Starting phenix.real_space_refine on Thu Jan 18 05:21:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8n_10125/01_2024/6s8n_10125_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8n_10125/01_2024/6s8n_10125.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8n_10125/01_2024/6s8n_10125_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8n_10125/01_2024/6s8n_10125_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8n_10125/01_2024/6s8n_10125_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8n_10125/01_2024/6s8n_10125.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8n_10125/01_2024/6s8n_10125.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8n_10125/01_2024/6s8n_10125_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8n_10125/01_2024/6s8n_10125_updated.pdb" } resolution = 3.1 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= -0.000 sd= 0.005 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 P 2 5.49 5 S 45 5.16 5 C 5092 2.51 5 N 1301 2.21 5 O 1391 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 21": "OD1" <-> "OD2" Residue "A ASP 63": "OD1" <-> "OD2" Residue "A ASP 64": "OD1" <-> "OD2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A ASP 132": "OD1" <-> "OD2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ASP 227": "OD1" <-> "OD2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "B ASP 21": "OD1" <-> "OD2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B ASP 63": "OD1" <-> "OD2" Residue "B ASP 108": "OD1" <-> "OD2" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "B PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B ASP 169": "OD1" <-> "OD2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "B ASP 185": "OD1" <-> "OD2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "C ARG 6": "NH1" <-> "NH2" Residue "F GLU 10": "OE1" <-> "OE2" Residue "F PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 40": "OD1" <-> "OD2" Residue "F GLU 58": "OE1" <-> "OE2" Residue "F TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 130": "OE1" <-> "OE2" Residue "F ARG 295": "NH1" <-> "NH2" Residue "F TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 8": "OD1" <-> "OD2" Residue "G PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 133": "NH1" <-> "NH2" Residue "G TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 7831 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1868 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 8, 'TRANS': 230} Chain: "B" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1857 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "C" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 187 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "F" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1864 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 9, 'TRANS': 229} Chain breaks: 1 Chain: "G" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1778 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 12, 'TRANS': 217} Chain breaks: 3 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'DCQ': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'LMN': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 26 Chain: "G" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 206 Unusual residues: {'DCQ': 1, 'L0W': 1, 'LMN': 1, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 20 Time building chain proxies: 4.72, per 1000 atoms: 0.60 Number of scatterers: 7831 At special positions: 0 Unit cell: (109.512, 78.078, 100.386, 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 45 16.00 P 2 15.00 O 1391 8.00 N 1301 7.00 C 5092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Atom "HETATM 7575 O3 DCQ B 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7575 O3 DCQ B 301 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 1.6 seconds 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1800 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 8 sheets defined 