Starting phenix.real_space_refine on Sat Jun 14 09:41:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbz_13314/06_2025/7pbz_13314.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbz_13314/06_2025/7pbz_13314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pbz_13314/06_2025/7pbz_13314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbz_13314/06_2025/7pbz_13314.map" model { file = "/net/cci-nas-00/data/ceres_data/7pbz_13314/06_2025/7pbz_13314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbz_13314/06_2025/7pbz_13314.cif" } resolution = 2.79 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= 0.008 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 886 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 84 5.16 5 C 9650 2.51 5 N 2408 2.21 5 O 2679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14822 Number of models: 1 Model: "" Number of chains: 17 Chain: "F" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 893 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 1 Chain: "A" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2695 Classifications: {'peptide': 334} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 319} Chain: "B" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2707 Classifications: {'peptide': 330} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2707 Classifications: {'peptide': 330} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2707 Classifications: {'peptide': 330} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2714 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 321} 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 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: "K" 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: "L" 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: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Unusual residues: {'HEX': 1, 'NAG': 1, 'OCT': 2, 'UND': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 1, 'ABU': 1, 'HEX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'D10': 1, 'HSM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Unusual residues: {'D10': 2, 'HEX': 2, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.99, per 1000 atoms: 0.81 Number of scatterers: 14822 At special positions: 0 Unit cell: (91.932, 119.968, 125.184, 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) Zn 1 29.99 S 84 16.00 O 2679 8.00 N 2408 7.00 C 9650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS F 409 " - pdb=" SG CYS F 483 " distance=2.04 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.04 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA H 3 " - " MAN H 4 " " BMA J 3 " - " MAN J 5 " " BMA L 3 " - " MAN L 5 " BETA1-4 " 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 J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A 501 " - " ASN A 111 " " NAG D 501 " - " ASN D 111 " " NAG G 1 " - " ASN B 80 " " NAG H 1 " - " ASN B 149 " " NAG I 1 " - " ASN C 80 " " NAG J 1 " - " ASN C 149 " " NAG K 1 " - " ASN E 80 " " NAG L 1 " - " ASN E 149 " Time building additional restraints: 4.59 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 503 " pdb="ZN ZN B 503 " - pdb=" NE2 HIS E 267 " pdb="ZN ZN B 503 " - pdb=" NE2 HIS C 267 " pdb="ZN ZN B 503 " - pdb=" NE2 HIS B 267 " 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 40.3% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'F' and resid 474 through 478 Processing helix chain 'F' and resid 495 through 499 Processing helix chain 'A' and resid 13 through 23 Processing helix chain 'A' and resid 73 through 76 Processing helix chain 'A' and resid 87 through 94 removed outlier: 3.645A pdb=" N ILE A 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 179 removed outlier: 4.415A pdb=" N VAL A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.589A pdb=" N SER A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 277 removed outlier: 4.096A pdb=" N ASN A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 310 removed outlier: 3.529A pdb=" N LEU A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 415 removed outlier: 3.634A pdb=" N ALA A 319 " --> pdb=" O PRO A 315 " (cutoff:3.500A) Proline residue: A 401 - end of helix Processing helix chain 'B' and resid 9 through 20 removed outlier: 3.553A pdb=" N LYS B 13 " --> pdb=" O MET B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.532A pdb=" N LEU B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 4.303A pdb=" N ARG B 142 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 225 through 243 removed outlier: 3.742A pdb=" N SER B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASN B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 270 Processing helix chain 'B' and resid 279 through 308 Processing helix chain 'B' and resid 420 through 429 Processing helix chain 'B' and resid 430 through 446 Processing helix chain 'C' and resid 9 through 21 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.571A pdb=" N LEU C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 removed outlier: 4.118A pdb=" N ARG C 142 " --> pdb=" O ASP C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 225 through 242 removed outlier: 3.978A pdb=" N SER C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE C 242 " --> pdb=" O VAL C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 271 Processing helix chain 'C' and resid 279 through 308 Processing helix chain 'C' and resid 420 through 446 Proline residue: C 432 - end of helix Processing helix chain 'E' and resid 9 through 21 Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 84 through 90 Processing helix chain 'E' and resid 139 through 143 removed outlier: 4.365A pdb=" N ARG E 142 " --> pdb=" O ASP E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 225 through 237 removed outlier: 4.152A pdb=" N SER E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR E 233 " --> pdb=" O SER E 229 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 242 removed outlier: 3.684A pdb=" N ILE E 242 " --> pdb=" O SER E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 272 removed outlier: 3.625A pdb=" N ARG E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 308 Processing helix chain 'E' and resid 423 through 449 Proline residue: E 435 - end of helix Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 73 through 76 removed outlier: 3.774A pdb=" N LYS D 76 " --> pdb=" O GLU D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 76' Processing helix chain 'D' and resid 88 through 93 removed outlier: 4.011A pdb=" N SER D 92 " --> pdb=" O ASN D 88 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 93' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.511A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 251 through 277 Processing helix chain 'D' and resid 284 through 310 removed outlier: 3.521A pdb=" N LEU D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 417 removed outlier: 3.707A pdb=" N ALA D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) Proline residue: D 401 - end of helix removed outlier: 3.799A pdb=" N ASN D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 2 through 7 Processing sheet with id=AA2, first strand: chain 'F' and resid 420 through 426 removed outlier: 6.652A pdb=" N