Starting phenix.real_space_refine on Fri Mar 22 18:54:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uk1_8563/03_2024/5uk1_8563_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uk1_8563/03_2024/5uk1_8563.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/5uk1_8563/03_2024/5uk1_8563.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uk1_8563/03_2024/5uk1_8563.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uk1_8563/03_2024/5uk1_8563_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uk1_8563/03_2024/5uk1_8563_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= 0.069 sd= 0.375 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 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s 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: 14.58, 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=2.05 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.02 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 648 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS D 637 " distance=1.96 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 278 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.02 Simple disulfide: pdb=" SG CYS D 644 " - pdb=" SG CYS D 648 " distance=2.03 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS F 637 " distance=2.06 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 278 " distance=2.03 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 71 " distance=2.04 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 306 " distance=2.02 Simple disulfide: pdb=" SG CYS F 644 " - pdb=" SG CYS F 648 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 89 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 89 " distance=2.04 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: 22.97 Conformation dependent library (CDL) restraints added in 3.6 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 48 sheets defined 18.4% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 removed outlier: 4.083A 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: 4.166A pdb=" N TRP A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.994A 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: 3.803A pdb=" N GLN B 625 " --> pdb=" O LYS B 621 " (cutoff:3.500A) removed outlier: 3.919A 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: 4.084A 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: 4.166A pdb=" N TRP C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.995A 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: 3.802A pdb=" N GLN D 625 " --> pdb=" O LYS D 621 " (cutoff:3.500A) removed outlier: 3.918A 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: 4.084A 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: 4.166A pdb=" N TRP E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 195 removed outlier: 3.994A 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: 3.803A pdb=" N GLN F 625 " --> pdb=" O LYS F 621 " (cutoff:3.500A) removed outlier: 3.919A 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 removed outlier: 3.535A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.534A pdb=" N PHE H 84 " --> pdb=" O PRO H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 215 Processing helix chain 'I' and resid 80 through 84 removed outlier: 3.534A pdb=" N PHE I 84 " --> pdb=" O PRO I 81 " (cutoff:3.500A) 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: 3.990A pdb=" N CYS B 637 " --> pdb=" O ILE B 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 22 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 47 through 48 removed outlier: 5.917A pdb=" N LEU A 47 " --> pdb=" O ALA A 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.601A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA7, first strand: chain 'A' and resid 136 through 140 removed outlier: 4.706A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 151 through 153 removed outlier: 8.152A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 153 removed outlier: 8.152A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 289 removed outlier: 3.921A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 531 through 536 removed outlier: 3.990A pdb=" N CYS D 637 " --> pdb=" O ILE D 633 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AB5, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AB6, first strand: chain 'C' and resid 47 through 48 removed outlier: 5.916A pdb=" N LEU C 47 " --> pdb=" O ALA C 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.601A pdb=" N LEU C 54 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AB9, first