Starting phenix.real_space_refine (version: dev) on Fri Mar 17 18:19:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3v_0827/03_2023/6l3v_0827_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3v_0827/03_2023/6l3v_0827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3v_0827/03_2023/6l3v_0827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3v_0827/03_2023/6l3v_0827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3v_0827/03_2023/6l3v_0827_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3v_0827/03_2023/6l3v_0827_trim_updated.pdb" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.276 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 Process input model Symmetric amino acids flipped Residue "A ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 171": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 171": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 171": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 171": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 171": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 171": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 209": "OE1" <-> "OE2" Residue "F ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 19416 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3167 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "B" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3167 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "C" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3167 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "D" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3167 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "E" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3167 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "F" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3167 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.34, per 1000 atoms: 0.48 Number of scatterers: 19416 At special positions: 0 Unit cell: (114.779, 121.683, 94.067, 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 66 16.00 O 1686 8.00 N 1620 7.00 C 6516 6.00 H 9528 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 180 " distance=2.04 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 169 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 180 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 169 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 180 " distance=2.04 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 169 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 180 " distance=2.04 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 174 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 169 " 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 Time building additional restraints: 14.97 Conformation dependent library (CDL) restraints added in 1.6 seconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 6 sheets defined 70.6% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 4.207A pdb=" N ALA A 11 " --> pdb=" O ARG A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 22 No H-bonds generated for 'chain 'A' and resid 19 through 22' Processing helix chain 'A' and resid 24 through 44 Proline residue: A 41 - end of helix Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 73 through 84 Processing helix chain 'A' and resid 86 through 106 removed outlier: 3.684A pdb=" N HIS A 102 " --> pdb=" O HIS A 98 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU A 104 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU A 105 " --> pdb=" O TRP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 158 removed outlier: 3.808A pdb=" N LEU A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 213 removed outlier: 3.612A pdb=" N LEU A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'B' and resid 3 through 13 removed outlier: 4.207A pdb=" N ALA B 11 " --> pdb=" O ARG B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 22 No H-bonds generated for 'chain 'B' and resid 19 through 22' Processing helix chain 'B' and resid 24 through 44 Proline residue: B 41 - end of helix Processing helix chain 'B' and resid 60 through 68 Processing helix chain 'B' and resid 73 through 84 Processing helix chain 'B' and resid 86 through 106 removed outlier: 3.685A pdb=" N HIS B 102 " --> pdb=" O HIS B 98 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU B 105 " --> pdb=" O TRP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 158 removed outlier: 3.808A pdb=" N LEU B 134 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA B 136 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 213 removed outlier: 3.613A pdb=" N LEU B 210 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 220 Processing helix chain 'C' and resid 3 through 13 removed outlier: 4.207A pdb=" N ALA C 11 " --> pdb=" O ARG C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 22 No H-bonds generated for 'chain 'C' and resid 19 through 22' Processing helix chain 'C' and resid 24 through 44 Proline residue: C 41 - end of helix Processing helix chain 'C' and resid 60 through 68 Processing helix chain 'C' and resid 73 through 84 Processing helix chain 'C' and resid 86 through 106 removed outlier: 3.685A pdb=" N HIS C 102 " --> pdb=" O HIS C 98 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU C 104 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU C 105 " --> pdb=" O TRP C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 158 removed outlier: 3.807A pdb=" N LEU C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TRP C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 213 removed outlier: 3.612A pdb=" N LEU C 210 " --> pdb=" O THR C 206 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 220 Processing helix chain 'D' and resid 3 through 13 removed outlier: 4.207A pdb=" N ALA D 11 " --> pdb=" O ARG D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 22 No H-bonds generated for 'chain 'D' and resid 19 through 22' Processing helix chain 'D' and resid 24 through 44 Proline residue: D 41 - end of helix Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 73 through 84 