Starting phenix.real_space_refine on Sun Mar 17 09:03:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a96_6998/03_2024/6a96_6998_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a96_6998/03_2024/6a96_6998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a96_6998/03_2024/6a96_6998.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a96_6998/03_2024/6a96_6998.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a96_6998/03_2024/6a96_6998_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a96_6998/03_2024/6a96_6998_updated.pdb" } resolution = 3.51 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= -0.023 sd= 0.837 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 160 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 11011 2.51 5 N 2753 2.21 5 O 3193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ARG 67": "NH1" <-> "NH2" Residue "K ARG 101": "NH1" <-> "NH2" Residue "L ARG 38": "NH1" <-> "NH2" Residue "L ARG 101": "NH1" <-> "NH2" Residue "O ARG 101": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17049 Number of models: 1 Model: "" Number of chains: 19 Chain: "K" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 957 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "O" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "B" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "A" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2706 Classifications: {'peptide': 337} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 321} Chain: "E" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "C" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" 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: "H" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "M" 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: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" 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: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" 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: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.00, per 1000 atoms: 0.53 Number of scatterers: 17049 At special positions: 0 Unit cell: (130.54, 121.98, 144.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 3193 8.00 N 2753 7.00 C 11011 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.04 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 296 " distance=2.04 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 6 " " MAN F 4 " - " MAN F 5 " " BMA H 3 " - " MAN H 4 " " BMA J 3 " - " MAN J 6 " " MAN J 4 " - " MAN J 5 " " BMA N 3 " - " MAN N 6 " " MAN N 4 " - " MAN N 5 " " BMA Q 3 " - " MAN Q 6 " " MAN Q 4 " - " MAN Q 5 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 5 " " BMA J 3 " - " MAN J 4 " " BMA N 3 " - " MAN N 4 " " BMA Q 3 " - " MAN Q 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG F 1 " - " ASN B 149 " " NAG G 1 " - " ASN B 80 " " NAG H 1 " - " ASN A 114 " " NAG I 1 " - " ASN A 205 " " NAG J 1 " - " ASN E 149 " " NAG M 1 " - " ASN E 80 " " NAG N 1 " - " ASN C 149 " " NAG P 1 " - " ASN C 80 " " NAG Q 1 " - " ASN D 149 " " NAG R 1 " - " ASN D 80 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.71 Conformation dependent library (CDL) restraints added in 2.9 seconds 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3828 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 32 sheets defined 27.9% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'K' and resid 109 through 111 No H-bonds generated for 'chain 'K' and resid 109 through 111' Processing helix chain 'L' and resid 88 through 90 No H-bonds generated for 'chain 'L' and resid 88 through 90' Processing helix chain 'L' and resid 109 through 111 No H-bonds generated for 'chain 'L' and resid 109 through 111' Processing helix chain 'O' and resid 88 through 90 No H-bonds generated for 'chain 'O' and resid 88 through 90' Processing helix chain 'B' and resid 10 through 20 removed outlier: 4.124A pdb=" N GLU B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.622A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 224 No H-bonds generated for 'chain 'B' and resid 221 through 224' Processing helix chain 'B' and resid 226 through 241 removed outlier: 3.977A pdb=" N THR B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 