strand: chain 'C' and resid 136 through 140 removed outlier: 4.706A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 151 through 153 removed outlier: 8.151A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 151 through 153 removed outlier: 8.151A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC4, first strand: chain 'C' and resid 287 through 289 removed outlier: 3.921A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 531 through 536 removed outlier: 3.990A pdb=" N CYS F 637 " --> pdb=" O ILE F 633 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 21 through 22 Processing sheet with id=AC7, first strand: chain 'E' and resid 33 through 35 Processing sheet with id=AC8, first strand: chain 'E' and resid 47 through 48 removed outlier: 5.916A pdb=" N LEU E 47 " --> pdb=" O ALA E 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.602A pdb=" N LEU E 54 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD2, first strand: chain 'E' and resid 136 through 140 removed outlier: 4.707A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 151 through 153 removed outlier: 8.151A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 151 through 153 removed outlier: 8.151A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD6, first strand: chain 'E' and resid 287 through 289 removed outlier: 3.922A pdb=" N CYS E 282 " --> pdb=" O ILE E 289 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AD8, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.264A pdb=" N GLN G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AE1, first strand: chain 'G' and resid 129 through 132 removed outlier: 5.809A pdb=" N GLY G 141 " --> pdb=" O ASN G 209 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 136 through 137 removed outlier: 6.991A pdb=" N MET G 159 " --> pdb=" O GLY G 175 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLY G 175 " --> pdb=" O MET G 159 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP G 161 " --> pdb=" O VAL G 173 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AE4, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.264A pdb=" N GLN H 38 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU H 47 " --> pdb=" O GLN H 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 13 Processing sheet with id=AE6, first strand: chain 'H' and resid 129 through 132 removed outlier: 5.810A pdb=" N GLY H 141 " --> pdb=" O ASN H 209 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 136 through 137 removed outlier: 6.992A pdb=" N MET H 159 " --> pdb=" O GLY H 175 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY H 175 " --> pdb=" O MET H 159 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP H 161 " --> pdb=" O VAL H 173 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 4 through 5 Processing sheet with id=AE9, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.264A pdb=" N GLN I 38 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU I 47 " --> pdb=" O GLN I 38 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AF2, first strand: chain 'I' and resid 129 through 132 removed outlier: 5.809A pdb=" N GLY I 141 " --> pdb=" O ASN I 209 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 136 through 137 removed outlier: 6.991A pdb=" N MET I 159 " --> pdb=" O GLY I 175 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLY I 175 " --> pdb=" O MET I 159 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP I 161 " --> pdb=" O VAL I 173 " (cutoff:3.500A) 687 hydrogen bonds defined for protein. 1845 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: 13.68 Time building geometry restraints manager: 24.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 16395 1.01 - 1.21: 6 1.21 - 1.42: 7627 1.42 - 1.62: 10214 1.62 - 1.82: 102 Bond restraints: 34344 Sorted by residual: bond pdb=" CA TRP I 36 " pdb=" CB TRP I 36 " ideal model delta sigma weight residual 1.532 1.483 0.048 1.82e-02 3.02e+03 7.03e+00 bond pdb=" CA TRP H 36 " pdb=" CB TRP H 36 " ideal model delta sigma weight residual 1.532 1.484 0.048 1.82e-02 3.02e+03 6.87e+00 bond pdb=" CA TRP G 36 " pdb=" CB TRP G 36 " ideal model delta sigma weight residual 1.532 1.484 0.047 1.82e-02 3.02e+03 6.80e+00 bond pdb=" NE1 TRP C 153 " pdb=" HE1 TRP C 153 " ideal model delta sigma weight residual 0.860 0.809 0.051 2.00e-02 2.50e+03 6.52e+00 bond pdb=" NE1 TRP A 153 " pdb=" HE1 TRP A 153 " ideal model delta sigma weight residual 0.860 0.810 0.050 2.00e-02 2.50e+03 6.34e+00 ... (remaining 34339 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.99: 1413 105.99 - 113.48: 