44.6% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 44 through 50 removed outlier: 3.938A pdb=" N VAL A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 75 No H-bonds generated for 'chain 'A' and resid 72 through 75' Processing helix chain 'A' and resid 95 through 103 removed outlier: 4.195A pdb=" N LEU A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 124 removed outlier: 4.079A pdb=" N ASN A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 152 Processing helix chain 'A' and resid 173 through 185 removed outlier: 3.833A pdb=" N ILE A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 224 No H-bonds generated for 'chain 'A' and resid 221 through 224' Processing helix chain 'A' and resid 230 through 233 No H-bonds generated for 'chain 'A' and resid 230 through 233' Processing helix chain 'B' and resid 41 through 50 removed outlier: 3.700A pdb=" N VAL B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 75 No H-bonds generated for 'chain 'B' and resid 72 through 75' Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 111 through 125 removed outlier: 4.075A pdb=" N GLU B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU B 123 " --> pdb=" O ASN B 119 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 151 removed outlier: 3.686A pdb=" N ARG B 144 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 146 " --> pdb=" O GLU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.589A pdb=" N LEU B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 200 No H-bonds generated for 'chain 'B' and resid 197 through 200' Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.588A pdb=" N LEU B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 225' Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.603A pdb=" N ARG B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL B 233 " --> pdb=" O HIS B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 228 through 233' Processing helix chain 'C' and resid 6 through 22 removed outlier: 3.670A pdb=" N VAL C 11 " --> pdb=" O TRP C 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 36 removed outlier: 3.531A pdb=" N LEU F 7 " --> pdb=" O ILE F 3 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS F 13 " --> pdb=" O ARG F 9 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER F 14 " --> pdb=" O GLU F 10 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU F 23 " --> pdb=" O LEU F 19 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 24 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG F 33 " --> pdb=" O GLN F 29 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE F 34 " --> pdb=" O LYS F 30 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU F 35 " --> pdb=" O LEU F 31 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY F 36 " --> pdb=" O VAL F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 53 No H-bonds generated for 'chain 'F' and resid 50 through 53' Processing helix chain 'F' and resid 56 through 81 removed outlier: 4.065A pdb=" N GLN F 61 " --> pdb=" O PRO F 57 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE F 63 " --> pdb=" O MET F 59 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) Proline residue: F 65 - end of helix removed outlier: 3.835A pdb=" N LEU F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR F 81 " --> pdb=" O GLY F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 96 through 110 removed outlier: 3.667A pdb=" N ILE F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 281 removed outlier: 3.807A pdb=" N LEU F 272 " --> pdb=" O TRP F 268 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL F 276 " --> pdb=" O LEU F 272 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE F 277 " --> pdb=" O VAL F 273 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA F 280 " --> pdb=" O VAL F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 317 removed outlier: 3.605A pdb=" N LEU F 300 " --> pdb=" O LEU F 297 " (cutoff:3.500A) Proline residue: F 301 - end of helix removed outlier: 4.453A pdb=" N LEU F 304 " --> pdb=" O PRO F 301 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR F 306 " --> pdb=" O MET F 303 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU F 307 " --> pdb=" O LEU F 304 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU F 308 " --> pdb=" O LEU F 305 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU F 311 " --> pdb=" O LEU F 308 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE F 312 " --> pdb=" O PHE F 309 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN F 313 " --> pdb=" O PHE F 310 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR F 314 " --> pdb=" O LEU F 311 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU F 316 " --> pdb=" O GLN F 313 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS F 317 " --> pdb=" O THR F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 322 No H-bonds generated for 'chain 'F' and resid 319 through 322' Processing helix chain 'F' and resid 329 through 346 removed outlier: 3.895A pdb=" N VAL F 334 " --> pdb=" O TRP F 330 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN F 335 " --> pdb=" O MET F 331 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN F 346 " --> pdb=" O ALA F 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 32 removed outlier: 3.574A pdb=" N GLY G 12 " --> pdb=" O ASP G 8 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS G 13 " --> pdb=" O ARG G 9 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR G 18 " --> pdb=" O THR G 14 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER G 30 " --> pdb=" O LEU G 26 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE G 32 " --> pdb=" O SER G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 58 No H-bonds generated for 'chain 'G' and resid 55 through 58' Processing helix chain 'G' and resid 60 through 66 Processing helix chain 'G' and resid 68 through 85 removed outlier: 3.732A pdb=" N LEU G 73 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU G 83 " --> pdb=" O GLY G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 107 removed outlier: 4.055A pdb=" N SER G 105 " --> pdb=" O GLN G 101 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL G 106 " --> pdb=" O VAL G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 117 removed outlier: 3.526A pdb=" N LEU G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 123 No H-bonds generated for 'chain 'G' and resid 120 through 123' Processing helix chain 'G' and resid 125 through 133 removed outlier: 3.523A pdb=" N GLU G 129 " --> pdb=" O ALA G 125 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET G 131 " --> pdb=" O GLN G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 279 removed outlier: 3.672A pdb=" N LYS G 278 " --> pdb=" O ASN G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 294 Processing helix chain 'G' and resid 305 through 324 removed outlier: 3.670A pdb=" N PHE G 319 " --> pdb=" O PHE G 315 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR G 320 " --> pdb=" O GLY G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 332 No H-bonds generated for 'chain 'G' and resid 329 through 332' Processing helix chain 'G' and resid 343 through 355 removed outlier: 3.841A pdb=" N PHE G 348 " --> pdb=" O PRO G 344 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU G 350 " --> pdb=" O ALA G 346 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE G 351 " --> pdb=" O SER G 347 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER G 352 " --> pdb=" O PHE G 348 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.280A pdb=" N VAL A 190 " --> pdb=" O VAL A 32 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 80 through 83 removed outlier: 6.334A pdb=" N PHE A 158 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU A 83 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU A 160 " --> pdb=" O LEU A 83 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 9 through 