Starting phenix.real_space_refine (version: dev) on Sun Dec 18 13:21:37 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/12_2022/6voy_21301.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/12_2022/6voy_21301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/12_2022/6voy_21301.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/12_2022/6voy_21301.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/12_2022/6voy_21301.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/12_2022/6voy_21301.pdb" } resolution = 3.7 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= 0.000 sd= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 31": "NH1" <-> "NH2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 47": "NH1" <-> "NH2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "C ARG 31": "NH1" <-> "NH2" Residue "C ARG 37": "NH1" <-> "NH2" Residue "C ARG 47": "NH1" <-> "NH2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D ARG 52": "NH1" <-> "NH2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D ARG 218": "NH1" <-> "NH2" Residue "D ARG 238": "NH1" <-> "NH2" Residue "D ARG 269": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E GLU 139": "OE1" <-> "OE2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E GLU 276": "OE1" <-> "OE2" Residue "E GLU 310": "OE1" <-> "OE2" Residue "E GLU 319": "OE1" <-> "OE2" Residue "E GLU 325": "OE1" <-> "OE2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F GLU 78": "OE1" <-> "OE2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F GLU 276": "OE1" <-> "OE2" Residue "F GLU 307": "OE1" <-> "OE2" Residue "F GLU 319": "OE1" <-> "OE2" Residue "F GLU 325": "OE1" <-> "OE2" Residue "F GLU 344": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 17556 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2200 Classifications: {'peptide': 276} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 257} Chain: "B" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2058 Classifications: {'peptide': 259} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 242} Chain breaks: 1 Chain: "C" Number of atoms: 2200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2200 Classifications: {'peptide': 276} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 257} Chain: "D" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2058 Classifications: {'peptide': 259} Link IDs: {'CIS': 2, 'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "E" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2676 Classifications: {'peptide': 327} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 304} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2676 Classifications: {'peptide': 327} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 304} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 966 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "J" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 504 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "K" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 371 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "L" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 966 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "M" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 504 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "N" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 371 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 246 SG CYS A 33 63.285 78.778 64.823 1.00116.78 S ATOM 267 SG CYS A 36 64.894 75.597 65.874 1.00 99.36 S ATOM 2439 SG CYS B 33 137.488 80.123 80.291 1.00299.42 S ATOM 2460 SG CYS B 36 138.441 77.611 78.802 1.00269.90 S ATOM 4504 SG CYS C 33 105.877 38.294 66.337 1.00107.32 S ATOM 4525 SG CYS C 36 104.269 41.389 64.821 1.00 95.45 S ATOM 6697 SG CYS D 33 31.902 36.894 81.648 1.00337.40 S ATOM 6718 SG CYS D 36 30.371 38.588 79.947 1.00308.22 S Time building chain proxies: 10.15, per 1000 atoms: 0.58 Number of scatterers: 17556 At special positions: 0 Unit cell: (170.62, 115.236, 139.355, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 54 16.00 P 178 15.00 Mg 2 11.99 O 3540 8.00 N 3072 7.00 C 10706 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.92 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 10 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 6 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 36 