Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 14 02:35:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zdg_11173/10_2023/6zdg_11173_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zdg_11173/10_2023/6zdg_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_11173/10_2023/6zdg_11173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zdg_11173/10_2023/6zdg_11173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zdg_11173/10_2023/6zdg_11173_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zdg_11173/10_2023/6zdg_11173_trim.pdb" } 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-1.21rc1-5097/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 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 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 chiralities: 1 Time building chain proxies: 11.84, per 1000 atoms: 0.41 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: 23.44 Conformation dependent library (CDL) restraints added in 2.4 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: 2.27 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: 11.79 Time building geometry restraints manager: 24.06 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: 11326 17.53 - 35.05: 384 35.05 - 52.58: 95 52.58 - 70.11: 14 70.11 - 87.63: 4 Dihedral angle restraints: 11823 sinusoidal: 5244 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 11820 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 1.850 nonbonded pdb=" H ALA A 363 " pdb=" O CYS A 525 " model vdw 1.519 1.850 nonbonded pdb=" H ALA D 363 " pdb=" O CYS D 525 " model vdw 1.520 1.850 nonbonded pdb=" H ALA E 363 " pdb=" O CYS E 525 " model vdw 1.520 1.850 nonbonded pdb=" HZ3 LYS D 356 " pdb=" O ARG D 357 " model vdw 1.533 1.850 ... (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 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: 16.330 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: 2.540 Extract box with map and model: 37.310 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 88.780 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.140 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.310 ------------------------------------------------------------------------------- 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 : 8.993 58.120 5277 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 *********************** 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 : 0.244 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 outliers start: 3 outliers final: 2 residues processed: 50 average time/residue: 0.4158 time to fit residues: 22.5294 Evaluate side-chains 33 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.250 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0482 time to fit residues: 0.4642 Evaluate side-chains 73 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.275 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 72 average time/residue: 0.4220 time to fit residues: 32.9353 Evaluate side-chains 50 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.256 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1534 time to fit residues: 1.0422 Evaluate side-chains 66 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.254 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 outliers start: 4 outliers final: 1 residues processed: 64 average time/residue: 0.3898 time to fit residues: 27.2703 Evaluate side-chains 36 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.255 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0529 time to fit residues: 0.4027 ------------------------------------------------------------------------------- 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: 1.9990 chunk 138 optimal weight: 0.4980 chunk 76 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 74 optimal weight: 0.0050 chunk 143 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 487 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.770 14907 Z= 1.227 Angle : 0.788 21.679 20271 Z= 0.501 Chirality : 0.044 0.185 2244 Planarity : 0.005 0.092 2601 Dihedral : 4.457 28.983 2052 Min Nonbonded Distance : 1.604 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.56 % Allowed : 2.22 % Favored : 97.22 % 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: -0.12 (0.19), residues: 1860 helix: -3.28 (0.32), residues: 135 sheet: 0.49 (0.18), residues: 729 loop : 0.08 (0.21), residues: 996 *********************** 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 44 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.240 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 outliers start: 2 outliers final: 0 residues processed: 43 average time/residue: 0.4752 time to fit residues: 22.0079 Evaluate side-chains 25 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.241 