38781 113.48 - 120.98: 12250 120.98 - 128.48: 8906 128.48 - 135.97: 207 Bond angle restraints: 61557 Sorted by residual: angle pdb=" C GLU I 1 " pdb=" N ILE I 2 " pdb=" CA ILE I 2 " ideal model delta sigma weight residual 120.35 127.76 -7.41 1.39e+00 5.18e-01 2.84e+01 angle pdb=" C GLU G 1 " pdb=" N ILE G 2 " pdb=" CA ILE G 2 " ideal model delta sigma weight residual 120.35 127.73 -7.38 1.39e+00 5.18e-01 2.82e+01 angle pdb=" C GLU H 1 " pdb=" N ILE H 2 " pdb=" CA ILE H 2 " ideal model delta sigma weight residual 120.35 127.69 -7.34 1.39e+00 5.18e-01 2.79e+01 angle pdb=" N SER H 30 " pdb=" CA SER H 30 " pdb=" C SER H 30 " ideal model delta sigma weight residual 113.28 121.54 -8.26 1.57e+00 4.06e-01 2.77e+01 angle pdb=" N SER I 30 " pdb=" CA SER I 30 " pdb=" C SER I 30 " ideal model delta sigma weight residual 113.28 121.53 -8.25 1.57e+00 4.06e-01 2.76e+01 ... (remaining 61552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.35: 15607 19.35 - 38.71: 867 38.71 - 58.06: 271 58.06 - 77.42: 46 77.42 - 96.77: 15 Dihedral angle restraints: 16806 sinusoidal: 9345 harmonic: 7461 Sorted by residual: dihedral pdb=" CA GLY I 58 " pdb=" C GLY I 58 " pdb=" N ILE I 59 " pdb=" CA ILE I 59 " ideal model delta harmonic sigma weight residual -180.00 -147.43 -32.57 0 5.00e+00 4.00e-02 4.24e+01 dihedral pdb=" CA GLY H 58 " pdb=" C GLY H 58 " pdb=" N ILE H 59 " pdb=" CA ILE H 59 " ideal model delta harmonic sigma weight residual -180.00 -147.47 -32.53 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA GLY G 58 " pdb=" C GLY G 58 " pdb=" N ILE G 59 " pdb=" CA ILE G 59 " ideal model delta harmonic sigma weight residual -180.00 -147.51 -32.49 0 5.00e+00 4.00e-02 4.22e+01 ... (remaining 16803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2235 0.081 - 0.163: 398 0.163 - 0.244: 43 0.244 - 0.326: 11 0.326 - 0.407: 7 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 -2.24 -0.16 2.00e-02 2.50e+03 6.76e+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 -2.24 -0.16 2.00e-02 2.50e+03 6.66e+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 -2.24 -0.16 2.00e-02 2.50e+03 6.53e+01 ... (remaining 2691 not shown) Planarity restraints: 5244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 248 " -0.149 2.00e-02 2.50e+03 1.75e-01 4.60e+02 pdb=" CG ASN E 248 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN E 248 " 0.157 2.00e-02 2.50e+03 pdb=" ND2 ASN E 248 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN E 248 " 0.260 2.00e-02 2.50e+03 pdb="HD22 ASN E 248 " -0.263 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 248 " -0.148 2.00e-02 2.50e+03 1.74e-01 4.56e+02 pdb=" CG ASN A 248 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN A 248 " 0.157 2.00e-02 2.50e+03 pdb=" ND2 ASN A 248 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN A 248 " 0.259 2.00e-02 2.50e+03 pdb="HD22 ASN A 248 " -0.262 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 248 " 0.148 2.00e-02 2.50e+03 1.74e-01 4.53e+02 pdb=" CG ASN C 248 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN C 248 " -0.157 2.00e-02 2.50e+03 pdb=" ND2 ASN C 248 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN C 248 " -0.258 2.00e-02 2.50e+03 pdb="HD22 ASN C 248 " 0.261 2.00e-02 2.50e+03 ... (remaining 5241 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 7614 2.31 - 2.88: 77229 2.88 - 3.45: 86327 3.45 - 4.03: 119135 4.03 - 4.60: 178874 Nonbonded interactions: 469179 Sorted by model distance: nonbonded pdb=" H GLY H 140 " pdb=" O LEU H 210 " model vdw 1.735 1.850 nonbonded pdb=" H THR E 31 " pdb=" O LEU E 321 " model vdw 1.736 1.850 nonbonded pdb=" H THR C 31 " pdb=" O LEU C 321 " model vdw 1.736 1.850 nonbonded pdb=" H THR A 31 " pdb=" O LEU A 321 " model vdw 1.737 1.850 nonbonded pdb=" H GLY G 140 " pdb=" O LEU G 210 " model vdw 1.738 1.850 ... (remaining 469174 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: 0.080 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: 2.340 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 100.990 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.260 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: 0.000 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 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 0.083 17943 Z= 0.663 Angle : 1.281 9.783 24318 Z= 0.747 Chirality : 0.065 0.407 2694 Planarity : 0.009 0.082 3132 Dihedral : 12.045 96.773 7023 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.06 % Favored : 91.80 % Rotamer: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.57 % 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: -3.97 (0.14), residues: 2172 helix: -1.38 (0.22), residues: 348 sheet: -2.97 (0.17), residues: 546 loop : -2.94 (0.14), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.005 TRP A 127 HIS 0.019 0.005 HIS D 611 PHE 0.036 0.004 PHE D 509 TYR 0.032 0.005 TYR C 95 ARG 0.026 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 70 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.417 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: A 35 ASN cc_start: 0.8881 (t0) cc_final: 0.8657 (t0) REVERT: A 84 VAL cc_start: 0.8884 (t) cc_final: 0.8237 (t) REVERT: A 184 HIS cc_start: 0.8971 (m90) cc_final: 0.8447 (m-70) REVERT: A 212 LYS cc_start: 0.7862 (mtmt) cc_final: 0.7656 (mmtm) outliers start: 1 outliers final: 1 residues processed: 70 average time/residue: 0.3800 time to fit residues: 30.5930 Evaluate side-chains 52 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.452 Evaluate side-chains 78 residues out of total 149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.247 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: B 542 GLN cc_start: 0.9504 (tp40) cc_final: 0.9098 (tp-100) REVERT: B 576 ARG cc_start: 0.8551 (mtm180) cc_final: 0.8189 (ttt180) REVERT: B 588 PHE cc_start: 0.8947 (m-80) cc_final: 0.8647 (m-80) REVERT: B 598 LEU cc_start: 0.9568 (mt) cc_final: 0.9017 (mt) REVERT: B 619 TYR cc_start: 0.7929 (t80) cc_final: 0.7718 (t80) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.4232 time to fit residues: 35.5328 Evaluate side-chains 45 residues out of total 149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.247 Evaluate side-chains 55 residues out of total 186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.281 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: symmetry clash REVERT: G 143 LEU cc_start: 0.9468 (tp) cc_final: 0.9063 (pp) REVERT: G 204 TYR cc_start: 0.8539 (m-80) cc_final: 0.7956 (m-80) REVERT: G 219 PHE cc_start: 0.8743 (m-80) cc_final: 0.7782 (m-80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.5056 time to fit residues: 30.2059 Evaluate side-chains 34 residues out of total 186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.297 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: 0.0030 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 : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0019 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=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 169 optimal weight: 0.0370 chunk 65 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 126 optimal weight: 0.0470 chunk 196 optimal weight: 9.9990 overall best weight: 2.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 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: B 542 GLN B 546 ASN ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.126 17943 Z= 0.334 Angle : 0.865 13.543 24318 Z= 0.469 Chirality : 0.046 0.207 2694 Planarity : 0.013 0.340 3132 Dihedral : 11.176 64.434 3075 Min Nonbonded Distance : 1.633 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.32 % Allowed : 2.27 % 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: -3.61 (0.15), residues: 2172 helix: -0.66 (0.27), residues: 339 sheet: -2.85 (0.17), residues: 561 loop : -2.75 (0.14), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 127 HIS 0.020 0.002 HIS C 32 PHE 0.019 0.002 PHE I 154 TYR 0.023 0.002 TYR E 102 ARG 0.036 0.002 ARG B 575 *********************** 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 B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 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 57 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.464 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: C 85 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7772 (mp0) REVERT: C 88 ASN cc_start: 0.9622 (t0) cc_final: 0.9359 (t0) REVERT: C 104 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6893 (mp0) REVERT: C 231 ASN cc_start: 0.9349 (m-40) cc_final: 0.9132 (m-40) outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 0.2231 time to fit residues: 16.1770 Evaluate side-chains 41 residues out of total 283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.387 Evaluate side-chains 59 residues out of total 149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 GLN cc_start: 0.9432 (tp-100) cc_final: 0.9089 (tp-100) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.3423 time to fit residues: 21.9351 Evaluate side-chains 42 residues out of total 149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.252 Evaluate side-chains 39 residues out of total 