Starting phenix.real_space_refine on Sat Aug 10 08:24:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zdg_11173/08_2024/6zdg_11173_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zdg_11173/08_2024/6zdg_11173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zdg_11173/08_2024/6zdg_11173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zdg_11173/08_2024/6zdg_11173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zdg_11173/08_2024/6zdg_11173_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zdg_11173/08_2024/6zdg_11173_trim.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 63 5.16 5 C 9210 2.51 5 N 2424 2.21 5 O 2856 1.98 5 H 13995 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 408": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 408": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 408": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 119": "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-5409/modules/chem_data/mon_lib" Total number of atoms: 28548 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "H" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3282 Classifications: {'peptide': 219} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Chain: "L" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3232 Classifications: {'peptide': 215} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "A" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "B" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3282 Classifications: {'peptide': 219} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Chain: "C" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3232 Classifications: {'peptide': 215} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "D" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "F" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3282 Classifications: {'peptide': 219} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Chain: "G" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3232 Classifications: {'peptide': 215} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "E" 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: "A" 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: "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 Time building chain proxies: 15.12, per 1000 atoms: 0.53 Number of scatterers: 28548 At special positions: 0 Unit cell: (146.91, 146.91, 81.34, 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 63 16.00 O 2856 8.00 N 2424 7.00 C 9210 6.00 H 13995 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 224 " - pdb=" SG CYS L 215 " distance=2.00 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS C 215 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 204 " distance=2.03 Simple disulfide: pdb=" SG CYS F 224 " - pdb=" SG CYS G 215 " distance=2.05 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 195 " 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 NAG-ASN " NAG A 601 " - " ASN A 343 " " NAG D 601 " - " ASN D 343 " " NAG E 601 " - " ASN E 343 " Time building additional restraints: 21.92 Conformation dependent library (CDL) restraints added in 3.2 seconds 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3486 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 42 sheets defined 10.8% alpha, 40.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 371 Processing helix chain 'E' and resid 384 through 388 removed outlier: 3.838A pdb=" N LEU E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 384 through 388' Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.024A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.614A pdb=" N ASN E 422 " --> pdb=" O ILE E 418 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.937A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 164 through 166 No H-bonds generated for 'chain 'H' and resid 164 through 166' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 93 through 97 removed outlier: 3.919A pdb=" N LEU L 97 " --> pdb=" O THR L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 129 Processing helix chain 'L' and resid 184 through 189 removed outlier: 3.738A pdb=" N LYS L 189 " --> pdb=" O ALA L 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.838A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.024A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.614A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.936A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 93 through 97 removed outlier: 3.918A pdb=" N LEU C 97 " --> pdb=" O THR C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 184 through 189 removed outlier: 3.737A pdb=" N LYS C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 