Starting phenix.real_space_refine (version: dev) on Mon Feb 20 10:44:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5h_10697/02_2023/6y5h_10697.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5h_10697/02_2023/6y5h_10697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5h_10697/02_2023/6y5h_10697.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5h_10697/02_2023/6y5h_10697.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5h_10697/02_2023/6y5h_10697.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5h_10697/02_2023/6y5h_10697.pdb" } resolution = 3.0 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= 0.003 sd= 0.253 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 ASP 31": "OD1" <-> "OD2" Residue "A ASP 63": "OD1" <-> "OD2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "B ASP 160": "OD1" <-> "OD2" Residue "C ASP 31": "OD1" <-> "OD2" Residue "C ASP 63": "OD1" <-> "OD2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 241": "OD1" <-> "OD2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E ASP 63": "OD1" <-> "OD2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 241": "OD1" <-> "OD2" Residue "E TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 46": "OD1" <-> "OD2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 158": "OD1" <-> "OD2" Residue "D ASP 160": "OD1" <-> "OD2" Residue "F PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 46": "OD1" <-> "OD2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 158": "OD1" <-> "OD2" Residue "F ASP 160": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11994 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "B" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "C" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "E" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "D" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "F" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.80, per 1000 atoms: 0.65 Number of scatterers: 11994 At special positions: 0 Unit cell: (86.11, 87.2, 149.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 2424 8.00 N 2055 7.00 C 7458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.11 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=1.96 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.01 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " 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 ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA J 3 " - " MAN J 5 " " BMA L 3 " - " MAN L 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 401 " - " ASN A 38 " " NAG A 409 " - " ASN A 81 " " NAG C 401 " - " ASN C 38 " " NAG C 409 " - " ASN C 81 " " NAG E 401 " - " ASN E 38 " " NAG E 409 " - " ASN E 81 " " NAG G 1 " - " ASN A 165 " " NAG H 1 " - " ASN A 285 " " NAG I 1 " - " ASN B 154 " " NAG J 1 " - " ASN C 165 " " NAG K 1 " - " ASN C 285 " " NAG L 1 " - " ASN E 165 " " NAG M 1 " - " ASN E 285 " " NAG N 1 " - " ASN D 154 " " NAG O 1 " - " ASN F 154 " Time building additional restraints: 5.09 Conformation dependent library (CDL) restraints added in 2.0 seconds 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2706 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 33 sheets defined 26.1% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.816A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 187 through 193 removed outlier: 3.802A pdb=" N GLN A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 56 removed outlier: 3.867A pdb=" N THR B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 126 removed outlier: 3.595A pdb=" N TYR B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 removed outlier: 3.850A pdb=" N GLU B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 161 removed outlier: 3.777A pdb=" N VAL B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 158 through 161' Processing helix chain 'B' and resid 162 through 172 removed outlier: 3.648A pdb=" N GLN B 172 " --> pdb=" O ASN B 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.816A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'C' and resid 187 through 193 removed outlier: 3.801A pdb=" N GLN C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 76 through 80 removed outlier: 3.815A pdb=" N GLN E 80 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 114 Processing helix chain 'E' and resid 187 through 193 removed outlier: 3.802A pdb=" N GLN E 191 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 56 removed outlier: 3.867A pdb=" N THR D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 126 removed outlier: 3.595A pdb=" N TYR D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.850A pdb=" N GLU D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 