Processing helix chain 'D' and resid 86 through 106 removed outlier: 3.685A pdb=" N HIS D 102 " --> pdb=" O HIS D 98 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU D 105 " --> pdb=" O TRP D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 158 removed outlier: 3.808A pdb=" N LEU D 134 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP D 135 " --> pdb=" O LEU D 131 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA D 136 " --> pdb=" O ARG D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 213 removed outlier: 3.613A pdb=" N LEU D 210 " --> pdb=" O THR D 206 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU D 213 " --> pdb=" O GLU D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 220 Processing helix chain 'E' and resid 3 through 13 removed outlier: 4.207A pdb=" N ALA E 11 " --> pdb=" O ARG E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 22 No H-bonds generated for 'chain 'E' and resid 19 through 22' Processing helix chain 'E' and resid 24 through 44 Proline residue: E 41 - end of helix Processing helix chain 'E' and resid 60 through 68 Processing helix chain 'E' and resid 73 through 84 Processing helix chain 'E' and resid 86 through 106 removed outlier: 3.685A pdb=" N HIS E 102 " --> pdb=" O HIS E 98 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU E 104 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU E 105 " --> pdb=" O TRP E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 158 removed outlier: 3.808A pdb=" N LEU E 134 " --> pdb=" O SER E 130 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA E 136 " --> pdb=" O ARG E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 213 removed outlier: 3.613A pdb=" N LEU E 210 " --> pdb=" O THR E 206 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU E 213 " --> pdb=" O GLU E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 220 Processing helix chain 'F' and resid 3 through 13 removed outlier: 4.207A pdb=" N ALA F 11 " --> pdb=" O ARG F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 22 No H-bonds generated for 'chain 'F' and resid 19 through 22' Processing helix chain 'F' and resid 24 through 44 Proline residue: F 41 - end of helix Processing helix chain 'F' and resid 60 through 68 Processing helix chain 'F' and resid 73 through 84 Processing helix chain 'F' and resid 86 through 106 removed outlier: 3.685A pdb=" N HIS F 102 " --> pdb=" O HIS F 98 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU F 104 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU F 105 " --> pdb=" O TRP F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 158 removed outlier: 3.807A pdb=" N LEU F 134 " --> pdb=" O SER F 130 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP F 135 " --> pdb=" O LEU F 131 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA F 136 " --> pdb=" O ARG F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 213 removed outlier: 3.612A pdb=" N LEU F 210 " --> pdb=" O THR F 206 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 220 Processing sheet with id= A, first strand: chain 'A' and resid 51 through 53 removed outlier: 3.530A pdb=" N ILE A 178 " --> pdb=" O CYS A 169 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS A 169 " --> pdb=" O ILE A 178 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 51 through 53 removed outlier: 3.530A pdb=" N ILE B 178 " --> pdb=" O CYS B 169 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS B 169 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 51 through 53 removed outlier: 3.530A pdb=" N ILE C 178 " --> pdb=" O CYS C 169 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS C 169 " --> pdb=" O ILE C 178 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 51 through 53 removed outlier: 3.530A pdb=" N ILE D 178 " --> pdb=" O CYS D 169 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS D 169 " --> pdb=" O ILE D 178 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 51 through 53 removed outlier: 3.530A pdb=" N ILE E 178 " --> pdb=" O CYS E 169 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS E 169 " --> pdb=" O ILE E 178 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 51 through 53 removed outlier: 3.530A pdb=" N ILE F 178 " --> pdb=" O CYS F 169 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS F 169 " --> pdb=" O ILE F 178 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1764 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: 6.93 Time building geometry restraints manager: 15.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9516 1.03 - 1.23: 22 1.23 - 1.42: 4350 1.42 - 1.62: 5738 1.62 - 1.82: 84 Bond restraints: 19710 Sorted by residual: bond pdb=" CBS LMN F 301 " pdb=" CCM LMN F 301 " ideal model delta sigma weight residual 1.529 1.617 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" CBS LMN B 301 " pdb=" CCM LMN B 301 " ideal model delta sigma weight residual 1.529 1.617 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" CBS LMN A 301 " pdb=" CCM LMN A 301 " ideal model delta sigma weight residual 1.529 1.617 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CBS LMN C 301 " pdb=" CCM LMN C 301 " ideal model delta sigma weight residual 1.529 1.617 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CBS LMN E 301 " pdb=" CCM LMN E 301 " ideal model delta sigma weight residual 1.529 1.617 -0.088 2.00e-02 2.50e+03 1.92e+01 ... (remaining 19705 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.07: 981 107.07 - 113.80: 21995 113.80 - 120.53: 7094 120.53 - 127.27: 5131 127.27 - 134.00: 169 Bond angle restraints: 35370 Sorted by residual: angle pdb=" CA ARG A 220 " pdb=" CB ARG A 220 " pdb=" CG ARG A 220 " ideal model delta sigma weight residual 114.10 120.12 -6.02 2.00e+00 2.50e-01 9.05e+00 angle pdb=" CA ARG C 220 " pdb=" CB ARG C 220 " pdb=" CG ARG C 220 " ideal model delta sigma weight residual 114.10 120.05 -5.95 2.00e+00 2.50e-01 8.86e+00 angle pdb=" CA ARG B 220 " pdb=" CB ARG B 220 " pdb=" CG ARG B 220 " ideal model delta sigma weight residual 114.10 120.05 -5.95 2.00e+00 2.50e-01 8.86e+00 angle pdb=" CA ARG D 220 " pdb=" CB ARG D 220 " pdb=" CG ARG D 220 " ideal