Starting phenix.real_space_refine on Tue Aug 6 22:16:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sms_25207/08_2024/7sms_25207.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sms_25207/08_2024/7sms_25207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sms_25207/08_2024/7sms_25207.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sms_25207/08_2024/7sms_25207.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sms_25207/08_2024/7sms_25207.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sms_25207/08_2024/7sms_25207.cif" } resolution = 3.18 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 85 5.16 5 C 11202 2.51 5 N 2640 2.21 5 O 3119 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 17051 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3140 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 366} Chain breaks: 1 Chain: "B" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3456 Classifications: {'peptide': 425} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 397} Chain breaks: 1 Chain: "C" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3294 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 382} Chain breaks: 1 Chain: "D" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3151 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 367} Chain breaks: 1 Chain: "E" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3317 Classifications: {'peptide': 409} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 386} Chain breaks: 1 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 127 Unusual residues: {'POV': 1, 'TC9': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'CLR': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 108 Unusual residues: {'CLR': 1, 'POV': 1, 'TC9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'POV': 1, 'TC9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" C1 CLR A 501 " occ=0.80 ... (26 atoms not shown) pdb=" O1 CLR A 501 " occ=0.80 residue: pdb=" N POV B 603 " occ=0.75 ... (35 atoms not shown) pdb="C311 POV B 603 " occ=0.75 residue: pdb=" N POV C 501 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV C 501 " occ=0.75 residue: pdb=" N POV C 502 " occ=0.75 ... (30 atoms not shown) pdb=" P POV C 502 " occ=0.75 residue: pdb=" C1 CLR C 503 " occ=0.89 ... (26 atoms not shown) pdb=" O1 CLR C 503 " occ=0.89 residue: pdb=" C1 CLR D 502 " occ=0.75 ... (26 atoms not shown) pdb=" O1 CLR D 502 " occ=0.75 residue: pdb=" N POV D 503 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV D 503 " occ=0.75 residue: pdb=" N POV E 602 " occ=0.75 ... (38 atoms not shown) pdb="C215 POV E 602 " occ=0.75 Time building chain proxies: 9.66, per 1000 atoms: 0.57 Number of scatterers: 17051 At special positions: 0 Unit cell: (162.549, 125.12, 100.524, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 5 15.00 O 3119 8.00 N 2640 7.00 C 11202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 193 " distance=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.04 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 5 " " BMA I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 5 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 143 " " NAG H 1 " - " ASN C 141 " " NAG I 1 " - " ASN D 141 " " NAG J 1 " - " ASN E 141 " Time building additional restraints: 7.32 Conformation dependent library (CDL) restraints added in 2.7 seconds 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3894 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 20 sheets defined 43.2% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 63 through 66 removed outlier: 3.697A pdb=" N ARG A 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.715A pdb=" N VAL A 85 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 218 through 228 removed outlier: 3.586A pdb=" N LEU A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.726A pdb=" N TYR A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 241 through 263 Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 317 removed outlier: 3.739A pdb=" N ILE A 315 " --> pdb=" O TRP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 426 removed outlier: 3.517A pdb=" N ALA A 375 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.504A pdb=" N VAL B 87 " --> pdb=" O PRO B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 232 through 246 removed outlier: 3.676A pdb=" N CYS B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 