161 removed outlier: 3.778A pdb=" N VAL D 161 " --> pdb=" O ASP D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 158 through 161' Processing helix chain 'D' and resid 162 through 172 removed outlier: 3.648A pdb=" N GLN D 172 " --> pdb=" O ASN D 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 56 removed outlier: 3.867A pdb=" N THR F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 126 removed outlier: 3.595A pdb=" N TYR F 94 " --> pdb=" O ASP F 90 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET F 115 " --> pdb=" O THR F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 154 removed outlier: 3.850A pdb=" N GLU F 150 " --> pdb=" O ASN F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 161 removed outlier: 3.777A pdb=" N VAL F 161 " --> pdb=" O ASP F 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 158 through 161' Processing helix chain 'F' and resid 162 through 172 removed outlier: 3.647A pdb=" N GLN F 172 " --> pdb=" O ASN F 168 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.064A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 61 removed outlier: 6.691A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 122 removed outlier: 6.686A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AB3, first strand: chain 'D' and resid 35 through 36 removed outlier: 3.517A pdb=" N GLY D 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY C 16 " --> pdb=" O GLY D 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.064A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.691A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 122 removed outlier: 6.686A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC2, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AC3, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC4, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AC5, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AC6, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AC7, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC8, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'E' and resid 51 through 52 removed outlier: 6.064A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 58 through 61 removed outlier: 6.690A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 120 through 122 removed outlier: 6.687A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD4, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AD5, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD6, first strand: chain 'E' and resid 286 through 287 427 hydrogen bonds defined for protein. 1173 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: 3.36 Time building geometry restraints manager: 5.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3868 1.34 - 1.46: 2158 1.46 - 1.58: 6130 1.58 - 1.70: 0 1.70 - 1.81: 78 Bond restraints: 12234 Sorted by residual: bond pdb=" N PHE E 79 " pdb=" CA PHE E 79 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.10e-02 8.26e+03 7.76e+00 bond pdb=" N PHE A 79 " pdb=" CA PHE A 79 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.10e-02 8.26e+03 7.75e+00 bond pdb=" N GLN E 80 " pdb=" CA GLN E 80 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.25e-02 6.40e+03 7.55e+00 bond pdb=" N ILE C 214 " pdb=" CA ILE C 214 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.23e-02 6.61e+03 7.53e+00 bond pdb=" N GLN A 80 " pdb=" CA GLN A 80 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.25e-02 6.40e+03 7.48e+00 ... (remaining 12229 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.26: 431 107.26 - 113.98: 7003 113.98 - 120.69: 4651 120.69 - 127.41: 4386 127.41 - 134.13: 119 Bond angle restraints: 16590 Sorted by residual: angle pdb=" CA ASN E 81 " pdb=" C ASN E 81 " pdb=" O ASN E 81 " ideal model delta sigma weight residual 121.28 117.58 3.70 1.19e+00 7.06e-01 9.68e+00 angle pdb=" CA ASN C 81 " pdb=" C ASN C 81 " pdb=" O ASN C 81 " ideal model delta sigma weight residual 121.28 117.60 3.68 1.19e+00 7.06e-01 9.58e+00 angle pdb=" CA ASN A 81 " pdb=" C ASN A 81 " pdb=" O ASN A 81 " ideal model delta sigma weight residual 121.28 117.60 3.68 1.19e+00 7.06e-01 9.55e+00 angle pdb=" C VAL A 78 " pdb=" N PHE A 79 " pdb=" CA PHE A 79 " ideal model delta sigma weight residual 122.83 118.65 4.18 1.54e+00 4.22e-01 7.38e+00 angle pdb=" C VAL C 78 " pdb=" N PHE C 79 " pdb=" CA PHE C 79 " ideal model delta sigma weight residual 122.83 118.66 4.17 1.54e+00 4.22e-01 7.34e+00 ... (remaining 16585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 6594 17.89 - 35.78: 533 35.78 - 53.68: 145 53.68 - 71.57: 27 71.57 - 89.46: 24 Dihedral angle restraints: 7323 sinusoidal: 3105 harmonic: 4218 Sorted by residual: dihedral pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual 93.00 3.54 89.46 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS B 148 " pdb=" CB CYS B 148 " ideal model delta sinusoidal sigma weight residual 93.00 3.60 89.40 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CB CYS F 144 " pdb=" SG CYS F 144 " pdb=" SG CYS F 148 " pdb=" CB CYS F 148 " ideal model delta sinusoidal sigma weight residual 93.00 3.62 89.38 1 1.00e+01 1.00e-02 9.50e+01 ... (remaining 7320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.236: 1908 0.236 - 0.472: 3 0.472 - 0.708: 6 0.708 - 0.943: 0 0.943 - 1.179: 3 Chirality restraints: 1920 Sorted by residual: chirality pdb=" C1 MAN J 4 " pdb=" O3 BMA J 3 " pdb=" C2 MAN J 4 " pdb=" O5 MAN J 4 " both_signs ideal model delta sigma weight residual False 2.40 1.22 1.18 2.00e-02 2.50e+03 3.48e+03 chirality pdb=" C1 MAN G 4 " pdb=" O3 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 1.22 1.18 2.00e-02 2.50e+03 3.48e+03 chirality pdb=" C1 MAN L 4 " pdb=" O3 BMA L 3 " pdb=" C2 MAN L 4 " pdb=" O5 MAN L 4 " both_signs ideal model delta sigma weight residual False 2.40 1.22 1.18 2.00e-02 2.50e+03 3.46e+03 ... (remaining 1917 not shown) Planarity restraints: 2142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 409 " -0.167 2.00e-02 2.50e+03 1.38e-01 2.38e+02 pdb=" C7 NAG E 409 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG E 409 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG E 409 " 0.223 2.00e-02 2.50e+03 pdb=" O7 NAG E 409 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 409 " -0.167 2.00e-02 2.50e+03 1.38e-01 2.37e+02 pdb=" C7 NAG A 409 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG A 409 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG A 409 " 0.222 2.00e-02 2.50e+03 pdb=" O7 NAG A 409 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 409 " -0.167 2.00e-02 2.50e+03 1.38e-01 2.37e+02 pdb=" C7 NAG C 409 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG C 409 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG C 409 " 0.222 2.00e-02 2.50e+03 pdb=" O7 NAG C 409 " 0.022 2.00e-02 2.50e+03 ... (remaining 2139 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1954 2.77 - 3.30: 9864 3.30 - 3.84: 18906 3.84 - 4.37: 22571 4.37 - 4.90: 40324 Nonbonded interactions: 93619 Sorted by model distance: nonbonded pdb=" N GLY F 1 " pdb=" OD2 ASP F 112 " model vdw 2.238 2.520 nonbonded pdb=" N GLY B 1 " pdb=" OD2 ASP B 112 " model vdw 2.238 2.520 nonbonded pdb=" N GLY D 1 " pdb=" OD2 ASP D 112 " model vdw 2.239 2.520 nonbonded pdb=" OD1 ASP C 68 " pdb=" OH TYR C 100 " model vdw 2.337 2.440 nonbonded pdb=" OD1 ASP E 68 " pdb=" OH TYR E 100 " model vdw 2.337 2.440 ... (remaining 93614 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 7458 2.51 5 N 2055 2.21 5 O 2424 1.98 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: 5.320 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: 0.010 Extract box with map and model: 13.630 Check model and map are aligned: 0.180 Process input model: 33.770 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5647 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 : 0.002 0.034 12234 Z= 0.165 Angle : 0.559 6.176 16590 Z= 0.337 Chirality : 0.073 1.179 1920 Planarity : 0.007 0.138 2127 Dihedral : 14.944 88.687 4563 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -2.50 (0.18), residues: 1458 helix: -0.26 (0.26), residues: 348 sheet: -0.34 (0.31), residues: 243 loop : -2.83 (0.15), residues: 867 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 267 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 274 average time/residue: 1.0095 time to fit residues: 305.1350 Evaluate side-chains 140 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.8753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 0.1980 chunk 84 optimal weight: 0.3980 chunk 130 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 216 ASN B 27 GLN C 18 HIS C 54 ASN C 132 GLN C 197 GLN C 211 GLN E 18 HIS E 54 ASN E 132 GLN E 188 ASN D 78 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.6630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.097 12234 Z= 0.449 Angle : 0.904 11.021 16590 Z= 0.481 Chirality : 0.058 0.651 1920 Planarity : 0.007 0.053 2127 Dihedral : 5.971 46.144 1818 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 6.