250 through 266 removed outlier: 3.562A pdb=" N THR B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B 258 " --> pdb=" O GLY B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 280 through 305 removed outlier: 3.624A pdb=" N VAL B 292 " --> pdb=" O CYS B 288 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 313 No H-bonds generated for 'chain 'B' and resid 310 through 313' Processing helix chain 'B' and resid 423 through 427 Processing helix chain 'B' and resid 431 through 445 removed outlier: 4.668A pdb=" N SER B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 26 removed outlier: 3.508A pdb=" N ARG A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 226 through 249 removed outlier: 3.513A pdb=" N PHE A 229 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN A 232 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A 233 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N TYR A 234 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU A 235 " --> pdb=" O GLN A 232 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 3.861A pdb=" N MET A 239 " --> pdb=" O PRO A 236 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL A 246 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.954A pdb=" N VAL A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 311 removed outlier: 4.357A pdb=" N VAL A 295 " --> pdb=" O TRP A 291 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL A 300 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 301 " --> pdb=" O TYR A 297 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 400 removed outlier: 4.171A pdb=" N ILE A 394 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASP A 395 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS A 396 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG A 399 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 417 removed outlier: 3.767A pdb=" N LEU A 411 " --> pdb=" O GLY A 407 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 417 " --> pdb=" O TYR A 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 20 removed outlier: 4.123A pdb=" N GLU E 14 " --> pdb=" O SER E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 90 removed outlier: 3.624A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 224 No H-bonds generated for 'chain 'E' and resid 221 through 224' Processing helix chain 'E' and resid 226 through 241 removed outlier: 3.977A pdb=" N THR E 233 " --> pdb=" O SER E 229 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE E 234 " --> pdb=" O ILE E 230 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N PHE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TRP E 241 " --> pdb=" O TRP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 250 through 266 removed outlier: 3.561A pdb=" N THR E 256 " --> pdb=" O ALA E 252 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL E 258 " --> pdb=" O GLY E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 271 No H-bonds generated for 'chain 'E' and resid 269 through 271' Processing helix chain 'E' and resid 280 through 305 removed outlier: 3.623A pdb=" N VAL E 292 " --> pdb=" O CYS E 288 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE E 301 " --> pdb=" O LEU E 297 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR E 304 " --> pdb=" O ALA E 300 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE E 305 " --> pdb=" O PHE E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 313 No H-bonds generated for 'chain 'E' and resid 310 through 313' Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'E' and resid 431 through 445 removed outlier: 4.668A pdb=" N SER E 436 " --> pdb=" O PRO E 432 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU E 444 " --> pdb=" O LEU E 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 20 removed outlier: 4.123A pdb=" N GLU C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 removed outlier: 3.624A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 224 No H-bonds generated for 'chain 'C' and resid 221 through 224' Processing helix chain 'C' and resid 226 through 241 removed outlier: 3.977A pdb=" N THR C 233 " --> pdb=" O SER C 229 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 234 