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2924 Evaluate side-chains 53 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.256 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 outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.4832 time to fit residues: 27.0843 Evaluate side-chains 49 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.265 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3147 Evaluate side-chains 41 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.263 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 outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.4158 time to fit residues: 18.6297 Evaluate side-chains 30 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.265 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3179 ------------------------------------------------------------------------------- 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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 771, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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: 53.4825 > 50: distance: 1 - 2: 8.486 distance: 1 - 9: 33.135 distance: 2 - 3: 27.462 distance: 2 - 5: 21.131 distance: 2 - 10: 24.699 distance: 3 - 4: 27.259 distance: 3 - 15: 42.604 distance: 5 - 6: 19.289 distance: 5 - 11: 16.292 distance: 5 - 12: 25.568 distance: 6 - 7: 13.339 distance: 6 - 8: 8.284 distance: 8 - 13: 13.134 distance: 8 - 14: 13.319 distance: 15 - 16: 49.174 distance: 15 - 27: 37.065 distance: 16 - 17: 28.867 distance: 16 - 19: 15.059 distance: 16 - 28: 29.604 distance: 17 - 18: 35.471 distance: 17 - 36: 28.220 distance: 19 - 20: 26.215 distance: 19 - 29: 27.095 distance: 19 - 30: 23.789 distance: 20 - 21: 7.348 distance: 20 - 22: 10.900 distance: 21 - 23: 5.914 distance: 21 - 31: 25.736 distance: 22 - 24: 8.947 distance: 22 - 32: 23.565 distance: 23 - 25: 14.481 distance: 23 - 33: 15.715 distance: 24 - 25: 14.664 distance: 24 - 34: 8.447 distance: 25 - 26: 19.198 distance: 26 - 35: 10.808 distance: 36 - 37: 26.484 distance: 36 - 44: 22.696 distance: 37 - 38: 16.451 distance: 37 - 40: 11.875 distance: 37 - 45: 19.035 distance: 38 - 39: 16.771 distance: 38 - 55: 10.669 distance: 40 - 41: 35.490 distance: 40 - 46: 45.064 distance: 40 - 47: 39.328 distance: 41 - 42: 21.037 distance: 41 - 43: 16.366 distance: 41 - 48: 34.387 distance: 42 - 49: 53.483 distance: 42 - 50: 10.086 distance: 42 - 51: 34.930 distance: 43 - 52: 29.503 distance: 43 - 53: 18.058 distance: 43 - 54: 16.384 distance: 55 - 56: 25.222 distance: 55 - 67: 7.856 distance: 56 - 57: 25.363 distance: 56 - 59: 28.995 distance: 56 - 68: 24.782 distance: 57 - 58: 18.725 distance: 57 - 76: 17.687 distance: 59 - 60: 18.324 distance: 59 - 69: 25.973 distance: 59 - 70: 13.697 distance: 60 - 61: 35.267 distance: 61 - 63: 14.775 distance: 61 - 71: 26.793 distance: 62 - 64: 25.821 distance: 62 - 72: 35.772 distance: 63 - 65: 15.232 distance: 63 - 73: 29.367 distance: 64 - 65: 11.067 distance: 64 - 74: 16.629 distance: 65 - 66: 15.096 distance: 66 - 75: 7.536 distance: 76 - 77: 17.187 distance: 76 - 87: 17.826 distance: 77 - 78: 26.601 distance: 77 - 80: 24.692 distance: 77 - 88: 32.346 distance: 78 - 79: 41.234 distance: 78 - 100: 31.566 distance: 80 - 81: 41.625 distance: 80 - 89: 30.164 distance: 80 - 90: 26.515 distance: 81 - 82: 22.405 distance: 81 - 91: 13.818 distance: 81 - 92: 41.761 distance: 82 - 83: 13.294 distance: 82 - 93: 11.521 distance: 82 - 94: 17.088 distance: 83 - 84: 13.433 distance: 83 - 95: 29.287 distance: 84 - 85: 11.422 distance: 84 - 86: 10.232 distance: 85 - 96: 30.303 distance: 85 - 97: 7.798 distance: 86 - 98: 14.503 distance: 86 - 99: 14.197 distance: 100 - 101: 17.471 distance: 100 - 108: 28.217 distance: 101 - 102: 24.847 distance: 101 - 104: 10.182 distance: 101 - 109: 22.677 distance: 102 - 103: 25.142 distance: 102 - 119: 19.774 distance: 104 - 105: 11.922 distance: 104 - 110: 9.660 distance: 104 - 111: 9.407 distance: 105 - 106: 24.904 distance: 105 - 107: 14.144 distance: 105 - 112: 24.968 distance: 106 - 113: 11.968 distance: 106 - 114: 15.359 distance: 106 - 115: 12.211 distance: 107 - 116: 10.427 distance: 107 - 117: 15.026 distance: 107 - 118: 17.652 distance: 119 - 120: 11.158 distance: 119 - 130: 23.477 distance: 120 - 121: 12.550 distance: 120 - 123: 13.335 distance: 120 - 131: 28.237 distance: 121 - 122: 32.559 distance: 121 - 139: 13.823 distance: 123 - 124: 4.857 distance: 123 - 132: 8.793 distance: 123 - 133: 27.036 distance: 124 - 125: 10.606 distance: 124 - 126: 10.305 distance: 125 - 127: 8.529 distance: 125 - 134: 6.980 distance: 126 - 128: 25.188 distance: 126 - 135: 21.654 distance: 127 - 129: 15.030 distance: 127 - 136: 7.758 distance: 128 - 129: 9.824 distance: 128 - 137: 6.518 distance: 129 - 138: 6.257 distance: 139 - 140: 9.489 distance: 140 - 141: 17.698