255 through 277 Processing helix chain 'B' and resid 286 through 314 Processing helix chain 'B' and resid 323 through 332 Processing helix chain 'B' and resid 333 through 338 Processing helix chain 'B' and resid 417 through 476 Proline residue: B 463 - end of helix Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 73 removed outlier: 4.073A pdb=" N GLU C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.965A pdb=" N PHE C 180 " --> pdb=" O LYS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 238 removed outlier: 4.679A pdb=" N ILE C 226 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.502A pdb=" N GLY C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 267 Processing helix chain 'C' and resid 278 through 306 Processing helix chain 'C' and resid 315 through 323 Processing helix chain 'C' and resid 325 through 331 removed outlier: 3.781A pdb=" N PHE C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 460 Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 63 through 66 Processing helix chain 'D' and resid 68 through 73 removed outlier: 4.156A pdb=" N GLY D 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 218 through 230 removed outlier: 4.136A pdb=" N GLY D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 236 through 240 Processing helix chain 'D' and resid 241 through 262 Processing helix chain 'D' and resid 272 through 300 Processing helix chain 'D' and resid 309 through 318 Processing helix chain 'D' and resid 319 through 324 removed outlier: 3.554A pdb=" N VAL D 323 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET D 324 " --> pdb=" O ILE D 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 319 through 324' Processing helix chain 'D' and resid 371 through 426 Processing helix chain 'E' and resid 3 through 13 removed outlier: 3.517A pdb=" N LEU E 7 " --> pdb=" O GLU E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 removed outlier: 3.927A pdb=" N GLU E 73 " --> pdb=" O SER E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 219 through 226 Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 236 through 242 removed outlier: 3.579A pdb=" N TYR E 241 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 271 Processing helix chain 'E' and resid 281 through 309 Processing helix chain 'E' and resid 318 through 328 removed outlier: 3.705A pdb=" N PHE E 328 " --> pdb=" O LEU E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 472 removed outlier: 3.610A pdb=" N LEU E 457 " --> pdb=" O TRP E 453 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.149A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.149A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE A 49 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER A 42 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLU A 51 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU A 40 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN A 53 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE A 61 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP A 30 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.557A pdb=" N CYS A 142 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP A 180 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 82 removed outlier: 4.931A pdb=" N GLY B 116 " --> pdb=" O ASP B 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 82 removed outlier: 4.931A pdb=" N GLY B 116 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N THR B 51 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU B 45 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR B 53 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TRP B 57 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU B 39 " --> pdb=" O TRP B 57 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP B 59 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU B 37 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ALA B 61 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU B 35 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N TYR B 63 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE B 33 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 11.508A pdb=" N HIS B 65 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 13.550A pdb=" N VAL B 31 " --> pdb=" O HIS B 65 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL B 31 " --> pdb=" O THR B 