186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.255 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: symmetry clash REVERT: H 156 ILE cc_start: 0.7816 (mm) cc_final: 0.7530 (mm) REVERT: H 204 TYR cc_start: 0.8657 (m-80) cc_final: 0.7957 (m-80) REVERT: H 219 PHE cc_start: 0.8991 (m-80) cc_final: 0.8229 (m-80) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.6621 time to fit residues: 27.4261 Evaluate side-chains 32 residues out of total 186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.276 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: 0.0032 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 : 0.001 ------------------------------------------------------------------------------- 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: 70.0634 > 50: distance: 0 - 9: 14.275 distance: 1 - 4: 17.315 distance: 1 - 10: 5.774 distance: 2 - 3: 15.323 distance: 2 - 15: 3.163 distance: 4 - 12: 8.846 distance: 5 - 6: 14.091 distance: 5 - 13: 7.778 distance: 6 - 7: 4.431 distance: 6 - 8: 6.967 distance: 15 - 16: 25.339 distance: 16 - 17: 8.313 distance: 16 - 19: 14.116 distance: 16 - 25: 20.998 distance: 17 - 18: 17.990 distance: 17 - 37: 20.827 distance: 19 - 20: 32.340 distance: 19 - 26: 15.518 distance: 19 - 27: 6.537 distance: 20 - 21: 37.301 distance: 20 - 28: 6.364 distance: 20 - 29: 27.878 distance: 21 - 22: 13.550 distance: 21 - 30: 12.085 distance: 21 - 31: 19.279 distance: 22 - 23: 45.386 distance: 22 - 32: 30.220 distance: 22 - 33: 13.744 distance: 23 - 34: 31.419 distance: 23 - 35: 20.904 distance: 23 - 36: 22.843 distance: 37 - 38: 17.115 distance: 37 - 46: 19.422 distance: 38 - 39: 12.243 distance: 38 - 41: 44.020 distance: 38 - 47: 17.190 distance: 39 - 40: 31.690 distance: 39 - 52: 13.194 distance: 41 - 42: 30.626 distance: 41 - 48: 14.658 distance: 41 - 49: 15.102 distance: 42 - 43: 9.010 distance: 42 - 51: 8.620 distance: 43 - 44: 3.120 distance: 52 - 53: 39.737 distance: 52 - 59: 32.183 distance: 53 - 54: 35.701 distance: 53 - 56: 17.904 distance: 53 - 60: 37.519 distance: 54 - 55: 41.184 distance: 54 - 68: 28.723 distance: 56 - 57: 23.471 distance: 56 - 58: 14.074 distance: 56 - 61: 19.572 distance: 57 - 62: 17.718 distance: 57 - 63: 15.595 distance: 57 - 64: 32.934 distance: 58 - 65: 26.943 distance: 58 - 66: 21.310 distance: 58 - 67: 32.317 distance: 68 - 69: 30.869 distance: 68 - 76: 13.352 distance: 69 - 70: 22.469 distance: 69 - 72: 32.830 distance: 69 - 77: 46.674 distance: 70 - 71: 20.296 distance: 70 - 87: 31.822 distance: 72 - 73: 15.994 distance: 72 - 78: 24.865 distance: 72 - 79: 16.435 distance: 73 - 74: 30.372 distance: 73 - 75: 39.845 distance: 73 - 80: 10.372 distance: 74 - 81: 30.662 distance: 74 - 83: 15.625 distance: 75 - 84: 5.602 distance: 75 - 85: 7.137 distance: 75 - 86: 17.223 distance: 87 - 88: 57.155 distance: 87 - 94: 6.293 distance: 88 - 89: 64.782 distance: 88 - 91: 8.295 distance: 88 - 95: 46.955 distance: 89 - 90: 57.816 distance: 89 - 103: 50.892 distance: 91 - 96: 25.275 distance: 92 - 97: 12.850 distance: 93 - 101: 5.305 distance: 93 - 102: 33.208 distance: 103 - 104: 42.049 distance: 103 - 111: 38.185 distance: 104 - 105: 39.830 distance: 104 - 112: 10.545 distance: 105 - 106: 15.627 distance: 105 - 122: 28.769 distance: 107 - 114: 4.764 distance: 108 - 109: 5.686 distance: 108 - 110: 30.775 distance: 109 - 116: 55.568 distance: 109 - 117: 12.294 distance: 109 - 118: 42.589 distance: 110 - 119: 6.685 distance: 110 - 120: 13.122 distance: 110 - 121: 9.354 distance: 122 - 123: 16.842 distance: 122 - 136: 30.835 distance: 123 - 124: 24.814 distance: 123 - 126: 30.899 distance: 123 - 137: 21.088 distance: 124 - 125: 17.980 distance: 124 - 146: 43.932 distance: 126 - 127: 23.369 distance: 126 - 138: 22.122 distance: 126 - 139: 7.602 distance: 127 - 128: 16.114 distance: 127 - 129: 20.334 distance: 128 - 130: 11.662 distance: 128 - 140: 37.436 distance: 129 - 131: 23.540 distance: 129 - 132: 12.297 distance: 130 - 131: 22.078 distance: 130 - 141: 36.825 distance: 131 - 133: 19.756 distance: 132 - 134: 4.147 distance: 132 - 142: 7.086 distance: 133 - 135: 32.541 distance: 133 - 143: 15.764 distance: 134 - 135: 4.270 distance: 134 - 144: 8.406 distance: 135 - 145: 12.333 distance: 146 - 147: 16.573 distance: 147 - 148: 25.766 distance: 147 - 151: 5.866 distance: 147 - 152: 18.182 distance: 148 - 149: 13.371 distance: 148 - 153: 21.946 distance: 153 - 154: 18.249 distance: 154 - 155: 19.655 distance: 154 - 157: 18.930 distance: 154 - 161: 4.391 distance: 155 - 156: 22.796 distance: 159 - 168: 7.366