365 through 371 Processing helix chain 'D' and resid 384 through 388 removed outlier: 3.838A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 384 through 388' Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.024A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 3.614A pdb=" N ASN D 422 " --> pdb=" O ILE D 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.937A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 164 through 166 No H-bonds generated for 'chain 'F' and resid 164 through 166' Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'G' and resid 93 through 97 removed outlier: 3.919A pdb=" N LEU G 97 " --> pdb=" O THR G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 129 Processing helix chain 'G' and resid 184 through 189 removed outlier: 3.738A pdb=" N LYS G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.592A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'E' and resid 465 through 467 removed outlier: 4.315A pdb=" N TRP G 149 " --> pdb=" O GLN G 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.788A pdb=" N TYR E 489 " --> pdb=" O TYR E 473 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.584A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.879A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 128 through 132 removed outlier: 6.214A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 128 through 132 removed outlier: 6.214A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 159 through 162 removed outlier: 4.431A pdb=" N TYR H 202 " --> pdb=" O VAL H 219 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 removed outlier: 12.177A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 12.193A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.832A pdb=" N GLN L 27 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.950A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.485A pdb=" N THR L 98 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 115 through 119 removed outlier: 6.108A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 206 through 211 removed outlier: 4.316A pdb=" N TRP L 149 " --> pdb=" O GLN L 156 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU L 155 " --> pdb=" O ARG A 466 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.591A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.788A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.584A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.879A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.215A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.215A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 159 through 162 removed outlier: 4.430A pdb=" N TYR B 202 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 4 through 7 removed outlier: 12.176A pdb=" N CYS C 23 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 11.230A pdb=" N THR C 74 " --> pdb=" O CYS C 23 " (cutoff:3.500A) removed outlier: 12.192A pdb=" N ALA C 25 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 12.042A pdb=" N THR C 72 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 10.831A pdb=" N GLN C 27 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP C 70 " --> pdb=" O GLN C 27 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.950A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 10 through 13 removed outlier: 4.486A pdb=" N THR C 98 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 115 through 119 removed outlier: 6.107A pdb=" N TYR C 174 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 206 through 211 removed outlier: 4.315A pdb=" N TRP C 149 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU C 155 " --> pdb=" O ARG D 466 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AD4, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.592A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.788A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.584A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.879A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 128 through 132 removed outlier: 6.215A pdb=" N TYR F 184 " --> pdb=" O ASP F 152 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 128 through 132 removed outlier: 6.215A pdb=" N TYR F 184 " --> pdb=" O ASP F 152 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 159 through 162 removed outlier: 4.431A pdb=" N TYR F 202 " --> pdb=" O VAL F 219 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 4 through 7 removed outlier: 12.176A pdb=" N CYS G 23 " --> pdb=" O THR G 74 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N THR G 74 " --> pdb=" O CYS G 23 " (cutoff:3.500A) removed outlier: 12.193A pdb=" N ALA G 25 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 12.042A pdb=" N THR G 72 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 10.831A pdb=" N GLN G 27 " --> pdb=" O ASP G 70 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP G 70 " --> pdb=" O GLN G 27 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.949A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 10 through 13 removed outlier: 4.486A pdb=" N THR G 98 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 115 through 119 removed outlier: 6.108A pdb=" N TYR G 174 " --> pdb=" O ASN G 139 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1419 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: 11.35 Time building geometry restraints manager: 23.