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.186A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG B 222 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILE B 192 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.186A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 80 removed outlier: 4.298A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 77 through 80 removed outlier: 4.298A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLU C 49 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C 42 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN C 53 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR C 61 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR C 30 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL C 29 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLN C 159 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL C 31 " --> pdb=" O GLN C 159 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.400A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 212 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.400A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 81 removed outlier: 4.821A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 81 removed outlier: 4.821A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE D 49 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL D 43 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLU D 51 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG D 55 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU D 37 " --> pdb=" O ARG D 55 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG D 57 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU D 35 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLN D 59 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N VAL D 33 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N ILE D 61 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE D 31 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 90 through 92 removed outlier: 3.614A pdb=" N CYS D 142 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE D 205 " --> pdb=" O CYS D 142 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP D 180 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLN D 208 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N MET D 178 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.825A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.825A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ALA E 49 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER E 42 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.204A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS E 188 " --> pdb=" O ILE E 214 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLN E 216 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE E 186 " --> pdb=" O GLN E 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.204A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 162 through 163 927 hydrogen bonds defined for protein. 2673 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.66 Time building geometry restraints manager: 7.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2633 1.31 - 1.45: 4895 1.45 - 1.58: 9844 1.58 - 1.71: 10 1.71 - 1.84: 139 Bond restraints: 17521 Sorted by residual: bond pdb=" C19 TC9 B 602 " pdb=" C24 TC9 B 602 " ideal model delta sigma weight residual 1.519 1.393 0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C19 TC9 E 601 " pdb=" C24 TC9 E 601 " ideal model delta sigma weight residual 1.519 1.393 0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" C19 TC9 B 601 " pdb=" C24 TC9 B 601 " ideal model delta sigma weight residual 1.519 1.394 0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C19 TC9 D 501 " pdb=" C24 TC9 D 501 " ideal model delta sigma weight residual 1.519 1.395 0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" C19 TC9 E 601 " pdb=" N20 TC9 E 601 " ideal model delta sigma weight residual 1.540 1.482 0.058 2.00e-02 2.50e+03 8.35e+00 ... (remaining 17516 not shown) Histogram of bond angle deviations from ideal: 98.07 - 105.27: 395 105.27 - 112.46: 9513 112.46 - 119.66: 5688 119.66 - 126.85: 8027 126.85 - 134.05: 307 Bond angle restraints: 23930 Sorted by residual: angle pdb=" O11 POV C 502 " pdb=" P POV C 502 " pdb=" O12 POV C 502 " ideal model delta sigma weight residual 97.67 110.10 -12.43 3.00e+00 1.11e-01 1.72e+01 angle pdb=" O11 POV B 603 " pdb=" P