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.74 (0.19), residues: 1458 helix: -0.13 (0.25), residues: 360 sheet: -0.09 (0.33), residues: 258 loop : -2.07 (0.17), residues: 840 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 234 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 18 residues processed: 297 average time/residue: 1.1075 time to fit residues: 359.8912 Evaluate side-chains 180 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 162 time to evaluate : 1.522 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 1 average time/residue: 0.2523 time to fit residues: 2.3295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 116 optimal weight: 0.4980 chunk 129 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 28 ASN B 34 GLN C 18 HIS C 75 HIS C 248 ASN C 312 ASN E 18 HIS E 191 GLN D 47 GLN D 78 GLN D 105 GLN D 125 GLN D 146 ASN F 12 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.8628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 12234 Z= 0.342 Angle : 0.643 9.077 16590 Z= 0.345 Chirality : 0.049 0.366 1920 Planarity : 0.005 0.051 2127 Dihedral : 5.344 37.670 1818 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 6.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.18 (0.20), residues: 1458 helix: 1.23 (0.28), residues: 357 sheet: 0.21 (0.33), residues: 234 loop : -2.08 (0.17), residues: 867 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 174 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 33 residues processed: 242 average time/residue: 0.9860 time to fit residues: 263.7010 Evaluate side-chains 188 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 155 time to evaluate : 1.372 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 28 residues processed: 5 average time/residue: 0.1502 time to fit residues: 3.1287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS C 75 HIS E 18 HIS E 295 GLN D 34 GLN D 47 GLN D 105 GLN F 28 ASN F 34 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.9800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 12234 Z= 0.346 Angle : 0.631 9.895 16590 Z= 0.340 Chirality : 0.048 0.264 1920 Planarity : 0.005 0.047 2127 Dihedral : 5.341 46.824 1818 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer Outliers : 6.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.06 (0.20), residues: 1458 helix: 1.31 (0.27), residues: 357 sheet: 0.63 (0.36), residues: 204 loop : -2.02 (0.17), residues: 897 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 167 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 38 residues processed: 233 average time/residue: 1.0291 time to fit residues: 264.8193 Evaluate side-chains 188 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 1.661 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 35 residues processed: 3 average time/residue: 0.1674 time to fit residues: 2.7577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/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-4877/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: 50.8005 > 50: distance: 38 - 226: 11.033 distance: 51 - 211: 11.120 distance: 54 - 208: 5.240 distance: 89 - 169: 26.832 distance: 92 - 166: 10.232 distance: 114 - 234: 12.468 distance: 117 - 231: 4.729 distance: 127 - 219: 8.414 distance: 161 - 166: 9.544 distance: 166 - 167: 9.264 distance: 167 - 168: 12.784 distance: 167 - 170: 14.890 distance: 168 - 169: 17.084 distance: 168 - 173: 33.948 distance: 170 - 171: 10.284 distance: 170 - 172: 9.501 distance: 173 - 174: 15.659 distance: 174 - 175: 9.430 distance: 174 - 177: 18.774 distance: 175 - 176: 26.351 distance: 175 - 182: 3.058 distance: 177 - 178: 23.844 distance: 178 - 179: 21.890 distance: 179 - 180: 7.006 distance: 180 - 181: 4.638 distance: 182 - 183: 7.992 distance: 182 - 188: 6.453 distance: 183 - 184: 6.624 distance: 183 - 186: 15.587 distance: 184 - 185: 13.184 distance: 184 - 189: 9.292 distance: 186 - 187: 16.106 distance: 187 - 188: 16.570 distance: 189 - 190: 16.563 distance: 190 - 191: 7.797 distance: 191 - 192: 12.897 distance: 191 - 193: 8.791 distance: 193 - 194: 3.442 distance: 194 - 195: 6.398 distance: 194 - 197: 3.204 distance: 195 - 196: 14.293 distance: 195 - 201: 5.407 distance: 197 - 198: 6.368 distance: 198 - 199: 5.980 distance: 198 - 200: 7.434 distance: 201 - 202: 8.704 distance: 202 - 203: 9.632 distance: 202 - 205: 8.130 distance: 203 - 204: 3.512 distance: 203 - 208: 7.462 distance: 205 - 206: 18.884 distance: 205 - 207: 14.029 distance: 208 - 209: 5.368 distance: 209 - 212: 5.423 distance: 210 - 211: 10.459 distance: 210 - 216: 4.694 distance: 212 - 213: 5.892 distance: 213 - 214: 14.236 distance: 213 - 215: 8.235 distance: 216 - 217: 6.965 distance: 217 - 218: 3.175 distance: 217 - 220: 9.328 distance: 218 - 219: 6.050 distance: 218 - 223: 5.874 distance: 220 - 221: 6.503 distance: 220 - 222: 12.667 distance: 223 - 224: 3.913 distance: 225 - 226: 7.090 distance: 227 - 228: 3.829 distance: 227 - 229: 5.900 distance: 231 - 232: 3.387 distance: 232 - 235: 4.651 distance: 233 - 234: 9.168