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 13995 1.03 - 1.23: 0 1.23 - 1.42: 6503 1.42 - 1.62: 8332 1.62 - 1.81: 72 Bond restraints: 28902 Sorted by residual: bond pdb=" C1 NAG E 601 " pdb=" O5 NAG E 601 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.54e+00 bond pdb=" C1 NAG D 601 " pdb=" O5 NAG D 601 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.53e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.43e+00 bond pdb=" CB PRO H 155 " pdb=" CG PRO H 155 " ideal model delta sigma weight residual 1.506 1.462 0.044 3.90e-02 6.57e+02 1.25e+00 bond pdb=" CB PRO B 155 " pdb=" CG PRO B 155 " ideal model delta sigma weight residual 1.506 1.462 0.044 3.90e-02 6.57e+02 1.24e+00 ... (remaining 28897 not shown) Histogram of bond angle deviations from ideal: 79.18 - 90.14: 4 90.14 - 101.11: 6 101.11 - 112.07: 32473 112.07 - 123.03: 15899 123.03 - 133.99: 3545 Bond angle restraints: 51927 Sorted by residual: angle pdb=" CB VAL C 58 " pdb=" CG1 VAL C 58 " pdb="HG12 VAL C 58 " ideal model delta sigma weight residual 109.00 79.18 29.82 3.00e+00 1.11e-01 9.88e+01 angle pdb="HG11 VAL C 58 " pdb=" CG1 VAL C 58 " pdb="HG12 VAL C 58 " ideal model delta sigma weight residual 110.00 80.47 29.53 3.00e+00 1.11e-01 9.69e+01 angle pdb=" CB VAL C 58 " pdb=" CG1 VAL C 58 " pdb="HG13 VAL C 58 " ideal model delta sigma weight residual 109.00 80.12 28.88 3.00e+00 1.11e-01 9.27e+01 angle pdb="HG11 VAL C 58 " pdb=" CG1 VAL C 58 " pdb="HG13 VAL C 58 " ideal model delta sigma weight residual 110.00 81.50 28.50 3.00e+00 1.11e-01 9.02e+01 angle pdb="HG12 VAL C 58 " pdb=" CG1 VAL C 58 " pdb="HG13 VAL C 58 " ideal model delta sigma weight residual 110.00 133.63 -23.63 3.00e+00 1.11e-01 6.21e+01 ... (remaining 51922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 13185 17.53 - 35.05: 545 35.05 - 52.58: 232 52.58 - 70.11: 53 70.11 - 87.63: 4 Dihedral angle restraints: 14019 sinusoidal: 7440 harmonic: 6579 Sorted by residual: dihedral pdb=" N GLN D 493 " pdb=" CA GLN D 493 " pdb=" CB GLN D 493 " pdb=" CG GLN D 493 " ideal model delta sinusoidal sigma weight residual -180.00 -122.32 -57.68 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N GLN A 493 " pdb=" CA GLN A 493 " pdb=" CB GLN A 493 " pdb=" CG GLN A 493 " ideal model delta sinusoidal sigma weight residual -180.00 -122.33 -57.67 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N GLN E 493 " pdb=" CA GLN E 493 " pdb=" CB GLN E 493 " pdb=" CG GLN E 493 " ideal model delta sinusoidal sigma weight residual -180.00 -122.34 -57.66 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 14016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1363 0.029 - 0.058: 597 0.058 - 0.088: 112 0.088 - 0.117: 148 0.117 - 0.146: 24 Chirality restraints: 2244 Sorted by residual: chirality pdb=" CA ILE L 75 " pdb=" N ILE L 75 " pdb=" C ILE L 75 " pdb=" CB ILE L 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ILE G 75 " pdb=" N ILE G 75 " pdb=" C ILE G 75 " pdb=" CB ILE G 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE C 75 " pdb=" N ILE C 75 " pdb=" C ILE C 75 " pdb=" CB ILE C 75 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 2241 not shown) Planarity restraints: 4383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 156 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO H 157 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO H 157 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 157 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 156 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO B 157 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 156 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO F 157 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 157 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 157 " -0.022 5.00e-02 4.00e+02 ... (remaining 4380 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 1061 2.12 - 2.74: 52820 2.74 - 3.36: 79316 3.36 - 3.98: 105482 3.98 - 4.60: 161091 Nonbonded interactions: 