POV B 603 " pdb=" O12 POV B 603 " ideal model delta sigma weight residual 97.67 109.37 -11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" O13 POV B 603 " pdb=" P POV B 603 " pdb=" O14 POV B 603 " ideal model delta sigma weight residual 121.11 109.47 11.64 3.00e+00 1.11e-01 1.51e+01 angle pdb=" O13 POV E 602 " pdb=" P POV E 602 " pdb=" O14 POV E 602 " ideal model delta sigma weight residual 121.11 109.51 11.60 3.00e+00 1.11e-01 1.50e+01 angle pdb=" O13 POV D 503 " pdb=" P POV D 503 " pdb=" O14 POV D 503 " ideal model delta sigma weight residual 121.11 109.52 11.59 3.00e+00 1.11e-01 1.49e+01 ... (remaining 23925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.02: 10468 31.02 - 62.05: 281 62.05 - 93.07: 88 93.07 - 124.10: 29 124.10 - 155.12: 6 Dihedral angle restraints: 10872 sinusoidal: 4892 harmonic: 5980 Sorted by residual: dihedral pdb=" CA CYS D 142 " pdb=" C CYS D 142 " pdb=" N THR D 143 " pdb=" CA THR D 143 " ideal model delta harmonic sigma weight residual 180.00 -151.41 -28.59 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA CYS A 192 " pdb=" C CYS A 192 " pdb=" N CYS A 193 " pdb=" CA CYS A 193 " ideal model delta harmonic sigma weight residual -180.00 -151.79 -28.21 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA CYS A 142 " pdb=" C CYS A 142 " pdb=" N THR A 143 " pdb=" CA THR A 143 " ideal model delta harmonic sigma weight residual -180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 10869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2324 0.060 - 0.119: 406 0.119 - 0.179: 53 0.179 - 0.238: 7 0.238 - 0.298: 7 Chirality restraints: 2797 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN D 141 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 2794 not shown) Planarity restraints: 2887 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C19 TC9 E 601 " -0.014 2.00e-02 2.50e+03 1.05e-02 3.04e+00 pdb=" C22 TC9 E 601 " 0.009 2.00e-02 2.50e+03 pdb=" C23 TC9 E 601 " -0.012 2.00e-02 2.50e+03 pdb=" C24 TC9 E 601 " 0.019 2.00e-02 2.50e+03 pdb=" C25 TC9 E 601 " 0.001 2.00e-02 2.50e+03 pdb=" C26 TC9 E 601 " 0.000 2.00e-02 2.50e+03 pdb=" C27 TC9 E 601 " -0.002 2.00e-02 2.50e+03 pdb=" C28 TC9 E 601 " -0.016 2.00e-02 2.50e+03 pdb=" O29 TC9 E 601 " 0.014 2.00e-02 2.50e+03 pdb=" O40 TC9 E 601 " 0.001 2.00e-02 2.50e+03 pdb=" O42 TC9 E 601 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C19 TC9 B 601 " -0.015 2.00e-02 2.50e+03 9.83e-03 2.66e+00 pdb=" C22 TC9 B 601 " 0.009 2.00e-02 2.50e+03 pdb=" C23 TC9 B 601 " -0.011 2.00e-02 2.50e+03 pdb=" C24 TC9 B 601 " 0.019 2.00e-02 2.50e+03 pdb=" C25 TC9 B 601 " 0.001 2.00e-02 2.50e+03 pdb=" C26 TC9 B 601 " 0.001 2.00e-02 2.50e+03 pdb=" C27 TC9 B 601 " -0.001 2.00e-02 2.50e+03 pdb=" C28 TC9 B 601 " -0.013 2.00e-02 2.50e+03 pdb=" O29 TC9 B 601 " 0.010 2.00e-02 2.50e+03 pdb=" O40 TC9 B 601 " -0.003 2.00e-02 2.50e+03 pdb=" O42 TC9 B 601 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 221 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C ILE C 221 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE C 221 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL C 222 " 0.009 2.00e-02 2.50e+03 ... (remaining 2884 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 954 2.73 - 3.27: 16922 3.27 - 3.81: 28271 3.81 - 4.36: 34505 4.36 - 4.90: 59822 Nonbonded interactions: 140474 Sorted by model distance: nonbonded pdb=" OE2 GLU D 45 " pdb=" NH2 ARG D 209 " model vdw 2.187 3.120 nonbonded pdb=" OG SER B 494 " pdb=" OD1 ASP B 496 " model vdw 2.202 3.040 nonbonded pdb=" OD2 ASP B 140 " pdb=" NE2 GLN B 142 " model vdw 2.211 3.120 nonbonded pdb=" OE2 GLU B 191 " pdb=" NH2 ARG B 222 " model vdw 2.235 3.120 nonbonded pdb=" OD2 ASP C 138 " pdb=" NE2 GLN C 140 " model vdw 2.239 3.120 ... (remaining 140469 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 426) selection = (chain 'D' and (resid 1 through 330 or resid 370 through 426)) } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'J' } 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=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 48.020 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 : 0.006 0.126 17521 Z= 0.410 Angle : 0.779 12.431 23930 Z= 0.342 Chirality : 0.049 0.298 2797 Planarity : 0.004 0.034 2882 Dihedral : 17.585 155.120 6957 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.19), residues: 1995 helix: 2.85 (0.18), residues: 756 sheet: -0.69 (0.24), residues: 422 loop : -0.28 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 60 HIS 0.005 0.001 HIS B 60 PHE 0.014 0.001 PHE D 256 TYR 0.011 0.001 TYR B 439 ARG 0.005 0.001 ARG C 198 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 293 PHE cc_start: 0.8312 (m-80) cc_final: 0.7897 (m-10) REVERT: D 226 SER cc_start: 0.8905 (m) cc_final: 0.8510 (p) REVERT: D 227 PHE cc_start: 0.7950 (t80) cc_final: 0.7200 (m-80) REVERT: D 325 PHE cc_start: 0.6617 (m-80) cc_final: 0.6397 (m-80) REVERT: E 317 LEU cc_start: 0.8513 (tp) cc_final: 0.8310 (tp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2746 time to fit residues: 64.3493 Evaluate side-chains 105 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS E 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17521 Z= 0.192 Angle : 0.558 8.008 23930 Z= 0.269 Chirality : 0.044 0.187 2797 Planarity : 0.004 0.035 2882 Dihedral : 14.822 132.009 3048 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.38 % Allowed : 3.76 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.19), residues: 1995 helix: 3.03 (0.18), residues: 762 sheet: -0.58 (0.25), residues: 410 loop : -0.36 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 60 HIS 0.006 0.001 HIS B 60 PHE 0.013 0.001 PHE D 256 TYR 0.010 0.001 TYR B 439 ARG 0.005 0.000 ARG C 198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 133 MET cc_start: 0.7967 (ttm) cc_final: 0.7684 (ttm) REVERT: C 293 PHE cc_start: 0.8287 (m-80) cc_final: 0.7881 (m-10) REVERT: C 436 ASP cc_start: 0.8026 (t0) cc_final: 0.7819 (t0) REVERT: D 227 PHE cc_start: 0.7953 (t80) cc_final: 0.7109 (m-80) REVERT: E 299 MET cc_start: 0.7186 (ttt) cc_final: 0.6784 (ttp) REVERT: E 317 LEU cc_start: 0.8403 (tp) cc_final: 0.8181 (tp) outliers start: 7 outliers final: 4 residues processed: 116 average time/residue: 0.2454 time to fit residues: 47.3765 Evaluate side-chains 103 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 132 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 0.0870 chunk 149 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 194 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17521 Z= 0.235 Angle : 0.536 7.007 23930 Z= 0.259 Chirality : 0.044 0.189 2797 Planarity : 0.003 0.033 2882 Dihedral : 12.665 127.470 3048 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.64 % Allowed : 6.01 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.19), residues: 1995 helix: 3.12 (0.18), residues: 761 sheet: -0.46 (0.25), residues: 398 loop : -0.34 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 60 HIS 0.004 0.001 HIS B 60 PHE 0.015 0.001 PHE D 325 TYR 0.011 0.001 TYR B 439 ARG 0.003 0.000 ARG C 198 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 133 MET cc_start: 0.7948 (ttm) cc_final: 0.7676 (ttm) REVERT: C 293 PHE cc_start: 0.8276 (m-80) cc_final: 0.7865 (m-10) REVERT: C 436 ASP cc_start: 0.8067 (t0) cc_final: 0.7772 (t0) REVERT: D 243 MET cc_start: 0.9299 (mmm) cc_final: 0.9052 (mmp) REVERT: E 299 MET cc_start: 0.7241 (ttt) cc_final: 0.6805 (ttp) REVERT: E 317 LEU cc_start: 0.8405 (tp) cc_final: 0.8171 (tp) outliers start: 12 outliers final: 7 residues processed: 117 average time/residue: 0.2689 time to fit residues: 51.6787 Evaluate side-chains 108 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 426 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 120 optimal weight: 0.0030 chunk 180 optimal weight: 0.9980 chunk 191 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 171 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17521 Z= 0.161 Angle : 0.495 7.095 23930 Z= 0.241 Chirality : 0.043 0.201 2797 Planarity : 0.003 0.035 2882 Dihedral : 11.683 130.306 3048 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.54 % Allowed : 7.41 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.19), residues: 1995 helix: 3.24 (0.18), residues: 761 sheet: -0.31 (0.25), residues: 400 loop : -0.27 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 60 HIS 0.003 0.001 HIS B 60 PHE 0.009 0.001 PHE C 219 TYR 0.013 0.001 TYR E 117 ARG 0.003 0.000 ARG C 198 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 133 MET cc_start: 0.7904 (ttm) cc_final: 0.7630 (ttm) REVERT: C 293 PHE cc_start: 0.8255 (m-80) cc_final: 0.7877 (m-10) REVERT: C 436 ASP cc_start: 0.8122 (t0) cc_final: 0.7806 (t0) REVERT: D 227 PHE cc_start: 0.7883 (t80) cc_final: 0.7124 (m-80) REVERT: D 243 MET cc_start: 0.9252 (mmm) cc_final: 