11 removed outlier: 7.609A pdb=" N LYS A 11 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLU A 20 " --> pdb=" O LYS A 11 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 24 through 27 Processing sheet with id= F, first strand: chain 'B' and resid 32 through 35 removed outlier: 6.933A pdb=" N ARG B 206 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LEU B 35 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR B 208 " --> pdb=" O LEU B 35 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 81 through 83 removed outlier: 3.553A pdb=" N LEU B 83 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU B 191 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 9 through 11 removed outlier: 3.786A pdb=" N VAL B 22 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS B 11 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLU B 20 " --> pdb=" O LYS B 11 " (cutoff:3.500A) 207 hydrogen bonds defined for protein. 597 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: 1.73 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 2500 1.36 - 1.50: 1891 1.50 - 1.63: 3477 1.63 - 1.77: 3 1.77 - 1.90: 87 Bond restraints: 7958 Sorted by residual: bond pdb=" CAR L0W G 401 " pdb=" CAT L0W G 401 " ideal model delta sigma weight residual 1.514 1.783 -0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" CB GLN B 136 " pdb=" CG GLN B 136 " ideal model delta sigma weight residual 1.520 1.903 -0.383 3.00e-02 1.11e+03 1.63e+02 bond pdb=" C3 DCQ B 301 " pdb=" O3 DCQ B 301 " ideal model delta sigma weight residual 1.341 1.596 -0.255 2.00e-02 2.50e+03 1.63e+02 bond pdb=" CG GLN B 136 " pdb=" CD GLN B 136 " ideal model delta sigma weight residual 1.516 1.825 -0.309 2.50e-02 1.60e+03 1.53e+02 bond pdb=" C3M DCQ B 301 " pdb=" O3 DCQ B 301 " ideal model delta sigma weight residual 1.428 1.617 -0.189 2.00e-02 2.50e+03 8.96e+01 ... (remaining 7953 not shown) Histogram of bond angle deviations from ideal: 77.71 - 91.94: 1 91.94 - 106.17: 238 106.17 - 120.40: 7621 120.40 - 134.63: 2870 134.63 - 148.86: 7 Bond angle restraints: 10737 Sorted by residual: angle pdb=" CB GLN B 136 " pdb=" CG GLN B 136 " pdb=" CD GLN B 136 " ideal model delta sigma weight residual 112.60 146.50 -33.90 1.70e+00 3.46e-01 3.98e+02 angle pdb=" C3 DCQ B 301 " pdb=" O3 DCQ B 301 " pdb=" C3M DCQ B 301 " ideal model delta sigma weight residual 115.29 148.86 -33.57 3.00e+00 1.11e-01 1.25e+02 angle pdb=" CAR L0W G 401 " pdb=" CAT L0W G 401 " pdb=" OAU L0W G 401 " ideal model delta sigma weight residual 109.51 77.71 31.80 3.00e+00 1.11e-01 1.12e+02 angle pdb=" C4 DCQ B 301 " pdb=" O4 DCQ B 301 " pdb=" C4M DCQ B 301 " ideal model delta sigma weight residual 115.20 146.76 -31.56 3.00e+00 1.11e-01 1.11e+02 angle pdb=" CAR L0W G 401 " pdb=" CAT L0W G 401 " pdb=" CAV L0W G 401 " ideal model delta sigma weight residual 109.43 139.45 -30.02 3.00e+00 1.11e-01 1.00e+02 ... (remaining 10732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.97: 4708 31.97 - 63.95: 158 63.95 - 95.92: 18 95.92 - 127.90: 4 127.90 - 159.87: 2 Dihedral angle restraints: 4890 sinusoidal: 2105 harmonic: 2785 Sorted by residual: dihedral pdb=" CA GLY B 39 " pdb=" C GLY B 39 " pdb=" N ALA B 40 " pdb=" CA ALA B 40 " ideal model delta harmonic sigma weight residual 180.00 -136.91 -43.09 0 5.00e+00 4.00e-02 7.43e+01 dihedral pdb=" CA ILE A 62 " pdb=" C ILE A 62 " pdb=" N ASP A 63 " pdb=" CA ASP A 63 " ideal model delta harmonic sigma weight residual -180.00 -147.76 -32.24 0 5.00e+00 4.00e-02 4.16e+01 dihedral pdb=" CA ASP G 37 " pdb=" C ASP G 37 " pdb=" N GLN G 38 " pdb=" CA GLN G 38 " ideal model delta harmonic sigma weight residual 180.00 148.88 31.12 0 5.00e+00 4.00e-02 3.87e+01 ... (remaining 4887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1188 0.105 - 0.211: 77 0.211 - 0.316: 6 0.316 - 0.421: 1 0.421 - 0.527: 1 Chirality restraints: 1273 Sorted by residual: chirality pdb=" CFM L0W G 401 " pdb=" CFL L0W G 401 " pdb=" CFN L0W G 401 " pdb=" OFZ L0W G 401 " both_signs ideal model delta sigma weight residual False -2.55 -2.03 -0.53 2.00e-01 2.50e+01 6.93e+00 chirality pdb=" CB ILE B 62 " pdb=" CA ILE B 62 " pdb=" CG1 ILE B 62 " pdb=" CG2 ILE B 62 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C2 L0W G 401 " pdb=" C1 L0W G 401 " pdb=" C3 L0W G 401 " pdb=" N2 L0W G 401 " both_signs ideal model delta sigma weight residual False -2.57 -2.87 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 1270 not shown) Planarity restraints: 1311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ B 301 " 0.006 2.00e-02 2.50e+03 4.50e-02 6.08e+01 pdb=" C1M DCQ B 301 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DCQ B 301 " -0.002 2.00e-02 2.50e+03 pdb=" C3 DCQ B 301 " -0.013 2.00e-02 2.50e+03 pdb=" C4 DCQ B 301 " 0.078 2.00e-02 2.50e+03 pdb=" C5 DCQ B 301 " -0.020 2.00e-02 2.50e+03 pdb=" C6 DCQ B 301 " -0.025 2.00e-02 2.50e+03 pdb=" C7 DCQ B 301 " -0.017 2.00e-02 2.50e+03 pdb=" O2 DCQ B 301 " -0.004 2.00e-02 2.50e+03 pdb=" O3 DCQ B 301 " 0.036 2.00e-02 2.50e+03 pdb=" O4 DCQ B 301 " -0.104 2.00e-02 2.50e+03 pdb=" O5 DCQ B 301 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 L0W G 401 " -0.000 2.00e-02 2.50e+03 2.95e-02 1.09e+01 pdb=" C7 L0W G 401 " 0.057 2.00e-02 2.50e+03 pdb=" C8 L0W G 401 " -0.016 2.00e-02 2.50e+03 pdb=" N2 L0W G 401 " -0.018 2.00e-02 2.50e+03 pdb=" O7 L0W G 401 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA G 125 " -0.054 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO G 126 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO G 126 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO G 126 " -0.045 5.00e-02 4.00e+02 ... (remaining 1308 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 10 2.41 - 3.03: 3891 3.03 - 3.66: 11156 3.66 - 4.28: 17524 4.28 - 4.90: 28628 Nonbonded interactions: 61209 Sorted by model distance: nonbonded pdb=" CAP L0W G 401 " pdb=" CAR L0W G 401 " model vdw 1.791 3.840 nonbonded pdb=" CD GLN B 136 " pdb=" O3 DCQ B 301 " model vdw 2.103 2.616 nonbonded pdb=" CAN L0W G 401 " pdb=" CAR L0W G 401 " model vdw 2.253 3.870 nonbonded pdb=" OCB LMN F 401 " pdb=" OAP LMN G 402 " model vdw 2.291 2.440 nonbonded pdb=" CB GLN B 136 " pdb=" O3 DCQ B 301 " model vdw 2.322 2.752 ... (remaining 61204 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' and resid 2 through 239) selection = (chain 'B' and resid 2 through 239) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 0.950 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: 3.280 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 24.020 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 : 0.012 0.383 7958 Z= 0.838 Angle : 1.727 33.899 10737 Z= 0.758 Chirality : 0.060 0.527 1273 Planarity : 0.008 0.081 1311 Dihedral : 16.963 159.870 3090 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.72 % Favored : 91.07 % Rotamer: Outliers : 0.12 % Allowed : 7.94 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -6.61 (0.17), residues: 952 helix: -4.76 (0.08), residues: 550 sheet: -1.65 (0.64), residues: 67 loop : -3.90 (0.26), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 123 HIS 0.008 0.002 HIS A 229 PHE 0.026 0.002 PHE G 280 TYR 0.025 0.002 TYR B 234 ARG 0.009 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 LYS cc_start: 0.8375 (mtmm) cc_final: 0.8168 (mtpt) REVERT: B 35 LEU cc_start: 0.8656 (pp) cc_final: 0.8430 (pt) REVERT: B 96 TYR cc_start: 0.8985 (t80) cc_final: 0.8665 (t80) REVERT: B 116 ASP cc_start: 0.7873 (m-30) cc_final: 0.7473 (m-30) REVERT: C 1 MET cc_start: 0.8209 (pmm) cc_final: 0.7990 (pmm) REVERT: F 9 ARG cc_start: 0.8065 (ttp-110) cc_final: 0.7849 (ttm170) REVERT: F 21 ILE cc_start: 0.8700 (mt) cc_final: 0.8459 (mt) REVERT: F 127 HIS cc_start: 0.7718 (t70) cc_final: 0.7442 (t-90) REVERT: F 261 ARG cc_start: 0.6048 (mmm160) cc_final: 0.5615 (mmm160) outliers start: 1 outliers final: 1 residues processed: 193 average time/residue: 0.3000 time to fit