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 250 through 266 removed outlier: 3.561A pdb=" N THR C 256 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 258 " --> pdb=" O GLY C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 280 through 305 removed outlier: 3.624A pdb=" N VAL C 292 " --> pdb=" O CYS C 288 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 313 No H-bonds generated for 'chain 'C' and resid 310 through 313' Processing helix chain 'C' and resid 423 through 427 Processing helix chain 'C' and resid 431 through 445 removed outlier: 4.668A pdb=" N SER C 436 " --> pdb=" O PRO C 432 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 20 removed outlier: 4.123A pdb=" N GLU D 14 " --> pdb=" O SER D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 90 removed outlier: 3.623A pdb=" N ASP D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 224 No H-bonds generated for 'chain 'D' and resid 221 through 224' Processing helix chain 'D' and resid 226 through 241 removed outlier: 3.977A pdb=" N THR D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE D 234 " --> pdb=" O ILE D 230 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N PHE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 250 through 266 removed outlier: 3.561A pdb=" N THR D 256 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL D 258 " --> pdb=" O GLY D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 271 No H-bonds generated for 'chain 'D' and resid 269 through 271' Processing helix chain 'D' and resid 280 through 305 removed outlier: 3.622A pdb=" N VAL D 292 " --> pdb=" O CYS D 288 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE D 301 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 313 No H-bonds generated for 'chain 'D' and resid 310 through 313' Processing helix chain 'D' and resid 423 through 427 Processing helix chain 'D' and resid 431 through 445 removed outlier: 4.668A pdb=" N SER D 436 " --> pdb=" O PRO D 432 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU D 444 " --> pdb=" O LEU D 440 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.503A pdb=" N GLN K 5 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 17 through 19 Processing sheet with id= C, first strand: chain 'K' and resid 97 through 99 removed outlier: 4.176A pdb=" N ILE K 33 " --> pdb=" O LYS K 99 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET K 34 " --> pdb=" O ILE K 51 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 93 through 98 removed outlier: 3.950A pdb=" N MET L 34 " --> pdb=" O ILE L 51 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG L 38 " --> pdb=" O PHE L 47 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N PHE L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 68 through 70 Processing sheet with id= F, first strand: chain 'O' and resid 3 through 7 Processing sheet with id= G, first strand: chain 'O' and resid 11 through 13 removed outlier: 6.544A pdb=" N THR O 122 " --> pdb=" O VAL O 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'O' and resid 96 through 99 removed outlier: 4.085A pdb=" N ILE O 33 " --> pdb=" O LYS O 99 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET O 34 " --> pdb=" O ILE O 51 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG O 38 " --> pdb=" O PHE O 47 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N PHE O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 166 through 168 removed outlier: 6.718A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.868A pdb=" N MET B 49 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 147 through 155 removed outlier: 3.651A pdb=" N CYS B 150 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 212 " --> pdb=" O CYS B 150 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 191 through 199 removed outlier: 3.569A pdb=" N SER B 211 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG B 207 " --> pdb=" O ARG B 196 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 101 through 106 removed outlier: 7.097A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.774A pdb=" N THR A 42 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 173 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL A 44 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 