Starting phenix.real_space_refine on Fri Mar 22 18:43:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ujz_8561/03_2024/5ujz_8561_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ujz_8561/03_2024/5ujz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ujz_8561/03_2024/5ujz_8561.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ujz_8561/03_2024/5ujz_8561.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ujz_8561/03_2024/5ujz_8561_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ujz_8561/03_2024/5ujz_8561_trim.pdb" } 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 Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 14.62, 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 - 3.50 Amino acid : False - 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: 25.83 Conformation dependent library (CDL) restraints added in 3.5 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: 2.94 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: 13.34 Time building geometry restraints manager: 26.89 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: 98.58 - 105.98: 1319 105.98 - 113.39: 38639 113.39 - 120.79: 12025 120.79 - 128.20: 9361 128.20 - 135.60: 213 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 1.850 nonbonded pdb=" H GLY H 140 " pdb=" O LEU H 210 " model vdw 1.746 1.850 nonbonded pdb=" HE2 HIS A 130 " pdb=" O PRO A 162 " model vdw 1.746 1.850 nonbonded pdb=" HE2 HIS C 130 " pdb=" O PRO C 162 " model vdw 1.746 1.850 nonbonded pdb=" HE2 HIS E 130 " pdb=" O PRO E 162 " model vdw 1.746 1.850 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } Set up NCS constraints Number of NCS constrained groups: 5 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } pdb_interpretation.ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } pdb_interpretation.ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } 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: 0.090 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: 0.480 Extract box with map and model: 2.210 Check model and map are aligned: 0.490 Set scattering table: 0.290 Process input model: 104.670 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.230 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.660 ------------------------------------------------------------------------------- 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 17943 Z= 0.645 Angle : 1.279 11.995 24318 Z= 0.753 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 *********************** 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 104 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.448 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: 0.3212 time to fit residues: 38.7680 Evaluate side-chains 67 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.405 Evaluate side-chains 73 residues out of total 149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.231 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: 0.2890 time to fit residues: 23.1081 Evaluate side-chains 44 residues out of total 149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.247 Evaluate side-chains 56 residues out of total 186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.300 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: 0.4451 time to fit residues: 27.1017 Evaluate side-chains 30 residues out of total 186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.274 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- 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: 8.9990 chunk 163 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 102 optimal weight: 0.4980 chunk 126 optimal weight: 0.4980 chunk 196 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 HIS E 183 HIS ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 614 ASN F 635 ASN Total number of N/Q/H flips: 2 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 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17943 Z= 0.266 Angle : 0.787 7.148 24318 Z= 0.431 Chirality : 0.045 0.154 2694 Planarity : 0.007 0.059 3132 Dihedral : 10.560 61.815 3075 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.16 % Allowed : 2.91 % Favored : 96.93 % 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: -3.09 (0.15), residues: 2172 helix: 0.16 (0.28), residues: 339 sheet: -2.77 (0.18), residues: 483 loop : -2.47 (0.14), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 592 HIS 0.004 0.001 HIS A 98 PHE 0.018 0.002 PHE H 154 TYR 0.043 0.002 TYR I 33 ARG 0.010 0.001 ARG E 226 *********************** 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 74 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.398 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: E 18 ASP cc_start: 0.9490 (m-30) cc_final: 0.8805 (p0) REVERT: E 88 ASN cc_start: 0.9152 (m-40) cc_final: 0.8770 (t0) REVERT: E 299 HIS cc_start: 0.7603 (t-90) cc_final: 0.6897 (t70) REVERT: E 317 MET cc_start: 0.8210 (tpp) cc_final: 0.7958 (tpp) outliers start: 1 outliers final: 1 residues processed: 74 average time/residue: 0.3080 time to fit residues: 26.7501 Evaluate side-chains 57 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.453 Evaluate side-chains 53 residues out of total 149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.207 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: 0.8591 (p) cc_final: 0.8244 (t) REVERT: F 551 LYS cc_start: 0.8211 (ttmt) cc_final: 0.7501 (mmtm) REVERT: F 575 ARG cc_start: 0.8131 (mmm-85) cc_final: 0.7680 (ptt180) REVERT: F 601 LEU cc_start: 0.8400 (tp) cc_final: 