residues: 71.3750 Evaluate side-chains 147 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 0.0010 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN A 98 ASN B 27 ASN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 HIS B 182 HIS F 89 HIS F 127 HIS F 267 ASN G 101 GLN G 274 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.214 7958 Z= 0.379 Angle : 0.768 15.413 10737 Z= 0.369 Chirality : 0.042 0.205 1273 Planarity : 0.005 0.066 1311 Dihedral : 13.898 153.360 1302 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.56 % Favored : 92.23 % Rotamer: Outliers : 1.83 % Allowed : 16.12 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.86 (0.22), residues: 952 helix: -3.22 (0.16), residues: 542 sheet: -1.16 (0.68), residues: 69 loop : -3.40 (0.29), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 119 HIS 0.002 0.001 HIS B 182 PHE 0.019 0.001 PHE G 295 TYR 0.016 0.001 TYR B 234 ARG 0.003 0.000 ARG F 295 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.7179 (m-80) REVERT: B 7 LYS cc_start: 0.8360 (mtmm) cc_final: 0.8154 (mtpt) REVERT: B 35 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8013 (pt) REVERT: B 47 TYR cc_start: 0.9014 (m-10) cc_final: 0.8808 (m-10) REVERT: F 100 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8249 (mtmt) REVERT: F 127 HIS cc_start: 0.7610 (t-90) cc_final: 0.7285 (t-170) outliers start: 15 outliers final: 11 residues processed: 156 average time/residue: 0.2444 time to fit residues: 49.0740 Evaluate side-chains 148 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 91 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 130 GLN G 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.213 7958 Z= 0.574 Angle : 0.872 15.910 10737 Z= 0.422 Chirality : 0.050 0.211 1273 Planarity : 0.006 0.059 1311 Dihedral : 13.997 147.130 1301 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.14 % Favored : 90.65 % Rotamer: Outliers : 3.66 % Allowed : 19.66 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -4.19 (0.24), residues: 952 helix: -2.56 (0.19), residues: 543 sheet: -1.00 (0.70), residues: 71 loop : -3.31 (0.29), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 119 HIS 0.006 0.002 HIS A 229 PHE 0.047 0.003 PHE G 295 TYR 0.019 0.002 TYR G 10 ARG 0.004 0.001 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 133 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 LYS cc_start: 0.8379 (mtmm) cc_final: 0.8178 (mtpt) REVERT: F 127 HIS cc_start: 0.7716 (t-90) cc_final: 0.7469 (t70) outliers start: 30 outliers final: 19 residues processed: 151 average time/residue: 0.2493 time to fit residues: 49.5542 Evaluate side-chains 141 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 294 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 0.2980 chunk 24 optimal weight: 0.0010 chunk 75 optimal weight: 0.6980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 ASN F 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.209 7958 Z= 0.357 Angle : 0.681 15.716 10737 Z= 0.331 Chirality : 0.042 0.284 1273 Planarity : 0.004 0.057 1311 Dihedral : 13.589 155.442 1301 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.93 % Favored : 92.96 % Rotamer: Outliers : 2.56 % Allowed : 22.22 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.25), residues: 952 helix: -1.88 (0.21), residues: 534 sheet: -0.71 (0.71), residues: 69 loop : -3.20 (0.29), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 123 HIS 0.003 0.001 HIS A 182 PHE 0.018 0.001 PHE G 295 TYR 0.010 0.001 TYR B 234 ARG 0.003 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 VAL cc_start: 0.9187 (m) cc_final: 0.8974 (p) REVERT: B 7 LYS cc_start: 0.8337 (mtmm) cc_final: 0.8109 (mtpt) REVERT: F 127 HIS cc_start: 0.7650 (t-90) cc_final: 0.7404 (t70) REVERT: G 319 PHE cc_start: 0.8876 (t80) cc_final: 0.8659 (t80) outliers start: 21 outliers final: 14 residues processed: 150 average time/residue: 0.2175 time to fit residues: 43.1283 Evaluate side-chains 139 