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 33 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 10 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 6 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 33 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 36 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 6 " pdb="ZN ZN C 301 " - pdb=" ND1 HIS C 10 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 33 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 36 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 10 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 6 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 36 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 33 " Number of angles added : 7 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3324 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 8 sheets defined 51.7% alpha, 4.1% beta 82 base pairs and 123 stacking pairs defined. Time for finding SS restraints: 5.36 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 12 through 20 Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 33 through 40 Processing helix chain 'A' and resid 96 through 108 Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 127 through 136 Processing helix chain 'A' and resid 148 through 151 Processing helix chain 'A' and resid 152 through 172 Processing helix chain 'A' and resid 179 through 191 Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 209 through 212 Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 16 through 20 Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 96 through 110 Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 127 through 135 Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 151 through 171 Processing helix chain 'B' and resid 179 through 190 Processing helix chain 'B' and resid 201 through 207 Processing helix chain 'C' and resid 2 through 10 Processing helix chain 'C' and resid 12 through 20 Processing helix chain 'C' and resid 22 through 30 Processing helix chain 'C' and resid 33 through 39 Processing helix chain 'C' and resid 96 through 108 Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 127 through 136 Processing helix chain 'C' and resid 148 through 151 Processing helix chain 'C' and resid 152 through 172 Processing helix chain 'C' and resid 177 through 192 Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 209 through 212 Processing helix chain 'C' and resid 267 through 271 Processing helix chain 'D' and resid 2 through 10 Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 22 through 32 Processing helix chain 'D' and resid 96 through 110 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 127 through 135 Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 151 through 171 Processing helix chain 'D' and resid 179 through 190 Processing helix chain 'D' and resid 201 through 206 Processing helix chain 'E' and resid 38 through 48 Processing helix chain 'E' and resid 63 through 83 Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 91 through 104 Processing helix chain 'E' and resid 130 through 146 Processing helix chain 'E' and resid 151 through 156 Processing helix chain 'E' and resid 160 through 169 Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 175 through 193 Processing helix chain 'E' and resid 194 through 213 Processing helix chain 'E' and resid 221 through 234 Processing helix chain 'E' and resid 241 through 251 Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 259 through 262 Processing helix chain 'E' and resid 263 through 276 Processing helix chain 'E' and resid 277 through 286 Proline residue: E 284 - end of helix Processing helix chain 'E' and resid 287 through 292 Processing helix chain 'E' and resid 298 through 310 Processing helix chain 'E' and resid 320 through 332 removed outlier: 4.731A pdb=" N GLU E 325 " --> pdb=" O VAL E 321 " (cutoff:3.500A) Proline residue: E 326 - end of helix removed outlier: 3.696A pdb=" N GLN E 330 " --> pdb=" O PRO E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 346 Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'F' and resid 38 through 48 Processing helix chain 'F' and resid 63 through 83 Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 91 through 104 Processing helix chain 'F' and resid 130 through 146 Processing helix chain 'F' and resid 151 through 156 Processing