0.8049 (tt) REVERT: F 603 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8883 (tp30) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2869 time to fit residues: 16.7368 Evaluate side-chains 41 residues out of total 149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.224 Evaluate side-chains 38 residues out of total 186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.251 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: H 29 ILE cc_start: 0.7128 (pt) cc_final: 0.6886 (pt) REVERT: H 181 ASP cc_start: 0.8866 (m-30) cc_final: 0.8505 (m-30) REVERT: H 235 PHE cc_start: 0.8872 (p90) cc_final: 0.8648 (p90) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.3372 time to fit residues: 14.4234 Evaluate side-chains 31 residues out of total 186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.271 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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: 0.0026 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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: 0.0023 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.0815 > 50: distance: 0 - 1: 9.385 distance: 0 - 6: 7.816 distance: 1 - 2: 9.008 distance: 1 - 4: 6.734 distance: 1 - 7: 17.564 distance: 2 - 3: 20.728 distance: 2 - 11: 9.864 distance: 4 - 5: 8.183 distance: 4 - 8: 15.644 distance: 4 - 9: 10.143 distance: 5 - 10: 7.718 distance: 11 - 12: 30.158 distance: 11 - 17: 7.516 distance: 12 - 13: 34.790 distance: 12 - 15: 11.730 distance: 12 - 18: 28.142 distance: 13 - 14: 7.054 distance: 13 - 22: 61.916 distance: 15 - 16: 4.160 distance: 15 - 19: 33.743 distance: 15 - 20: 25.252 distance: 16 - 21: 23.287 distance: 22 - 23: 12.367 distance: 22 - 33: 21.964 distance: 23 - 24: 13.990 distance: 23 - 26: 28.260 distance: 23 - 34: 38.541 distance: 24 - 25: 14.894 distance: 24 - 42: 32.686 distance: 26 - 27: 26.019 distance: 26 - 35: 10.865 distance: 26 - 36: 56.616 distance: 27 - 28: 16.794 distance: 27 - 29: 12.239 distance: 28 - 30: 13.786 distance: 28 - 37: 18.851 distance: 29 - 31: 10.619 distance: 29 - 38: 6.804 distance: 30 - 32: 13.303 distance: 30 - 39: 18.413 distance: 31 - 32: 3.732 distance: 31 - 40: 6.404 distance: 32 - 41: 3.045 distance: 42 - 43: 17.307 distance: 42 - 51: 12.264 distance: 43 - 44: 20.198 distance: 43 - 46: 15.118 distance: 43 - 52: 24.822 distance: 44 - 45: 16.906 distance: 44 - 57: 44.976 distance: 46 - 47: 34.284 distance: 46 - 53: 49.471 distance: 46 - 54: 14.966 distance: 47 - 48: 55.138 distance: 47 - 55: 21.229 distance: 47 - 56: 16.321 distance: 48 - 50: 55.897 distance: 57 - 58: 25.737 distance: 58 - 59: 24.611 distance: 58 - 61: 28.712 distance: 58 - 69: 31.456 distance: 59 - 60: 12.057 distance: 59 - 81: 35.590 distance: 61 - 62: 16.693 distance: 61 - 70: 18.389 distance: 61 - 71: 16.654 distance: 62 - 63: 9.362 distance: 62 - 72: 6.901 distance: 62 - 73: 12.740 distance: 63 - 64: 3.299 distance: 63 - 74: 3.638 distance: 64 - 65: 3.142 distance: 64 - 76: 4.053 distance: 65 - 67: 4.728 distance: 66 - 77: 7.454 distance: 66 - 78: 5.103 distance: 67 - 79: 4.655 distance: 67 - 80: 7.480 distance: 81 - 82: 21.865 distance: 81 - 92: 23.968 distance: 82 - 83: 24.455 distance: 82 - 85: 25.183 distance: 82 - 93: 42.290 distance: 83 - 84: 24.912 distance: 83 - 101: 16.436 distance: 85 - 86: 44.108 distance: 85 - 94: 12.938 distance: 85 - 95: 18.613 distance: 86 - 87: 27.253 distance: 86 - 88: 49.108 distance: 87 - 89: 34.091 distance: 87 - 96: 54.734 distance: 88 - 90: 36.893 distance: 88 - 97: 44.852 distance: 89 - 91: 15.581 distance: 89 - 98: 14.423 distance: 90 - 91: 13.899 distance: 90 - 99: 19.375 distance: 91 - 100: 8.974 distance: 101 - 102: 22.416 distance: 101 - 110: 8.920 distance: 102 - 103: 25.987 distance: 102 - 105: 13.627 distance: 102 - 111: 33.009 distance: 103 - 104: 55.509 distance: 103 - 116: 3.381 distance: 105 - 106: 34.094 distance: 105 - 112: 23.570 distance: 105 - 113: 34.520 distance: 106 - 107: 57.820 distance: 106 - 114: 42.239 distance: 106 - 115: 42.128 distance: 107 - 108: 23.313 distance: 107 - 109: 31.787 distance: 116 - 117: 30.083 distance: 116 - 124: 12.571 distance: 117 - 118: 15.822 distance: 117 - 120: 15.360 distance: 117 - 125: 43.420 distance: 118 - 119: 29.328 distance: 118 - 135: 30.381 distance: 120 - 121: 50.142 distance: 120 - 122: 34.971 distance: 120 - 126: 36.173 distance: 121 - 123: 47.711 distance: 121 - 127: 27.192 distance: 121 - 128: 32.639 distance: 122 - 129: 11.755 distance: 122 - 130: 14.616 distance: 122 - 131: 19.099 distance: 123 - 132: 34.361 distance: 123 - 133: 27.769 distance: 123 - 134: 41.259 distance: 135 - 136: 13.255 distance: 135 - 146: 19.940 distance: 136 - 137: 22.312 distance: 136 - 139: 25.481 distance: 136 - 147: 9.237 distance: 137 - 155: 59.969 distance: 139 - 140: 19.497 distance: 139 - 148: 22.877 distance: 139 - 149: 16.560 distance: 140 - 141: 25.180 distance: 140 - 142: 14.396 distance: 141 - 143: 5.878 distance: 141 - 150: 18.246 distance: 142 - 144: 7.919 distance: 142 - 151: 6.528 distance: 143 - 145: 22.597 distance: 143 - 152: 11.453 distance: 144 - 145: 11.743 distance: 144 - 153: 8.547 distance: 155 - 156: 10.619 distance: 155 - 161: 4.411 distance: 156 - 157: 13.020 distance: 156 - 159: 11.615 distance: 156 - 162: 11.923 distance: 157 - 158: 22.509 distance: 159 - 160: 5.171 distance: 159 - 163: 10.554 distance: 159 - 164: 5.672 distance: 160 - 161: 24.431 distance: 160 - 165: 5.883 distance: 160 - 166: 5.604 distance: 161 - 167: 19.897 distance: 161 - 168: 24.598