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 294 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 77 optimal weight: 0.0980 chunk 62 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 22 optimal weight: 0.0040 chunk 30 optimal weight: 0.0980 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.208 7958 Z= 0.372 Angle : 0.682 15.466 10737 Z= 0.331 Chirality : 0.042 0.303 1273 Planarity : 0.004 0.053 1311 Dihedral : 13.364 170.470 1301 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.83 % Favored : 93.07 % Rotamer: Outliers : 3.42 % Allowed : 21.98 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.88 (0.26), residues: 952 helix: -1.35 (0.22), residues: 525 sheet: -0.46 (0.71), residues: 69 loop : -2.97 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 123 HIS 0.004 0.001 HIS A 195 PHE 0.022 0.001 PHE G 295 TYR 0.013 0.001 TYR G 10 ARG 0.003 0.000 ARG G 9 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 139 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8001 (mm) REVERT: A 115 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6869 (tm-30) REVERT: B 7 LYS cc_start: 0.8344 (mtmm) cc_final: 0.8114 (mtpt) REVERT: F 127 HIS cc_start: 0.7643 (t-90) cc_final: 0.7392 (t70) REVERT: F 249 MET cc_start: 0.5824 (tpt) cc_final: 0.4891 (pmm) REVERT: G 319 PHE cc_start: 0.8892 (t80) cc_final: 0.8668 (t80) outliers start: 28 outliers final: 19 residues processed: 161 average time/residue: 0.2125 time to fit residues: 45.3993 Evaluate side-chains 153 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 263 ARG Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 294 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.676 > 50: distance: 40 - 45: 26.232 distance: 45 - 46: 17.625 distance: 45 - 51: 14.802 distance: 46 - 47: 15.958 distance: 46 - 49: 26.383 distance: 47 - 48: 6.588 distance: 47 - 52: 42.011 distance: 49 - 50: 39.798 distance: 50 - 51: 34.693 distance: 52 - 53: 14.050 distance: 53 - 54: 26.531 distance: 53 - 56: 21.062 distance: 54 - 55: 7.305 distance: 54 - 59: 21.199 distance: 56 - 57: 42.560 distance: 56 - 58: 20.485 distance: 59 - 60: 25.596 distance: 60 - 61: 41.063 distance: 60 - 63: 16.414 distance: 61 - 62: 29.312 distance: 61 - 68: 29.526 distance: 63 - 64: 12.998 distance: 64 - 65: 17.107 distance: 65 - 66: 12.789 distance: 65 - 67: 17.128 distance: 68 - 69: 13.448 distance: 69 - 70: 20.944 distance: 69 - 72: 17.126 distance: 70 - 71: 19.387 distance: 70 - 76: 24.003 distance: 72 - 73: 44.492 distance: 72 - 74: 48.003 distance: 73 - 75: 49.913 distance: 76 - 77: 18.239 distance: 77 - 78: 37.489 distance: 77 - 80: 36.733 distance: 78 - 79: 21.087 distance: 78 - 84: 19.738 distance: 80 - 81: 28.262 distance: 81 - 82: 5.837 distance: 81 - 83: 17.307 distance: 84 - 85: 12.855 distance: 85 - 86: 26.339 distance: 85 - 88: 31.775 distance: 86 - 87: 37.057 distance: 86 - 93: 31.774 distance: 88 - 89: 50.786 distance: 89 - 90: 40.495 distance: 90 - 91: 19.495 distance: 90 - 92: 40.431 distance: 93 - 94: 41.219 distance: 94 - 95: 55.813 distance: 94 - 97: 43.504 distance: 95 - 96: 40.469 distance: 95 - 101: 57.123 distance: 97 - 98: 22.666 distance: 98 - 99: 27.226 distance: 98 - 100: 32.515 distance: 101 - 102: 67.092 distance: 102 - 103: 67.080 distance: 102 - 105: 50.427 distance: 103 - 104: 32.390 distance: 103 - 110: 30.645 distance: 105 - 106: 11.203 distance: 106 - 107: 26.072 distance: 107 - 108: 4.315 distance: 107 - 109: 24.863 distance: 110 - 111: 18.828 distance: 111 - 112: 35.992 distance: 111 - 114: 30.704 distance: 112 - 113: 24.636 distance: 112 - 120: 8.213 distance: 114 - 115: 39.014 distance: 115 - 116: 57.423 distance: 115 - 117: 54.644 distance: 116 - 118: 40.169 distance: 117 - 119: 48.946 distance: 118 - 119: 41.317 distance: 120 - 121: 19.377 distance: 121 - 122: 15.090 distance: 121 - 124: 13.357 distance: 122 - 123: 39.036 distance: 122 - 127: 12.071 distance: 124 - 125: 15.726 distance: 124 - 126: 28.615