helix chain 'F' and resid 160 through 169 Processing helix chain 'F' and resid 170 through 173 Processing helix chain 'F' and resid 175 through 193 Processing helix chain 'F' and resid 194 through 213 Processing helix chain 'F' and resid 221 through 234 Processing helix chain 'F' and resid 241 through 251 Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 259 through 262 Processing helix chain 'F' and resid 263 through 276 Processing helix chain 'F' and resid 277 through 286 Proline residue: F 284 - end of helix Processing helix chain 'F' and resid 287 through 292 Processing helix chain 'F' and resid 298 through 310 Processing helix chain 'F' and resid 320 through 332 removed outlier: 4.702A pdb=" N GLU F 325 " --> pdb=" O VAL F 321 " (cutoff:3.500A) Proline residue: F 326 - end of helix removed outlier: 3.701A pdb=" N GLN F 330 " --> pdb=" O PRO F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 346 Processing helix chain 'F' and resid 353 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65 Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 230 Processing sheet with id=AA3, first strand: chain 'A' and resid 254 through 258 Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 65 Processing sheet with id=AA5, first strand: chain 'B' and resid 228 through 230 removed outlier: 4.195A pdb=" N GLN B 244 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N PHE B 230 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLY B 242 " --> pdb=" O PHE B 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 61 through 66 Processing sheet with id=AA7, first strand: chain 'D' and resid 62 through 65 Processing sheet with id=AA8, first strand: chain 'D' and resid 116 through 117 589 hydrogen bonds defined for protein. 1653 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 198 hydrogen bonds 392 hydrogen bond angles 0 basepair planarities 82 basepair parallelities 123 stacking parallelities Total time for adding SS restraints: 5.55 Time building geometry restraints manager: 9.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3018 1.32 - 1.45: 5935 1.45 - 1.58: 9006 1.58 - 1.70: 347 1.70 - 1.83: 80 Bond restraints: 18386 Sorted by residual: bond pdb=" CG PRO D 243 " pdb=" CD PRO D 243 " ideal model delta sigma weight residual 1.503 1.348 0.155 3.40e-02 8.65e+02 2.09e+01 bond pdb=" CB TRP A 240 " pdb=" CG TRP A 240 " ideal model delta sigma weight residual 1.498 1.362 0.136 3.10e-02 1.04e+03 1.94e+01 bond pdb=" CB TRP C 60 " pdb=" CG TRP C 60 " ideal model delta sigma weight residual 1.498 1.368 0.130 3.10e-02 1.04e+03 1.76e+01 bond pdb=" CB ASN B 118 " pdb=" CG ASN B 118 " ideal model delta sigma weight residual 1.516 1.419 0.097 2.50e-02 1.60e+03 1.52e+01 bond pdb=" CB TRP C 240 " pdb=" CG TRP C 240 " ideal model delta sigma weight residual 1.498 1.388 0.110 3.10e-02 1.04e+03 1.25e+01 ... (remaining 18381 not shown) Histogram of bond angle deviations from ideal: 78.86 - 93.21: 2 93.21 - 107.56: 2489 107.56 - 121.91: 19516 121.91 - 136.26: 3760 136.26 - 150.62: 1 Bond angle restraints: 25768 Sorted by residual: angle pdb=" N PHE A 230 " pdb=" CA PHE A 230 " pdb=" CB PHE A 230 " ideal model delta sigma weight residual 110.63 78.86 31.77 1.94e+00 2.66e-01 2.68e+02 angle pdb=" N PHE C 230 " pdb=" CA PHE C 230 " pdb=" C PHE C 230 " ideal model delta sigma weight residual 112.12 132.09 -19.97 1.34e+00 5.57e-01 2.22e+02 angle pdb=" N PHE A 230 " pdb=" CA PHE A 230 " pdb=" C PHE A 230 " ideal model delta sigma weight residual 112.12 131.73 -19.61 1.34e+00 5.57e-01 2.14e+02 angle pdb=" N PHE C 230 " pdb=" CA PHE C 230 " pdb=" CB PHE C 230 " ideal model delta sigma weight residual 110.63 83.38 27.25 1.94e+00 2.66e-01 1.97e+02 angle pdb=" C GLN A 91 " pdb=" N LYS A 92 " pdb=" CA LYS A 92 " ideal model delta sigma weight residual 122.17 104.37 17.80 1.54e+00 4.22e-01 1.34e+02 ... (remaining 25763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 9265 35.22 - 70.43: 963 70.43 - 105.65: 52 105.65 - 140.86: 5 140.86 - 176.08: 9 Dihedral angle restraints: 10294 sinusoidal: 5190 harmonic: 5104 Sorted by residual: dihedral pdb=" CA GLU E 276 " pdb=" C GLU E 276 " pdb=" N LYS E 277 " pdb=" CA LYS E 277 " ideal model delta harmonic sigma weight residual -180.00 -49.46 -130.54 0 5.00e+00 4.00e-02 6.82e+02 dihedral pdb=" CA GLU F 276 " pdb=" C GLU F 276 " pdb=" N LYS F 277 " pdb=" CA LYS F 277 " ideal model delta harmonic sigma weight residual -180.00 -50.02 -129.98 0 5.00e+00 4.00e-02 6.76e+02 dihedral pdb=" CA GLN A 244 " pdb=" C GLN A 244 " pdb=" N GLU A 245 " pdb=" CA GLU A 245 " ideal model delta harmonic sigma weight residual -180.00 -83.94 -96.06 0 5.00e+00 4.00e-02 3.69e+02 ... (remaining 10291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 2853 0.336 - 0.672: 23 0.672 - 1.009: 4 1.009 - 1.345: 1 1.345 - 1.681: 1 Chirality restraints: 2882 Sorted by residual: chirality pdb=" CA TYR D 228 " pdb=" N TYR D 228 " pdb=" C TYR D 228 " pdb=" CB TYR D 228 " both_signs ideal model delta sigma weight residual False 2.51 0.83 1.68 2.00e-01 2.50e+01 7.06e+01 chirality pdb=" CA PRO C 243 " pdb=" N PRO C 243 " pdb=" C PRO C 243 " pdb=" CB PRO C 243 " both_signs ideal model delta sigma weight residual False 2.72 1.71 1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" CA PRO A 243 " pdb=" N PRO A 243 " pdb=" C PRO A 243 " pdb=" CB PRO A 243 " both_signs ideal model delta sigma weight residual False 2.72 1.72 1.00 2.00e-01 2.50e+01 2.49e+01 ... (remaining 2879 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 153 " 0.043 2.00e-02 2.50e+03 8.63e-02 7.45e+01 pdb=" C GLY B 153 " -0.149 2.00e-02 2.50e+03 pdb=" O GLY B 153 " 0.056 2.00e-02 2.50e+03 pdb=" N LEU B 154 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 132 " -0.041 2.00e-02 2.50e+03 8.00e-02 6.40e+01 pdb=" C PRO F 132 " 0.138 2.00e-02 2.50e+03 pdb=" O PRO F 132 " -0.051 2.00e-02 2.50e+03 pdb=" N HIS F 133 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 132 " 0.041 2.00e-02 2.50e+03 8.00e-02 6.39e+01 pdb=" C PRO E 132 " -0.138 2.00e-02 2.50e+03 pdb=" O PRO E 132 " 0.051 2.00e-02 2.50e+03 pdb=" N HIS E 133 " 0.047 2.00e-02 2.50e+03 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.25: 47 2.25 - 2.91: 8538 2.91 - 3.57: 28016 3.57 - 4.24: 42570 4.24 - 4.90: 62808 Nonbonded interactions: 141979 Sorted by model distance: nonbonded pdb=" O TRP A 60 " pdb=" O VAL A 80 " model vdw 1.583 3.040 nonbonded pdb=" CD2 HIS B 6 " pdb=" CD2 HIS B 10 " model vdw 1.769 3.480 nonbonded pdb=" O GLY C 122 " pdb=" N TYR C 125 " model vdw 1.971 2.520 nonbonded pdb=" OD2 ASP A 63 " pdb="MG MG A 302 " model vdw 1.992 2.170 nonbonded pdb=" NE2 GLN A 44 " pdb=" OP1 DT J 10 " model vdw 2.005 2.520 ... (remaining 141974 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 1 through 37 or resid 53 through 274)) selection = (chain 'B' and resid 1 through 274) selection = (chain 'C' and (resid 1 through 37 or resid 53 through 274)) selection = (chain 'D' and resid 1 through 274) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'N' } 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 178 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 10706 2.51 5 N 3072 2.21 5 O 3540 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 5.600 Check model and map are aligned: 0.230 Convert atoms to be neutral: 0.150 Process input model: 54.070 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 : 0.013 0.155 18386 Z= 0.778 Angle : 1.520 31.766 25768 Z= 0.883 Chirality : 0.100 1.681 2882 Planarity : 0.013 0.095 2630 Dihedral : 24.389 176.075 6970 Min Nonbonded Distance : 1.583 Molprobity Statistics. All-atom Clashscore : 35.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.46 % Cbeta Deviations : 1.81 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.96 % Twisted General : 1.49 % 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: -6.32 (0.14), residues: 1700 helix: -4.02 (0.11), residues: 784 sheet: -3.45 (0.47), residues: 100 loop : -4.53 (0.16), residues: 816 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 433 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 437 average time/residue: 0.3035 time to fit residues: 193.5875 Evaluate side-chains 363 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 1.636 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 47 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 142 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 chunk 165 optimal weight: 0.0010 overall best weight: 4.