Starting phenix.real_space_refine on Mon Dec 11 10:44:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/12_2023/6voy_21301.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/12_2023/6voy_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_2023/6voy_21301.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/12_2023/6voy_21301.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/12_2023/6voy_21301.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/12_2023/6voy_21301.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 9.78, per 1000 atoms: 0.56 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: 8.39 Conformation dependent library (CDL) restraints added in 2.7 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: 6.11 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: 5.37 Time building geometry restraints manager: 8.88 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=" C TRP D 227 " pdb=" N TYR D 228 " pdb=" CA TYR D 228 " ideal model delta sigma weight residual 121.70 150.62 -28.92 1.80e+00 3.09e-01 2.58e+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 ... (remaining 25763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 9409 35.22 - 70.43: 1023 70.43 - 105.65: 52 105.65 - 140.86: 5 140.86 - 176.08: 9 Dihedral angle restraints: 10498 sinusoidal: 5394 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 10495 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 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: 0.910 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: 5.050 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 55.120 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.120 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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 : 1.522 31.766 25768 Z= 0.887 Chirality : 0.100 1.681 2882 Planarity : 0.013 0.095 2630 Dihedral : 24.618 176.075 7174 Min Nonbonded Distance : 1.583 Molprobity Statistics. All-atom Clashscore : 35.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.46 % Allowed : 13.41 % Favored : 86.12 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP A 227 HIS 0.052 0.003 HIS B 10 PHE 0.031 0.003 PHE A 230 TYR 0.058 0.004 TYR D 228 ARG 0.010 0.001 ARG A 51 *********************** 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 : 2.039 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: 0.3232 time to fit residues: 204.8617 Evaluate side-chains 363 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 1.437 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3012 ------------------------------------------------------------------------------- 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: 5.9990 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: 4.5994 ------------------------------------------------------------------------------- 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** ** 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 226 HIS C 236 ASN D 61 GLN D 77 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: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 18386 Z= 0.419 Angle : 0.971 17.334 25768 Z= 0.524 Chirality : 0.053 0.443 2882 Planarity : 0.007 0.073 2630 Dihedral : 28.399 176.740 3844 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 25.16 Ramachandran Plot: Outliers : 0.59 % Allowed : 16.47 % Favored : 82.94 % Rotamer: Outliers : 3.85 % Allowed : 23.11 % Favored : 73.04 % 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: -4.44 (0.18), residues: 1700 helix: -2.14 (0.15), residues: 768 sheet: -2.87 (0.44), residues: 108 loop : -3.84 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP F 131 HIS 0.015 0.002 HIS B 10 PHE 0.022 0.003 PHE B 170 TYR 0.035 0.003 TYR D 228 ARG 0.008 0.001 ARG F 201 *********************** 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 469 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 411 time to evaluate : 1.704 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: 58 outliers final: 41 residues processed: 435 average time/residue: 0.2789 time to fit residues: 183.7923 Evaluate side-chains 420 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 379 time to evaluate : 1.777 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 41 outliers final: 1 residues processed: 41 average time/residue: 0.1526 time to fit residues: 13.8888 ------------------------------------------------------------------------------- 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: 4.9990 chunk 51 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 165 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 164 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 132 optimal weight: 0.0370 overall best weight: 1.5664 ------------------------------------------------------------------------------- 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 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 207 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 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18386 