 8112.083| |-----------------------------------------------------------------------------| r_work (final): 0.3649 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.053568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.052348 restraints weight = 349.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.052713 restraints weight = 90.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.052997 restraints weight = 44.425| |-----------------------------------------------------------------------------| r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 17997 Z= 0.185 Angle : 0.834 8.707 24459 Z= 0.445 Chirality : 0.047 0.193 2694 Planarity : 0.007 0.088 3132 Dihedral : 10.812 62.988 3075 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.16 % Allowed : 2.43 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.20 (0.15), residues: 2172 helix: -0.07 (0.27), residues: 342 sheet: -2.69 (0.19), residues: 480 loop : -2.57 (0.14), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 521 HIS 0.004 0.001 HIS C 184 PHE 0.020 0.002 PHE H 154 TYR 0.046 0.002 TYR I 33 ARG 0.009 0.001 ARG A 226 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 24) link_NAG-ASN : angle 2.39073 ( 72) link_BETA1-4 : bond 0.00977 ( 9) link_BETA1-4 : angle 4.14515 ( 27) hydrogen bonds : bond 0.04991 ( 675) hydrogen bonds : angle 7.97456 ( 1935) SS BOND : bond 0.01693 ( 21) SS BOND : angle 1.79171 ( 42) covalent geometry : bond 0.00398 (17943) covalent geometry : angle 0.81141 (24318) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** pdbres="ILE F 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE F 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE F 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE F 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE F 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE F 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE F 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE F 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE F 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0028 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Evaluate side-chains 56 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 515 THR cc_start: 0.8726 (p) cc_final: 0.8363 (t) REVERT: F 551 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7535 (mmtt) REVERT: F 575 ARG cc_start: 0.8131 (mmm-85) cc_final: 0.7717 (ptt180) REVERT: F 601 LEU cc_start: 0.8267 (tp) cc_final: 0.7962 (tt) REVERT: F 603 GLU cc_start: 0.9365 (mm-30) cc_final: 0.9044 (tp30) REVERT: F 638 PHE cc_start: 0.6875 (m-80) cc_final: 0.6569 (m-80) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.3116 time to fit residues: 19.1673 Evaluate side-chains 43 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.224 Evaluate side-chains 77 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 18 ASP cc_start: 0.9537 (m-30) cc_final: 0.8911 (p0) REVERT: E 88 ASN cc_start: 0.9188 (m-40) cc_final: 0.8820 (t0) REVERT: E 299 HIS cc_start: 0.7347 (t-90) cc_final: 0.6790 (t70) REVERT: E 315 LEU cc_start: 0.8246 (mt) cc_final: 0.8010 (mt) outliers start: 1 outliers final: 1 residues processed: 77 average time/residue: 0.3065 time to fit residues: 27.8730 Evaluate side-chains 59 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.438 Evaluate side-chains 40 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 181 ASP cc_start: 0.8582 (m-30) cc_final: 0.8317 (m-30) REVERT: H 235 PHE cc_start: 0.8727 (p90) cc_final: 0.8516 (p90) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.3439 time to fit residues: 15.5007 Evaluate side-chains 26 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.334 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0033 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 122 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 84 optimal weight: 0.0970 chunk 87 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 191 GLN A 250 ASN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.069024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.068954 restraints weight = 226.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.068994 restraints weight = 19.