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN A 132 ASN A 141 HIS ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN A 204 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN A 226 HIS A 236 ASN B 34 HIS B 141 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 ASN ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN D 61 GLN D 77 HIS D 141 HIS ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 133 HIS E 187 HIS E 205 ASN E 233 ASN E 306 ASN E 330 GLN F 48 GLN F 85 ASN F 187 HIS F 205 ASN F 233 ASN F 306 ASN F 330 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.084 18386 Z= 0.443 Angle : 0.991 31.370 25768 Z= 0.528 Chirality : 0.053 0.353 2882 Planarity : 0.007 0.072 2630 Dihedral : 28.344 176.449 3640 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 25.97 Ramachandran Plot: Outliers : 0.71 % Allowed : 16.82 % Favored : 82.47 % Rotamer Outliers : 3.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.93 % 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: -4.45 (0.18), residues: 1700 helix: -2.14 (0.16), residues: 766 sheet: -2.99 (0.43), residues: 110 loop : -3.85 (0.20), residues: 824 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 410 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 43 residues processed: 435 average time/residue: 0.2474 time to fit residues: 164.5161 Evaluate side-chains 421 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 378 time to evaluate : 1.722 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 43 outliers final: 1 residues processed: 43 average time/residue: 0.1592 time to fit residues: 14.8816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 132 optimal weight: 0.0670 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 ASN ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN D 226 HIS ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 18386 Z= 0.352 Angle : 0.911 29.698 25768 Z= 0.483 Chirality : 0.050 0.282 2882 Planarity : 0.006 0.050 2630 Dihedral : 28.147 177.462 3640 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.41 % Allowed : 13.24 % Favored : 86.35 % Rotamer Outliers : 4.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.68 % 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: -3.69 (0.19), residues: 1700 helix: -1.25 (0.17), residues: 784 sheet: -3.09 (0.39), residues: 132 loop : -3.67 (0.20), residues: 784 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 399 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 34 residues processed: 436 average time/residue: 0.2654 time to fit residues: 176.3621 Evaluate side-chains 400 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 366 time to evaluate : 1.612 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1609 time to fit residues: 11.5877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 6.9990 chunk 124 optimal weight: 0.3980 chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 79 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 chunk 166 optimal weight: 20.0000 chunk 175 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 47 optimal weight: 0.4980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 GLN ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 159 ASN ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN F 38 GLN F 206 ASN F 264 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 18386 Z= 0.256 Angle : 0.860 27.020 25768 Z= 0.451 Chirality : 0.048 0.320 2882 Planarity : 0.005 0.047 2630 Dihedral : 27.936 177.324 3640 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.41 % Favored : 86.24 % Rotamer Outliers : 4.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: -3.26 (0.19), residues: 1700 helix: -0.83 (0.18), residues: 794 sheet: -2.38 (0.45), residues: 108 loop : -3.66 (0.20), residues: 798 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 406 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 34 residues processed: 435 average time/residue: 0.2707 time to fit residues: 178.0345 Evaluate side-chains 416 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 382 time to evaluate : 1.668 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1595 time to fit residues: 12.3778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 89 optimal weight: 0.0970 chunk 157 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 132 ASN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 18386 Z= 0.352 Angle : 0.887 24.688 25768 Z= 0.468 Chirality : 0.049 0.263 2882 Planarity : 0.006 0.051 2630 Dihedral : 27.894 178.008 3640 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 23.04 Ramachandran Plot: Outliers : 0.29 % Allowed : 14.00 % Favored : 85.71 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -3.08 (0.19), residues: 1700 helix: -0.58 (0.18), residues: 778 sheet: -2.61 (0.43), residues: 120 loop : -3.59 (0.20), residues: 802 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 392 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 26 residues processed: 421 average time/residue: 0.2801 time to fit residues: 178.8310 Evaluate side-chains 398 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 372 time to evaluate : 1.848 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1547 time to fit residues: 9.8174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 chunk 146 optimal weight: 0.1980 chunk 81 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 92 optimal weight: 0.0370 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 190 ASN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN F 38 GLN F 233 ASN ** F 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 18386 Z= 0.224 Angle : 0.853 23.147 25768 Z= 0.442 Chirality : 0.048 0.289 2882 Planarity : 0.005 0.059 2630 Dihedral : 27.633 176.703 3640 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.00 % Favored : 87.65 % Rotamer Outliers : 3.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -2.83 (0.20), residues: 1700 helix: -0.39 (0.19), residues: 780 sheet: -2.47 (0.40), residues: 132 loop : -3.45 (0.21), residues: 788 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 426 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 31 residues processed: 450 average time/residue: 0.2734 time to fit residues: 185.8661 Evaluate side-chains 423 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 392 time to evaluate : 1.864 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1550 time to fit residues: 11.2211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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: 56.9923 > 50: distance: 9 - 13: 22.626 distance: 13 - 14: 6.727 distance: 14 - 15: 12.531 distance: 14 - 17: 10.376 distance: 15 - 16: 16.015 distance: 15 - 20: 7.545 distance: 17 - 18: 26.193 distance: 17 - 19: 37.269 distance: 20 - 21: 11.099 distance: 21 - 22: 9.049 distance: 21 - 24: 20.332 distance: 22 - 23: 16.615 distance: 22 - 30: 10.779 distance: 24 - 25: 15.879 distance: 25 - 26: 4.916 distance: 25 - 27: 10.400 distance: 27 - 29: 4.361 distance: 28 - 29: 3.370 distance: 30 - 31: 21.371 distance: 31 - 32: 42.202 distance: 31 - 34: 44.110 distance: 32 - 33: 24.816 distance: 32 - 44: 16.782 distance: 34 - 35: 19.356 distance: 35 - 36: 14.081 distance: 35 - 37: 16.363 distance: 36 - 38: 4.796 distance: 37 - 39: 6.478 distance: 37 - 40: 13.122 distance: 39 - 41: 7.355 distance: 40 - 42: 15.584 distance: 42 - 43: 17.455 distance: 44 - 45: 33.169 distance: 45 - 46: 13.790 distance: 45 - 48: 31.280 distance: 46 - 47: 53.016 distance: 46 - 56: 13.761 distance: 48 - 49: 22.397 distance: 49 - 50: 16.659 distance: 49 - 51: 13.993 distance: 50 - 52: 17.561 distance: 51 - 53: 10.669 distance: 52 - 54: 6.408 distance: 53 - 54: 5.289 distance: 54 - 55: 4.602 distance: 56 - 57: 13.554 distance: 57 - 58: 6.368 distance: 57 - 60: 15.916 distance: 58 - 59: 15.128 distance: 58 - 68: 33.687 distance: 60 - 61: 11.329 distance: 61 - 62: 22.674 distance: 61 - 63: 18.320 distance: 62 - 64: 6.869 distance: 63 - 65: 8.089 distance: 64 - 66: 5.001 distance: 65 - 66: 37.444 distance: 68 - 69: 6.110 distance: 69 - 70: 14.646 distance: 69 - 72: 22.708 distance: 70 - 71: 11.467 distance: 70 - 79: 17.254 distance: 72 - 73: 10.677 distance: 73 - 74: 3.281 distance: 73 - 75: 6.190 distance: 74 - 76: 9.060 distance: 75 - 77: 7.393 distance: 76 - 78: 4.490 distance: 79 - 80: 7.455 distance: 80 - 81: 3.115 distance: 81 - 82: 21.851 distance: 81 - 88: 22.108 distance: 83 - 84: 9.106 distance: 84 - 85: 7.774 distance: 85 - 86: 5.505 distance: 86 - 87: 4.147 distance: 88 - 89: 7.444 distance: 89 - 90: 16.541 distance: 89 - 92: 10.619 distance: 90 - 91: 21.675 distance: 90 - 96: 23.820 distance: 92 - 93: 5.620 distance: 93 - 95: 6.165 distance: 96 - 97: 23.638 distance: 96 - 102: 17.933 distance: 97 - 98: 26.641 distance: 97 - 100: 28.156 distance: 98 - 99: 27.471 distance: 98 - 103: 43.423 distance: 100 - 101: 30.142 distance: 101 - 102: 19.692 distance: 103 - 104: 8.654 distance: 104 - 105: 26.321 distance: 105 - 107: 28.975