399770 Sorted by model distance: nonbonded pdb=" HZ2 LYS A 386 " pdb=" O LEU B 103 " model vdw 1.499 2.450 nonbonded pdb=" H ALA A 363 " pdb=" O CYS A 525 " model vdw 1.519 2.450 nonbonded pdb=" H ALA D 363 " pdb=" O CYS D 525 " model vdw 1.520 2.450 nonbonded pdb=" H ALA E 363 " pdb=" O CYS E 525 " model vdw 1.520 2.450 nonbonded pdb=" HZ3 LYS D 356 " pdb=" O ARG D 357 " model vdw 1.533 2.450 ... (remaining 399765 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'L' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'L' } 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: 9.310 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: 0.470 Extract box with map and model: 1.180 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 92.570 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 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 : 0.004 0.044 14907 Z= 0.230 Angle : 0.503 4.254 20271 Z= 0.285 Chirality : 0.041 0.146 2244 Planarity : 0.003 0.044 2601 Dihedral : 9.076 58.120 5340 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.41 % Allowed : 3.52 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1860 helix: -1.71 (0.44), residues: 117 sheet: 0.56 (0.19), residues: 726 loop : -0.04 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 353 HIS 0.003 0.001 HIS C 190 PHE 0.009 0.001 PHE E 400 TYR 0.013 0.001 TYR F 95 ARG 0.003 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9134 (pt0) cc_final: 0.8923 (mp0) REVERT: A 342 PHE cc_start: 0.8657 (m-80) cc_final: 0.7891 (m-80) REVERT: A 357 ARG cc_start: 0.6900 (ttt-90) cc_final: 0.6691 (tpt-90) REVERT: A 369 TYR cc_start: 0.4380 (m-10) cc_final: 0.3226 (t80) REVERT: A 457 ARG cc_start: 0.9064 (ttt-90) cc_final: 0.8779 (ttt-90) REVERT: A 486 PHE cc_start: 0.8536 (t80) cc_final: 0.7922 (t80) outliers start: 3 outliers final: 2 residues processed: 50 average time/residue: 0.4184 time to fit residues: 22.6744 Evaluate side-chains 34 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.216 Evaluate side-chains 73 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.234 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: B 32 TYR cc_start: 0.8060 (m-80) cc_final: 0.7840 (m-80) REVERT: B 59 TYR cc_start: 0.8156 (m-80) cc_final: 0.7572 (m-80) REVERT: B 83 MET cc_start: 0.6850 (mtm) cc_final: 0.6607 (mtm) REVERT: B 98 LYS cc_start: 0.7827 (tttt) cc_final: 0.7536 (ttmm) REVERT: B 108 PHE cc_start: 0.6401 (m-10) cc_final: 0.4416 (p90) REVERT: B 113 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8620 (mm-40) outliers start: 6 outliers final: 4 residues processed: 72 average time/residue: 0.4055 time to fit residues: 31.6227 Evaluate side-chains 55 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.269 Evaluate side-chains 66 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.274 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: C 182 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7432 (pp) outliers start: 4 outliers final: 1 residues processed: 64 average time/residue: 0.3856 time to fit residues: 26.8742 Evaluate side-chains 36 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 93 optimal weight: 0.3980 chunk 74 optimal weight: 0.0570 chunk 143 optimal weight: 0.1980 chunk 55 optimal weight: 0.0030 chunk 87 optimal weight: 0.2980 chunk 106 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 overall best weight: 0.1908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 450 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.794 14907 Z= 1.234 Angle : 0.749 20.409 20271 Z= 0.482 Chirality : 0.045 0.150 2244 Planarity : 0.006 0.092 2601 Dihedral : 4.782 43.370 2115 Min Nonbonded Distance : 1.604 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.56 % Allowed : 2.04 % Favored : 97.41 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 1860 helix: -2.66 (0.36), residues: 135 sheet: 0.67 (0.18), residues: 750 loop : 0.19 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.004 TRP H 104 HIS 0.005 0.002 HIS B 35 PHE 0.017 0.001 PHE B 130 TYR 0.016 0.001 TYR B 184 ARG 0.004 0.001 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.220 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: E 369 TYR cc_start: 0.4144 (m-10) cc_final: 0.2374 (t80) REVERT: E 396 TYR cc_start: 0.7152 (m-10) cc_final: 0.6601 (m-10) REVERT: E 465 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7687 (tm-30) outliers start: 2 outliers final: 0 residues processed: 45 average time/residue: 0.4474 time to fit residues: 21.9529 Evaluate side-chains 26 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.252 Evaluate side-chains 56 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.267 