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.069022 restraints weight = 2.578 | |-----------------------------------------------------------------------------| r_work (final): 0.2720 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.098954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.086436 restraints weight = 13123.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.089611 restraints weight = 6408.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.091795 restraints weight = 3647.991| |-----------------------------------------------------------------------------| r_work (final): 0.3656 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.104125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.089355 restraints weight = 23798.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.093933 restraints weight = 11198.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.097079 restraints weight = 6191.902| |-----------------------------------------------------------------------------| r_work (final): 0.3602 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.075015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.064817 restraints weight = 29479.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.067887 restraints weight = 14493.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.069915 restraints weight = 8350.123| |-----------------------------------------------------------------------------| r_work (final): 0.3611 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.060729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.059259 restraints weight = 313.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.059789 restraints weight = 98.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.060151 restraints weight = 51.620| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.170 17997 Z= 0.311 Angle : 1.074 23.973 24459 Z= 0.544 Chirality : 0.053 0.575 2694 Planarity : 0.009 0.089 3132 Dihedral : 10.385 60.024 3075 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.65 % Allowed : 1.78 % Favored : 97.57 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.36 (0.15), residues: 2172 helix: -0.11 (0.28), residues: 342 sheet: -2.78 (0.18), residues: 486 loop : -2.71 (0.13), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 153 HIS 0.016 0.002 HIS A 32 PHE 0.043 0.003 PHE E 118 TYR 0.187 0.005 TYR C 95 ARG 0.010 0.001 ARG E 322 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 24) link_NAG-ASN : angle 2.42536 ( 72) link_BETA1-4 : bond 0.00920 ( 9) link_BETA1-4 : angle 3.53873 ( 27) hydrogen bonds : bond 0.05881 ( 675) hydrogen bonds : angle 8.01271 ( 1935) SS BOND : bond 0.02705 ( 21) SS BOND : angle 4.39319 ( 42) covalent geometry : bond 0.00731 (17943) covalent geometry : angle 1.04626 (24318) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** pdbres="ILE F 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE F 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE F 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE F 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE F 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE F 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE F 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE F 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE F 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 51 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 515 THR cc_start: 0.8586 (p) cc_final: 0.8215 (t) REVERT: F 551 LYS cc_start: 0.8121 (ttmt) cc_final: 0.7425 (mmtt) REVERT: F 575 ARG cc_start: 0.8032 (mmm-85) cc_final: 0.7777 (ptt180) REVERT: F 585 ASP cc_start: 0.7846 (m-30) cc_final: 0.7526 (m-30) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.3005 time to fit residues: 16.8649 Evaluate side-chains 44 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.211 Evaluate side-chains 70 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.9491 (m-30) cc_final: 0.8579 (p0) REVERT: A 36 LEU cc_start: 0.8798 (mm) cc_final: 0.8430 (mm) REVERT: A 88 ASN cc_start: 0.9315 (m-40) cc_final: 0.8985 (t0) REVERT: A 103 GLU cc_start: 0.8919 (mp0) cc_final: 0.8309 (tt0) REVERT: A 119 GLU cc_start: 0.8926 (pt0) cc_final: 0.8545 (pp20) REVERT: A 164 LEU cc_start: 0.8763 (pp) cc_final: 0.8553 (mm) REVERT: A 178 VAL cc_start: 0.8785 (t) cc_final: 0.8562 (p) outliers start: 4 outliers final: 