67 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP A 73 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR A 133 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 121 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU A 122 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 48 through 50 Processing sheet with id= P, first strand: chain 'A' and resid 159 through 161 removed outlier: 3.897A pdb=" N THR A 200 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 107 through 112 removed outlier: 7.025A pdb=" N SER A 139 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER A 110 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR A 137 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 166 through 168 removed outlier: 6.718A pdb=" N VAL E 38 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 49 through 51 removed outlier: 3.867A pdb=" N MET E 49 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 147 through 155 removed outlier: 3.650A pdb=" N CYS E 150 " --> pdb=" O PHE E 212 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE E 212 " --> pdb=" O CYS E 150 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 191 through 199 removed outlier: 3.570A pdb=" N SER E 211 " --> pdb=" O ARG E 192 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG E 207 " --> pdb=" O ARG E 196 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 101 through 106 removed outlier: 7.097A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 166 through 168 removed outlier: 6.717A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.868A pdb=" N MET C 49 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 147 through 155 removed outlier: 3.650A pdb=" N CYS C 150 " --> pdb=" O PHE C 212 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 212 " --> pdb=" O CYS C 150 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 191 through 199 removed outlier: 3.570A pdb=" N SER C 211 " --> pdb=" O ARG C 192 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG C 207 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 101 through 106 removed outlier: 7.097A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 166 through 168 removed outlier: 6.717A pdb=" N VAL D 38 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 49 through 51 removed outlier: 3.867A pdb=" N MET D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 147 through 155 removed outlier: 3.651A pdb=" N CYS D 150 " --> pdb=" O PHE D 212 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE D 212 " --> pdb=" O CYS D 150 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 191 through 199 removed outlier: 3.569A pdb=" N SER D 211 " --> pdb=" O ARG D 192 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG D 207 " --> pdb=" O ARG D 196 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 101 through 106 removed outlier: 7.098A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) 505 hydrogen bonds defined for protein. 1386 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: 4.82 Time building geometry restraints manager: 8.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5173 1.34 - 1.46: 4848 1.46 - 1.59: 7306 1.59 - 1.71: 0 1.71 - 1.84: 158 Bond restraints: 17485 Sorted by residual: bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C1 MAN H 4 " pdb=" C2 MAN H 4 " ideal model delta sigma weight residual 1.526 1.587 -0.061 2.00e-02 2.50e+03 9.31e+00 bond pdb=" C5 MAN N 5 " pdb=" O5 MAN N 5 " ideal model delta sigma weight residual 1.418 1.474 -0.056 2.00e-02 2.50e+03 7.74e+00 bond pdb=" C3 BMA N 3 " pdb=" O3 BMA N 3 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.71e+00 bond pdb=" C5 MAN J 5 " pdb=" O5 MAN J 5 " ideal model delta sigma weight residual 1.418 1.474 -0.056 2.00e-02 2.50e+03 7.70e+00 ... (remaining 17480 not shown) Histogram of bond angle deviations from ideal: 98.03 - 105.26: 334 105.26 - 112.49: 9045 112.49 - 119.72: 5817 119.72 - 126.95: 8364 126.95 - 134.18: 217 Bond angle restraints: 23777 Sorted by residual: angle pdb=" C LYS K 65 " pdb=" N ASP K 66 " pdb=" CA ASP K 66 " ideal model delta sigma weight residual 121.54 131.31 -9.77 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C MET A 84 " pdb=" N GLN A 85 " pdb=" CA