0.9006 (mmp) REVERT: D 278 MET cc_start: 0.7760 (tpp) cc_final: 0.7484 (tpp) REVERT: E 299 MET cc_start: 0.7239 (ttt) cc_final: 0.6814 (ttp) REVERT: E 317 LEU cc_start: 0.8395 (tp) cc_final: 0.8172 (tp) REVERT: E 467 PHE cc_start: 0.6915 (m-10) cc_final: 0.6448 (t80) outliers start: 10 outliers final: 5 residues processed: 117 average time/residue: 0.2700 time to fit residues: 51.1834 Evaluate side-chains 107 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 407 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 78 optimal weight: 0.0170 chunk 163 optimal weight: 5.9990 chunk 132 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17521 Z= 0.168 Angle : 0.493 6.894 23930 Z= 0.240 Chirality : 0.043 0.190 2797 Planarity : 0.003 0.035 2882 Dihedral : 11.287 131.185 3048 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.43 % Allowed : 8.27 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.19), residues: 1995 helix: 3.26 (0.18), residues: 761 sheet: -0.21 (0.25), residues: 387 loop : -0.27 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 60 HIS 0.005 0.001 HIS B 60 PHE 0.009 0.001 PHE C 219 TYR 0.011 0.001 TYR E 117 ARG 0.002 0.000 ARG C 198 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 2.114 Fit side-chains revert: symmetry clash REVERT: C 133 MET cc_start: 0.7893 (ttm) cc_final: 0.7630 (ttm) REVERT: C 293 PHE cc_start: 0.8241 (m-80) cc_final: 0.7865 (m-10) REVERT: C 436 ASP cc_start: 0.8132 (t0) cc_final: 0.7792 (t0) REVERT: C 468 PHE cc_start: 0.7854 (m-80) cc_final: 0.7636 (m-80) REVERT: D 227 PHE cc_start: 0.7890 (t80) cc_final: 0.7139 (m-80) REVERT: E 299 MET cc_start: 0.7259 (ttt) cc_final: 0.6846 (ttp) REVERT: E 317 LEU cc_start: 0.8420 (tp) cc_final: 0.8202 (tp) REVERT: E 467 PHE cc_start: 0.6879 (m-10) cc_final: 0.6452 (t80) outliers start: 8 outliers final: 4 residues processed: 116 average time/residue: 0.2637 time to fit residues: 49.6450 Evaluate side-chains 104 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 407 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 64.4126 > 50: distance: 71 - 75: 27.535 distance: 75 - 76: 18.217 distance: 75 - 189: 28.994 distance: 76 - 77: 35.007 distance: 76 - 79: 19.646 distance: 77 - 78: 27.968 distance: 77 - 83: 22.381 distance: 78 - 186: 26.834 distance: 79 - 80: 12.148 distance: 79 - 81: 21.171 distance: 80 - 82: 10.390 distance: 83 - 84: 7.753 distance: 83 - 89: 15.119 distance: 84 - 85: 21.627 distance: 84 - 87: 26.001 distance: 85 - 86: 26.485 distance: 85 - 90: 28.435 distance: 87 - 88: 15.046 distance: 88 - 89: 8.461 distance: 90 - 91: 14.798 distance: 91 - 92: 18.505 distance: 91 - 94: 24.162 distance: 92 - 93: 26.884 distance: 92 - 96: 9.341 distance: 94 - 95: 18.376 distance: 96 - 97: 9.118 distance: 97 - 98: 13.303 distance: 97 - 100: 8.436 distance: 98 - 99: 9.172 distance: 98 - 102: 12.098 distance: 102 - 103: 9.925 distance: 103 - 104: 4.107 distance: 103 - 106: 10.778 distance: 104 - 105: 20.085 distance: 104 - 110: 10.599 distance: 106 - 107: 15.387 distance: 107 - 108: 15.439 distance: 107 - 109: 3.110 distance: 110 - 111: 20.457 distance: 111 - 112: 22.782 distance: 111 - 114: 6.480 distance: 112 - 113: 36.731 distance: 112 - 117: 16.714 distance: 114 - 115: 9.313 distance: 114 - 116: 12.603 distance: 117 - 118: 27.437 distance: 118 - 119: 24.141 distance: 118 - 121: 30.787 distance: 119 - 120: 29.929 distance: 119 - 131: 36.330 distance: 121 - 122: 14.391 distance: 122 - 123: 10.874 distance: 122 - 124: 7.841 distance: 123 - 125: 27.253 distance: 124 - 126: 19.189 distance: 124 - 127: 6.064 distance: 125 - 126: 5.402 distance: 126 - 128: 17.405 distance: 127 - 129: 18.413 distance: 128 - 130: 5.147 distance: 129 - 130: 17.016 distance: 131 - 132: 32.227 distance: 132 - 133: 27.454 distance: 132 - 135: 20.212 distance: 133 - 134: 33.839 distance: 133 - 140: 31.459 distance: 135 - 136: 34.868 distance: 136 - 137: 9.379 distance: 137 - 138: 31.048 distance: 137 - 139: 13.642 distance: 140 - 141: 23.733 distance: 140 - 146: 22.162 distance: 141 - 142: 17.082 distance: 141 - 144: 28.759 distance: 142 - 143: 6.561 distance: 142 - 147: 21.990 distance: 144 - 145: 33.783 distance: 145 - 146: 33.226 distance: 147 - 148: 13.432 distance: 148 - 149: 12.509 distance: 148 - 151: 16.454 distance: 149 - 150: 13.482 distance: 149 - 155: 7.433 distance: 151 - 152: 6.688 distance: 152 - 153: 10.199 distance: 152 - 154: 12.353