2 residues processed: 70 average time/residue: 0.2361 time to fit residues: 20.4276 Evaluate side-chains 55 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.381 Evaluate side-chains 32 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 171 GLU cc_start: 0.8177 (pt0) cc_final: 0.7843 (pt0) REVERT: H 181 ASP cc_start: 0.8861 (m-30) cc_final: 0.8419 (m-30) REVERT: H 235 PHE cc_start: 0.8865 (p90) cc_final: 0.8588 (p90) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.2960 time to fit residues: 10.9228 Evaluate side-chains 27 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.245 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0025 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.1429 > 50: distance: 0 - 4: 3.820 distance: 2 - 3: 10.292 distance: 7 - 16: 6.967 distance: 8 - 9: 4.211 distance: 8 - 11: 3.521 distance: 8 - 17: 5.628 distance: 9 - 10: 13.238 distance: 9 - 22: 8.672 distance: 11 - 12: 8.324 distance: 11 - 18: 14.960 distance: 11 - 19: 4.462 distance: 12 - 20: 9.365 distance: 12 - 21: 7.819 distance: 13 - 14: 9.235 distance: 13 - 15: 7.528 distance: 22 - 28: 3.365 distance: 23 - 24: 8.376 distance: 23 - 26: 9.356 distance: 23 - 29: 24.295 distance: 24 - 25: 7.228 distance: 24 - 33: 7.474 distance: 26 - 27: 4.141 distance: 26 - 30: 6.846 distance: 26 - 31: 7.402 distance: 27 - 32: 5.442 distance: 33 - 34: 3.526 distance: 33 - 39: 17.723 distance: 34 - 35: 4.510 distance: 34 - 37: 8.366 distance: 34 - 40: 20.387 distance: 35 - 36: 6.403 distance: 37 - 38: 17.859 distance: 37 - 41: 15.925 distance: 37 - 42: 10.116 distance: 38 - 43: 25.534 distance: 44 - 55: 7.271 distance: 45 - 46: 4.380 distance: 45 - 48: 3.170 distance: 45 - 56: 16.743 distance: 46 - 47: 8.031 distance: 46 - 64: 11.255 distance: 48 - 49: 6.552 distance: 48 - 57: 10.080 distance: 48 - 58: 18.492 distance: 49 - 50: 7.515 distance: 49 - 51: 10.862 distance: 50 - 52: 6.327 distance: 50 - 59: 3.508 distance: 51 - 53: 14.443 distance: 51 - 60: 18.757 distance: 52 - 54: 7.884 distance: 52 - 61: 4.333 distance: 53 - 54: 22.408 distance: 53 - 62: 37.939 distance: 54 - 63: 8.684 distance: 64 - 65: 5.379 distance: 64 - 76: 17.257 distance: 65 - 66: 8.370 distance: 65 - 68: 11.483 distance: 65 - 77: 7.897 distance: 66 - 67: 16.460 distance: 66 - 85: 13.421 distance: 68 - 69: 4.631 distance: 68 - 78: 13.183 distance: 68 - 79: 8.625 distance: 69 - 70: 5.928 distance: 69 - 71: 4.322 distance: 70 - 72: 6.597 distance: 70 - 80: 7.750 distance: 71 - 73: 5.333 distance: 72 - 74: 3.866 distance: 72 - 82: 6.781 distance: 73 - 74: 4.312 distance: 74 - 75: 4.664 distance: 75 - 84: 5.755 distance: 85 - 94: 6.993 distance: 86 - 87: 10.647 distance: 86 - 89: 13.276 distance: 86 - 95: 4.208 distance: 87 - 88: 5.551 distance: 87 - 107: 5.412 distance: 89 - 90: 10.258 distance: 89 - 96: 4.234 distance: 89 - 97: 12.188 distance: 90 - 91: 12.327 distance: 90 - 98: 9.486 distance: 90 - 99: 34.940 distance: 91 - 92: 14.438 distance: 91 - 100: 24.261 distance: 91 - 101: 42.565 distance: 92 - 93: 7.662 distance: 92 - 102: 6.397 distance: 92 - 103: 6.175 distance: 93 - 104: 4.075 distance: 93 - 105: 3.094 distance: 107 - 108: 3.092 distance: 107 - 115: 18.761 distance: 108 - 109: 4.865 distance: 108 - 111: 3.914 distance: 108 - 116: 3.013 distance: 109 - 110: 9.569 distance: 109 - 121: 8.360 distance: 111 - 112: 3.083 distance: 111 - 117: 8.219 distance: 111 - 118: 11.879 distance: 112 - 113: 6.118 distance: 112 - 114: 3.680 distance: 114 - 119: 5.801 distance: 114 - 120: 5.933 distance: 121 - 122: 3.585 distance: 121 - 129: 7.695 distance: 122 - 123: 3.889 distance: 122 - 125: 3.471 distance: 122 - 130: 5.956 distance: 123 - 124: 18.413 distance: 123 - 140: 3.706 distance: 125 - 126: 4.254 distance: 125 - 131: 5.514 distance: 125 - 132: 7.915 distance: 126 - 127: 3.278 distance: 126 - 128: 8.482 distance: 126 - 133: 12.635 distance: 127 - 134: 5.862 distance: 127 - 136: 5.530 distance: 128 - 137: 8.606 distance: 128 - 138: 10.062 distance: 128 - 139: 5.728 distance: 140 - 141: 8.729 distance: 140 - 148: 10.140 distance: 141 - 142: 6.980 distance: 141 - 144: 3.355 distance: 141 - 149: 8.422 distance: 142 - 143: 5.280 distance: 144 - 145: 3.017 distance: 144 - 150: 7.970 distance: 144 - 151: 4.246 distance: 145 - 152: 3.758