GLN A 85 " ideal model delta sigma weight residual 121.54 129.36 -7.82 1.91e+00 2.74e-01 1.68e+01 angle pdb=" CB MET A 115 " pdb=" CG MET A 115 " pdb=" SD MET A 115 " ideal model delta sigma weight residual 112.70 102.29 10.41 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C2 NAG I 1 " pdb=" N2 NAG I 1 " pdb=" C7 NAG I 1 " ideal model delta sigma weight residual 124.56 134.18 -9.62 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C2 NAG Q 2 " pdb=" N2 NAG Q 2 " pdb=" C7 NAG Q 2 " ideal model delta sigma weight residual 124.56 134.05 -9.49 3.00e+00 1.11e-01 1.00e+01 ... (remaining 23772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.87: 10326 23.87 - 47.74: 276 47.74 - 71.61: 75 71.61 - 95.48: 66 95.48 - 119.34: 41 Dihedral angle restraints: 10784 sinusoidal: 4787 harmonic: 5997 Sorted by residual: dihedral pdb=" CB CYS A 237 " pdb=" SG CYS A 237 " pdb=" SG CYS A 296 " pdb=" CB CYS A 296 " ideal model delta sinusoidal sigma weight residual 93.00 141.02 -48.02 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CA PHE O 37 " pdb=" C PHE O 37 " pdb=" N ARG O 38 " pdb=" CA ARG O 38 " ideal model delta harmonic sigma weight residual 180.00 152.72 27.28 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA TYR D 66 " pdb=" C TYR D 66 " pdb=" N TRP D 67 " pdb=" CA TRP D 67 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 10781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 2703 0.140 - 0.281: 48 0.281 - 0.421: 13 0.421 - 0.561: 1 0.561 - 0.701: 1 Chirality restraints: 2766 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 205 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CB VAL K 64 " pdb=" CA VAL K 64 " pdb=" CG1 VAL K 64 " pdb=" CG2 VAL K 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" C2 NAG J 2 " pdb=" C1 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" N2 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.09 -0.41 2.00e-01 2.50e+01 4.10e+00 ... (remaining 2763 not shown) Planarity restraints: 2923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 431 " 0.046 5.00e-02 4.00e+02 6.85e-02 7.50e+00 pdb=" N PRO B 432 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 432 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 432 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 431 " -0.046 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO D 432 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 432 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 432 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 431 " -0.045 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO E 432 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 432 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 432 " -0.039 5.00e-02 4.00e+02 ... (remaining 2920 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 749 2.71 - 3.25: 16092 3.25 - 3.80: 26963 3.80 - 4.35: 32162 4.35 - 4.90: 53246 Nonbonded interactions: 129212 Sorted by model distance: nonbonded pdb=" OG1 THR C 110 " pdb=" O THR D 96 " model vdw 2.158 2.440 nonbonded pdb=" OG1 THR B 110 " pdb=" O THR C 96 " model vdw 2.193 2.440 nonbonded pdb=" O2 BMA H 3 " pdb=" O6 MAN H 5 " model vdw 2.247 2.440 nonbonded pdb=" OG SER L 7 " pdb=" OG SER L 21 " model vdw 2.266 2.440 nonbonded pdb=" O PRO A 256 " pdb=" OG1 THR A 259 " model vdw 2.270 2.440 ... (remaining 129207 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 'B' and resid 8 through 447) selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'M' selection = chain 'P' selection = chain 'R' } ncs_group { reference = (chain 'K' and resid 1 through 124) selection = chain 'L' selection = (chain 'O' and resid 1 through 124) } 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 4.110 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 46.700 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 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 : 0.008 0.073 17485 Z= 0.506 Angle : 1.017 10.414 23777 Z= 0.504 Chirality : 0.063 0.701 2766 Planarity : 0.007 0.068 2913 Dihedral : 16.063 119.344 6929 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.22 % Allowed : 1.57 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % 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: -3.71 (0.16), residues: 2027 helix: -3.69 (0.13), residues: 395 sheet: -2.02 (0.21), residues: 551 loop : -2.17 (0.18), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 92 HIS 0.011 0.002 HIS A 113 PHE 0.023 0.003 PHE O 37 TYR 0.024 0.003 TYR K 108 ARG 0.015 0.001 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 866 time to evaluate : 1.842 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 11 LEU cc_start: 0.9576 (pp) cc_final: 0.9063 (tp) REVERT: K 18 LEU cc_start: 0.8930 (tm) cc_final: 0.8553 (tm) REVERT: K 39 GLN cc_start: 0.8278 (mm110) cc_final: 0.8003 (mm110) REVERT: K 73 ASP cc_start: 0.7495 (t0) cc_final: 0.6052 (t0) REVERT: K 74 ASN cc_start: 0.9253 (t0) cc_final: 0.9021 (t0) REVERT: K 76 LYS cc_start: 0.9402 (mttt) cc_final: 0.9168 (mtmm) REVERT: K 81 LEU cc_start: 0.7669 (mp) cc_final: 0.6856 (mp) REVERT: K 82 GLU cc_start: 0.9020 (tt0) cc_final: 0.8775 (tt0) REVERT: K 83 MET cc_start: 0.8436 (mpm) cc_final: 0.8150 (mpp) REVERT: K 90 ASP cc_start: 0.9125 (m-30) cc_final: 0.8906 (m-30) REVERT: K 95 TYR cc_start: 0.8571 (m-80) cc_final: 0.8345 (m-80) REVERT: L 43 LYS cc_start: 0.8977 (tttt) cc_final: 0.8619 (tttm) REVERT: L 48 VAL cc_start: 0.9184 (m) cc_final: 0.8930 (m) REVERT: O 22 CYS cc_start: 0.3909 (t) cc_final: 0.3572 (t) REVERT: O 30 ASN cc_start: 0.9054 (p0) cc_final: 0.8395 (p0) REVERT: O 36 TRP cc_start: 0.8709 (m100) cc_final: 0.8404 (m100) REVERT: O 38 ARG cc_start: 0.8619 (ptt180) cc_final: 0.8255 (mtm180) REVERT: O 58 THR cc_start: 0.9113 (p) cc_final: 0.8890 (t) REVERT: O 85 ASN cc_start: 0.8720 (m110) cc_final: 0.8175 (m-40) REVERT: O 87 LYS cc_start: 0.9197 (mtpp) cc_final: 0.8963 (mtpp) REVERT: O 89 GLU cc_start: 0.8931 (pt0) cc_final: 0.8620 (pm20) REVERT: O 99 LYS cc_start: 0.8225 (ttpm) cc_final: 0.7877 (tttp) REVERT: O 101 ARG cc_start: 0.8997 (ttm110) cc_final: 0.8781 (ttm110) REVERT: O 103 SER cc_start: 0.7950 (t) cc_final: 0.7222 (m) REVERT: O 115 TRP cc_start: 0.7017 (m-10) cc_final: 0.6639 (m-10) REVERT: B 21 LYS cc_start: 0.9540 (tttt) cc_final: 0.9294 (ptmt) REVERT: B 30 ASP cc_start: 0.9082 (m-30) cc_final: 0.8135 (t0) REVERT: B 37 CYS cc_start: 0.8206 (t) cc_final: 0.6906 (t) REVERT: B 40 MET cc_start: 0.7937 (mtm) cc_final: 0.7526 (mtt) REVERT: B 46 SER cc_start: 0.9294 (p) cc_final: 0.9010 (p) REVERT: B 49 MET cc_start: 0.9181 (ptm) cc_final: 0.8511 (ppp) REVERT: B 55 MET cc_start: 0.9359 (mtt) cc_final: 0.8591 (mmm) REVERT: B 89 ASP cc_start: 0.9007 (m-30) cc_final: 0.8759 (m-30) REVERT: B 90 GLN cc_start: 0.9150 (mt0) cc_final: 0.8596 (mp10) REVERT: B 95 ASP cc_start: 0.8433 (p0) cc_final: 0.8116 (p0) REVERT: B 115 MET cc_start: 0.8357 (ttp) cc_final: 0.8143 (ttp) REVERT: B 165 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8361 (tm-30) REVERT: B 168 TRP cc_start: 0.9387 (m100) cc_final: 0.8963 (m100) REVERT: B 208 LEU cc_start: 0.8770 (mt) cc_final: 0.8550 (mp) REVERT: B 215 LYS cc_start: 0.8807 (tttt) cc_final: 0.8601 (ttpt) REVERT: B 229 SER cc_start: 0.9349 (m) cc_final: 0.8948 (t) REVERT: B 230 ILE cc_start: 0.9376 (mt) cc_final: 0.9176 (mt) REVERT: B 261 MET cc_start: 0.9562 (mmm) cc_final: 0.9179 (mmp) REVERT: A 20 ARG cc_start: 0.9293 (mtt180) cc_final: 0.8956 (mtp-110) REVERT: A 75 ASP cc_start: 0.8484 (t0) cc_final: 0.8156 (t70) REVERT: A 90 ASN cc_start: 0.8605 (t0) cc_final: 0.8182 (t0) REVERT: A 98 TRP cc_start: 0.8941 (t60) cc_final: 0.8683 (t60) REVERT: A 125 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8275 (mm-30) REVERT: A 193 GLN cc_start: 0.8145 (tt0) cc_final: 0.7662 (tp-100) REVERT: A 225 LYS cc_start: 0.8695 (mmtt) cc_final: 0.8482 (mmmt) REVERT: E 14 GLU cc_start: 0.9029 (pt0) cc_final: 0.8786 (pp20) REVERT: E 24 ASP cc_start: 0.8956 (t0) cc_final: 0.8542 (t70) REVERT: E 49 MET cc_start: 0.9131 (ptm) cc_final: 0.8325 (ppp) REVERT: E 97 TYR cc_start: 0.8706 (p90) cc_final: 0.8230 (p90) REVERT: E 208 LEU cc_start: 0.9145 (mt) cc_final: 0.8500 (mt) REVERT: E 312 ARG cc_start: 0.7961 (tpp-160) cc_final: 0.7620 (ttt180) REVERT: C 44 ILE cc_start: 0.9139 (mt) cc_final: 0.8932 (mp) REVERT: C 119 HIS cc_start: 0.8829 (m90) cc_final: 0.8474 (m90) REVERT: C 148 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7513 (mm110) REVERT: C 151 THR cc_start: 0.9679 (p) cc_final: 0.9454 (t) REVERT: C 163 ASP cc_start: 0.8976 (m-30) cc_final: 0.8352 (p0) REVERT: C 191 HIS cc_start: 0.7909 (m-70) cc_final: 0.7552 (m-70) REVERT: C 217 ASN cc_start: 0.8734 (m-40) cc_final: 0.8462 (m110) REVERT: C 224 GLN cc_start: 0.8920 (mm110) cc_final: 0.8579 (mp10) REVERT: C 226 TYR cc_start: 0.9378 (m-10) cc_final: 0.8967 (m-10) REVERT: C 227 MET cc_start: 0.8687 (mtt) cc_final: 0.8374 (mmt) REVERT: C 229 SER cc_start: 0.9596 (m) cc_final: 0.9389 (p) REVERT: C 261 MET cc_start: 0.9157 (mmm) cc_final: 0.8391 (mmm) REVERT: C 282 ASP cc_start: 0.8991 (m-30) cc_final: 0.8315 (m-30) REVERT: C 288 CYS cc_start: 0.9500 (m) cc_final: 0.8068 (t) REVERT: C 289 PHE cc_start: 0.8846 (t80) cc_final: 0.8549 (t80) REVERT: C 303 ASN cc_start: 0.8875 (t160) cc_final: 0.8552 (m-40) REVERT: C 444 LEU cc_start: 0.9392 (mt) cc_final: 0.9128 (mt) REVERT: D 13 LYS cc_start: 0.9402 (tttm) cc_final: 0.9077 (tttp) REVERT: D 17 ASP cc_start: 0.9343 (m-30) cc_final: 0.9125 (m-30) REVERT: D 55 MET cc_start: 0.9364 (mtt) cc_final: 0.8917 (mtp) REVERT: D 85 ASN cc_start: 0.8884 (p0) cc_final: 0.8466 (p0) REVERT: D 100 ASN cc_start: 0.8394 (p0) cc_final: 0.8132 (p0) REVERT: D 137 MET cc_start: 0.9127 (mmm) cc_final: 0.8810 (mmm) REVERT: D 190 GLU cc_start: 0.8328 (tt0) cc_final: 0.7889 (tm-30) REVERT: D 191 HIS cc_start: 0.7815 (m-70) cc_final: 0.7151 (m-70) REVERT: D 208 LEU cc_start: 0.8585 (mt) cc_final: 0.8344 (mp) REVERT: D 235 LEU cc_start: 0.8580 (mp) cc_final: 0.8345 (tt) REVERT: D 261 MET cc_start: 0.8832 (mmm) cc_final: 0.8581 (tpp) REVERT: D 282 ASP cc_start: 0.9107 (m-30) cc_final: 0.8739 (m-30) REVERT: D 299 TYR cc_start: 0.6468 (t80) cc_final: 0.6204 (t80) outliers start: 4 outliers final: 1 residues processed: 870 average time/residue: 0.3162 time to fit residues: 393.8239 Evaluate side-chains 514 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 513 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.2274 > 50: distance: 28 - 49: 7.074 distance: 36 - 57: 29.219 distance: 40 - 66: 16.855 distance: 44 - 49: 7.308 distance: 45 - 74: 16.186 distance: 49 - 50: 20.583 distance: 50 - 51: 21.289 distance: 50 - 53: 8.817 distance: 51 - 52: 10.503 distance: 51 - 57: 27.250 distance: 53 - 54: 12.524 distance: 54 - 55: 16.493 distance: 54 - 56: 8.911 distance: 57 - 58: 16.245 distance: 58 - 59: 18.465 distance: 58 - 61: 16.012 distance: 59 - 60: 12.242 distance: 59 - 66: 19.811 distance: 61 - 62: 6.187 distance: 62 - 63: 21.826 distance: 63 - 64: 32.651 distance: 64 - 65: 23.078 distance: 66 - 67: 20.504 distance: 67 - 68: 21.471 distance: 67 - 70: 9.587 distance: 68 - 69: 28.252 distance: 68 - 74: 10.999 distance: 70 - 71: 14.283 distance: 71 - 72: 18.784 distance: 71 - 73: 41.306 distance: 74 - 75: 13.052 distance: 75 - 76: 7.732 distance: 75 - 78: 16.021 distance: 76 - 77: 14.815 distance: 76 - 82: 10.411 distance: 78 - 79: 30.659 distance: 79 - 80: 21.407 distance: 79 - 81: 22.600 distance: 82 - 83: 14.360 distance: 83 - 84: 33.770 distance: 83 - 86: 13.672 distance: 84 - 85: 19.202 distance: 84 - 91: 26.867 distance: 86 - 87: 21.233 distance: 87 - 88: 12.521 distance: 88 - 89: 23.297 distance: 91 - 92: 6.606 distance: 92 - 93: 22.105 distance: 93 - 94: 16.178 distance: 93 - 95: 23.011 distance: 95 - 96: 14.039 distance: 96 - 97: 4.667 distance: 96 - 99: 9.772 distance: 97 - 98: 15.583 distance: 97 - 107: 23.420 distance: 99 - 100: 9.727 distance: 100 - 101: 3.544 distance: 100 - 102: 4.264 distance: 102 - 104: 8.246 distance: 103 - 105: 5.700 distance: 107 - 108: 6.489 distance: 108 - 109: 13.239 distance: 108 - 111: 11.567 distance: 109 - 110: 11.047 distance: 111 - 112: 19.230 distance: 112 - 113: 5.707 distance: 112 - 114: 6.752 distance: 115 - 116: 7.811 distance: 116 - 117: 9.450 distance: 116 - 119: 13.328 distance: 117 - 118: 6.549 distance: 117 - 123: 7.746 distance: 119 - 120: 17.663 distance: 119 - 121: 12.997 distance: 120 - 122: 16.933 distance: 123 - 124: 4.419 distance: 124 - 125: 3.445 distance: 124 - 127: 11.318 distance: 125 - 126: 4.904 distance: 125 - 134: 18.078 distance: 127 - 128: 16.799 distance: 128 - 129: 21.394 distance: 129 - 130: 3.657 distance: 130 - 131: 18.297 distance: 131 - 132: 4.189 distance: 131 - 133: 4.308