Z= 0.266 Angle : 0.864 15.746 25768 Z= 0.465 Chirality : 0.049 0.379 2882 Planarity : 0.005 0.050 2630 Dihedral : 28.117 177.509 3844 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.76 % Favored : 87.88 % Rotamer: Outliers : 3.92 % Allowed : 24.37 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -3.50 (0.19), residues: 1700 helix: -1.07 (0.18), residues: 766 sheet: -2.85 (0.40), residues: 128 loop : -3.59 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 268 HIS 0.012 0.002 HIS D 207 PHE 0.021 0.002 PHE B 170 TYR 0.032 0.002 TYR E 209 ARG 0.005 0.001 ARG F 201 *********************** 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: 59 poor density : 411 time to evaluate : 1.687 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 outliers start: 59 outliers final: 25 residues processed: 438 average time/residue: 0.2839 time to fit residues: 187.4728 Evaluate side-chains 414 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 389 time to evaluate : 1.658 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1879 time to fit residues: 10.7081 ------------------------------------------------------------------------------- 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: 5.9990 chunk 124 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 47 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 ** 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 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 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 264 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 18386 Z= 0.422 Angle : 0.913 14.046 25768 Z= 0.491 Chirality : 0.051 0.393 2882 Planarity : 0.006 0.053 2630 Dihedral : 28.061 178.652 3844 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 24.62 Ramachandran Plot: Outliers : 0.41 % Allowed : 15.65 % Favored : 83.94 % Rotamer: Outliers : 5.31 % Allowed : 27.09 % Favored : 67.60 % 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: -3.46 (0.19), residues: 1700 helix: -1.05 (0.17), residues: 806 sheet: -2.37 (0.48), residues: 106 loop : -3.74 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 268 HIS 0.011 0.002 HIS D 207 PHE 0.023 0.002 PHE B 170 TYR 0.032 0.003 TYR F 209 ARG 0.006 0.001 ARG F 70 *********************** 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 457 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 377 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 39 residues processed: 416 average time/residue: 0.2886 time to fit residues: 181.4983 Evaluate side-chains 397 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 358 time to evaluate : 1.845 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.1542 time to fit residues: 13.6264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 71.8381 > 50: distance: 23 - 50: 21.230 distance: 31 - 58: 29.300 distance: 42 - 50: 21.356 distance: 50 - 51: 52.790 distance: 51 - 52: 41.187 distance: 51 - 54: 55.965 distance: 52 - 53: 62.300 distance: 52 - 58: 21.484 distance: 54 - 55: 68.414 distance: 55 - 56: 52.373 distance: 55 - 57: 55.438 distance: 58 - 59: 44.846 distance: 59 - 62: 41.459 distance: 60 - 61: 56.918 distance: 60 - 67: 40.392 distance: 62 - 63: 54.407 distance: 63 - 64: 65.620 distance: 64 - 65: 52.810 distance: 64 - 66: 35.710 distance: 67 - 68: 55.731 distance: 68 - 69: 8.808 distance: 68 - 71: 57.510 distance: 69 - 70: 40.369 distance: 69 - 73: 7.018 distance: 71 - 72: 68.328 distance: 73 - 74: 42.394 distance: 73 - 79: 56.938 distance: 74 - 75: 37.191 distance: 74 - 77: 60.550 distance: 75 - 76: 12.437 distance: 75 - 80: 44.757 distance: 77 - 78: 59.303 distance: 78 - 79: 56.999 distance: 80 - 81: 50.542 distance: 81 - 82: 41.388 distance: 81 - 84: 43.745 distance: 82 - 83: 41.014 distance: 82 - 88: 15.869 distance: 84 - 85: 37.408 distance: 85 - 86: 27.539 distance: 85 - 87: 32.093 distance: 88 - 89: 45.481 distance: 89 - 90: 38.724 distance: 90 - 91: 6.994 distance: 90 - 99: 57.817 distance: 92 - 93: 66.177 distance: 93 - 94: 49.821 distance: 93 - 95: 36.746 distance: 94 - 96: 62.239 distance: 95 - 97: 48.069 distance: 96 - 98: 22.349 distance: 97 - 98: 53.088 distance: 99 - 100: 31.474 distance: 100 - 101: 58.725 distance: 100 - 103: 29.452 distance: 101 - 102: 55.606 distance: 101 - 105: 40.221 distance: 102 - 128: 33.886 distance: 103 - 104: 43.340 distance: 105 - 106: 30.232 distance: 105 - 111: 13.852 distance: 106 - 107: 57.134 distance: 106 - 109: 45.923 distance: 107 - 108: 51.577 distance: 107 - 112: 56.706 distance: 108 - 133: 25.674 distance: 109 - 110: 40.613 distance: 110 - 111: 43.284 distance: 112 - 113: 39.829 distance: 113 - 114: 40.554 distance: 113 - 116: 63.155 distance: 114 - 115: 20.329 distance: 114 - 120: 41.077 distance: 116 - 117: 38.790 distance: 117 - 118: 56.504 distance: 117 - 119: 53.251 distance: 120 - 121: 4.439 distance: 121 - 122: 56.781 distance: 121 - 124: 40.898 distance: 122 - 123: 39.295 distance: 122 - 128: 33.683 distance: 124 - 125: 57.923 distance: 124 - 126: 39.022 distance: 125 - 127: 37.733