model delta sigma weight residual 114.10 120.05 -5.95 2.00e+00 2.50e-01 8.85e+00 angle pdb=" CA ARG F 220 " pdb=" CB ARG F 220 " pdb=" CG ARG F 220 " ideal model delta sigma weight residual 114.10 120.05 -5.95 2.00e+00 2.50e-01 8.84e+00 ... (remaining 35365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.56: 7257 21.56 - 43.11: 483 43.11 - 64.67: 96 64.67 - 86.22: 12 86.22 - 107.78: 12 Dihedral angle restraints: 7860 sinusoidal: 3570 harmonic: 4290 Sorted by residual: dihedral pdb=" CAZ LMN F 301 " pdb=" CBB LMN F 301 " pdb=" CBD LMN F 301 " pdb=" CBF LMN F 301 " ideal model delta sinusoidal sigma weight residual -179.71 -71.93 -107.78 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" CAZ LMN B 301 " pdb=" CBB LMN B 301 " pdb=" CBD LMN B 301 " pdb=" CBF LMN B 301 " ideal model delta sinusoidal sigma weight residual -179.71 -71.94 -107.77 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" CAZ LMN C 301 " pdb=" CBB LMN C 301 " pdb=" CBD LMN C 301 " pdb=" CBF LMN C 301 " ideal model delta sinusoidal sigma weight residual -179.71 -71.94 -107.77 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 7857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1272 0.044 - 0.087: 198 0.087 - 0.131: 75 0.131 - 0.174: 9 0.174 - 0.218: 18 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CCQ LMN C 301 " pdb=" CCF LMN C 301 " pdb=" CCH LMN C 301 " pdb=" OCB LMN C 301 " both_signs ideal model delta sigma weight residual False -2.61 -2.39 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CCQ LMN A 301 " pdb=" CCF LMN A 301 " pdb=" CCH LMN A 301 " pdb=" OCB LMN A 301 " both_signs ideal model delta sigma weight residual False -2.61 -2.39 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CCQ LMN D 301 " pdb=" CCF LMN D 301 " pdb=" CCH LMN D 301 " pdb=" OCB LMN D 301 " both_signs ideal model delta sigma weight residual False -2.61 -2.39 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1569 not shown) Planarity restraints: 2778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 18 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO F 19 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO F 19 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 19 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 18 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO C 19 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 19 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 19 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 18 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO B 19 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 19 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 19 " 0.023 5.00e-02 4.00e+02 ... (remaining 2775 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 3151 2.30 - 2.88: 40234 2.88 - 3.45: 43556 3.45 - 4.03: 61066 4.03 - 4.60: 94281 Nonbonded interactions: 242288 Sorted by model distance: nonbonded pdb=" O CYS B 202 " pdb=" HG1 THR B 206 " model vdw 1.725 1.850 nonbonded pdb=" O CYS D 202 " pdb=" HG1 THR D 206 " model vdw 1.726 1.850 nonbonded pdb=" O CYS E 202 " pdb=" HG1 THR E 206 " model vdw 1.726 1.850 nonbonded pdb=" O CYS F 202 " pdb=" HG1 THR F 206 " model vdw 1.727 1.850 nonbonded pdb=" O CYS C 202 " pdb=" HG1 THR C 206 " model vdw 1.728 1.850 ... (remaining 242283 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 66 5.16 5 C 6516 2.51 5 N 1620 2.21 5 O 1686 1.98 5 H 9528 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic 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: 1.760 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: 0.260 Extract box with map and model: 9.110 Check model and map are aligned: 0.280 Process input model: 58.460 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.180 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 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 : 0.009 0.088 10182 Z= 0.582 Angle : 0.925 7.353 13818 Z= 0.402 Chirality : 0.043 0.218 1572 Planarity : 0.006 0.042 1644 Dihedral : 17.165 107.778 3528 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer Outliers : 5.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -5.00 (0.16), residues: 1182 helix: -3.18 (0.11), residues: 858 sheet: -1.56 (0.56), residues: 60 loop : -3.20 (0.29), residues: 264 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 149 time to evaluate : 1.726 Fit side-chains outliers start: 54 outliers final: 4 residues processed: 184 average time/residue: 3.5367 time to fit residues: 679.4534 Evaluate side-chains 125 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 0.935 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.1604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.023 10182 Z= 0.273 Angle : 0.722 4.969 13818 Z= 0.363 Chirality : 0.039 0.133 1572 Planarity : 0.006 0.037 1644 Dihedral : 13.515 94.150 1434 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.73 (0.22), residues: 1182 helix: 0.39 (0.16), residues: 864 sheet: -1.22 (0.56), residues: 60 loop : -3.14 (0.29), residues: 258 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 1.679 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 141 average time/residue: 2.5588 time to fit residues: 378.9662 Evaluate side-chains 126 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 0.934 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 1.1343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 10182 Z= 0.226 Angle : 0.602 4.375 13818 Z= 0.292 Chirality : 0.036 0.119 1572 Planarity : 0.005Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 152 average time/residue: 2.9820 time to fit residues: 478.4892 Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 294, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 600, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 180, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 132, in run_one_one result.show(prefix=" ") File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 112, in show self.log.flush() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/libtbx/utils.py", line 1570, in flush if (flush is not None): flush() IOError: [Errno 28] No space left on device