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 156 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7488 (mt-10) outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.4811 time to fit residues: 28.4794 Evaluate side-chains 50 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.273 Evaluate side-chains 46 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.275 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: L 49 TYR cc_start: 0.8840 (p90) cc_final: 0.8616 (p90) REVERT: L 70 ASP cc_start: 0.8754 (m-30) cc_final: 0.8529 (m-30) REVERT: L 191 LYS cc_start: 0.7787 (tppp) cc_final: 0.7421 (tppt) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2960 time to fit residues: 15.3493 Evaluate side-chains 31 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 800, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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: 67.7182 > 50: distance: 5 - 6: 17.492 distance: 5 - 12: 20.227 distance: 6 - 7: 8.605 distance: 6 - 9: 30.373 distance: 6 - 13: 15.571 distance: 7 - 8: 16.824 distance: 7 - 21: 31.712 distance: 9 - 10: 15.721 distance: 9 - 11: 29.015 distance: 9 - 14: 12.824 distance: 10 - 15: 4.403 distance: 10 - 17: 3.433 distance: 11 - 18: 24.559 distance: 11 - 19: 28.394 distance: 11 - 20: 41.052 distance: 21 - 22: 20.726 distance: 21 - 29: 44.508 distance: 22 - 23: 27.256 distance: 22 - 25: 17.440 distance: 22 - 30: 29.987 distance: 23 - 24: 52.460 distance: 23 - 40: 5.869 distance: 25 - 26: 34.154 distance: 25 - 27: 23.572 distance: 25 - 31: 47.437 distance: 26 - 28: 12.620 distance: 26 - 32: 24.492 distance: 26 - 33: 15.021 distance: 27 - 34: 18.726 distance: 27 - 35: 14.023 distance: 27 - 36: 15.955 distance: 28 - 37: 28.013 distance: 28 - 38: 17.512 distance: 28 - 39: 20.846 distance: 40 - 41: 17.523 distance: 40 - 51: 26.405 distance: 41 - 42: 13.289 distance: 41 - 44: 30.257 distance: 41 - 52: 33.334 distance: 42 - 43: 29.015 distance: 42 - 64: 23.487 distance: 44 - 45: 30.426 distance: 44 - 53: 29.047 distance: 44 - 54: 33.586 distance: 45 - 46: 21.406 distance: 45 - 55: 38.272 distance: 45 - 56: 43.515 distance: 46 - 47: 12.842 distance: 46 - 57: 7.642 distance: 46 - 58: 15.885 distance: 47 - 59: 4.770 distance: 64 - 65: 16.351 distance: 64 - 68: 14.314 distance: 65 - 66: 22.380 distance: 65 - 69: 29.667 distance: 65 - 70: 24.486 distance: 66 - 67: 7.152 distance: 66 - 71: 36.517 distance: 71 - 72: 28.937 distance: 71 - 79: 37.356 distance: 72 - 73: 25.760 distance: 72 - 75: 17.726 distance: 72 - 80: 47.670 distance: 73 - 74: 46.344 distance: 73 - 83: 58.223 distance: 75 - 76: 20.253 distance: 75 - 81: 46.540 distance: 75 - 82: 33.859 distance: 76 - 77: 19.053 distance: 76 - 78: 16.530 distance: 83 - 84: 34.391 distance: 83 - 92: 56.427 distance: 84 - 85: 13.400 distance: 84 - 87: 31.378 distance: 84 - 93: 53.260 distance: 85 - 86: 56.619 distance: 85 - 98: 31.686 distance: 86 - 138: 59.421 distance: 87 - 88: 43.212 distance: 87 - 94: 52.851 distance: 87 - 95: 38.953 distance: 88 - 89: 20.182 distance: 88 - 96: 20.594 distance: 88 - 97: 14.832 distance: 89 - 90: 11.604 distance: 89 - 91: 42.033 distance: 98 - 99: 40.255 distance: 98 - 105: 34.067 distance: 99 - 100: 54.647 distance: 99 - 102: 32.550 distance: 99 - 106: 38.292 distance: 100 - 101: 23.098 distance: 100 - 114: 42.377 distance: 101 - 155: 53.276 distance: 102 - 103: 27.162 distance: 102 - 104: 21.233 distance: 102 - 107: 29.870 distance: 103 - 108: 5.464 distance: 103 - 109: 8.117 distance: 103 - 110: 8.083 distance: 104 - 111: 32.462 distance: 104 - 112: 10.771 distance: 104 - 113: 49.889 distance: 114 - 115: 21.078 distance: 114 - 125: 59.986 distance: 115 - 116: 41.494 distance: 115 - 118: 57.895 distance: 115 - 126: 58.260 distance: 116 - 117: 39.954 distance: 116 - 138: 37.922 distance: 118 - 119: 39.075 distance: 118 - 127: 39.787 distance: 118 - 128: 53.221 distance: 119 - 120: 21.017 distance: 119 - 129: 24.270 distance: 119 - 130: 43.630 distance: 120 - 121: 8.257 distance: 120 - 131: 11.452 distance: 120 - 132: 8.766 distance: 121 - 122: 4.679 distance: 121 - 133: 3.674 distance: 138 - 139: 22.986 distance: 138 - 147: 44.483 distance: 139 - 140: 46.818 distance: 139 - 142: 30.347 distance: 139 - 148: 40.012 distance: 140 - 141: 46.239 distance: 140 - 155: 54.660 distance: 142 - 143: 12.510 distance: 142 - 149: 13.083 distance: 142 - 150: 15.315 distance: 143 - 144: 23.194 distance: 143 - 151: 13.111 distance: 143 - 152: 5.382 distance: 144 - 145: 24.572 distance: 144 - 146: 23.256 distance: 146 - 153: 5.634 distance: 146 - 154: 4.158 distance: 155 - 156: 39.354 distance: 156 - 157: 30.108 distance: 156 - 159: 24.470 distance: 157 - 158: 18.689