MET F 421 " --> pdb=" O ALA F 437 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA F 437 " --> pdb=" O MET F 421 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP F 423 " --> pdb=" O VAL F 435 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 445 through 447 current: chain 'F' and resid 501 through 502 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 54 removed outlier: 6.540A pdb=" N GLU A 40 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS A 71 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP A 63 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N PHE A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR A 61 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLU A 59 " --> pdb=" O PRO A 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 59 through 71 current: chain 'A' and resid 126 through 138 Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.253A pdb=" N SER A 159 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL A 211 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY A 195 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LYS A 220 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU A 193 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 36 through 51 removed outlier: 6.373A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 56 through 68 current: chain 'B' and resid 123 through 135 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.797A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 36 through 46 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 36 through 46 current: chain 'C' and resid 56 through 68 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 68 current: chain 'C' and resid 123 through 135 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 98 removed outlier: 4.138A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 36 through 51 removed outlier: 6.394A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 56 through 68 current: chain 'E' and resid 123 through 135 Processing sheet with id=AB1, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.692A pdb=" N CYS E 150 " --> pdb=" O PHE E 212 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE E 212 " --> pdb=" O CYS E 150 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR E 205 " --> pdb=" O ASN E 197 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN E 197 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG E 207 " --> pdb=" O SER E 195 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER E 195 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER E 209 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU E 193 " --> pdb=" O SER E 209 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER E 211 " --> pdb=" O HIS E 191 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N HIS E 191 " --> pdb=" O SER E 211 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG E 213 " --> pdb=" O VAL E 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 39 through 49 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 39 through 49 current: chain 'D' and resid 59 through 71 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 71 current: chain 'D' and resid 126 through 138 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.303A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR D 210 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE D 202 " --> pdb=" O TYR D 210 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL D 212 " --> pdb=" O SER D 200 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N SER D 200 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR D 214 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL D 198 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N HIS D 216 " --> pdb=" O GLN D 196 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLN D 196 " --> pdb=" O HIS D 216 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N HIS D 218 " --> pdb=" O LEU D 194 " (cutoff:3.500A) 593 hydrogen bonds defined for protein. 1671 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: 4.04 Time building geometry restraints manager: 5.30 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: 4508 1.34 - 1.46: 3892 1.46 - 1.58: 6639 1.58 - 1.70: 0 1.70 - 1.82: 146 Bond restraints: 15185 Sorted by residual: bond pdb=" CG HSM C 601 " pdb=" ND1 HSM C 601 " ideal model delta sigma weight residual 1.383 1.313 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" CD2 HSM C 601 " pdb=" NE2 HSM C 601 " ideal model delta sigma weight residual 1.376 1.314 0.062 2.00e-02 2.50e+03 9.67e+00 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.09e+00 bond pdb=" N GLN F 1 " pdb=" CA GLN F 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.75e+00 ... (remaining 15180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 20305 2.88 - 5.77: 268 5.77 - 8.65: 23 8.65 - 11.54: 1 11.54 - 14.42: 1 Bond angle restraints: 20598 Sorted by residual: angle pdb=" C ALA A 316 " pdb=" N ARG A 317 " pdb=" CA ARG A 317 " ideal model delta sigma weight residual 120.28 131.67 -11.39 1.34e+00 5.57e-01 7.23e+01 angle pdb=" CA CYS E 150 " pdb=" CB CYS E 150 " pdb=" SG CYS E 150 " ideal model delta sigma weight residual 114.40 128.82 -14.42 2.30e+00 1.89e-01 3.93e+01 angle pdb=" C THR C 110 " pdb=" N VAL C 111 " pdb=" CA VAL C 111 " ideal model delta sigma weight residual 122.11 128.27 -6.16 1.12e+00 7.97e-01 3.03e+01 angle pdb=" C VAL C 109 " pdb=" N THR C 110 " pdb=" CA THR C 110 " ideal model delta sigma weight residual 121.54 129.28 -7.74 1.91e+00 2.74e-01 1.64e+01 angle pdb=" C MET A 112 " pdb=" N THR A 113 " pdb=" CA THR A 113 " ideal model delta sigma weight residual 121.54 129.07 -7.53 1.91e+00 2.74e-01 1.55e+01 ... (remaining 20593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.34: 8705 23.34 - 46.67: 406 46.67 - 70.01: 40 70.01 - 93.35: 27 93.35 - 116.68: 26 Dihedral angle restraints: 9204 sinusoidal: 3975 harmonic: 5229 Sorted by residual: dihedral pdb=" CA LEU E 223 " pdb=" C LEU E 223 " pdb=" N GLN E 224 " pdb=" CA GLN E 224 " ideal model delta harmonic sigma weight residual -180.00 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA VAL D 64 " pdb=" C VAL D 64 " pdb=" N PHE D 65 " pdb=" CA PHE D 65 " ideal model delta harmonic sigma weight residual 180.00 156.57 23.43 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA PRO C 276 " pdb=" C PRO C 276 " pdb=" N TYR C 277 " pdb=" CA TYR C 277 " ideal model delta harmonic sigma weight residual 180.00 158.01 21.99 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 9201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.837: 2364 0.837 - 1.675: 6 1.675 - 2.512: 0 2.512 - 3.349: 0 3.349 - 4.186: 1 Chirality restraints: 2371 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.74 -1.66 2.00e-02 2.50e+03 6.91e+03 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-02 2.50e+03 2.67e+03 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-02 2.50e+03 2.48e+03 ... (remaining 2368 not shown) Planarity restraints: 2530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 111 " 0.219 2.00e-02 2.50e+03 2.14e-01 5.72e+02 pdb=" CG ASN A 111 " -0.076 2.00e-02 2.50e+03 pdb=" OD1 ASN A 111 " -0.083 2.00e-02 2.50e+03 pdb=" ND2 ASN A 111 " -0.319 2.00e-02 2.50e+03 pdb=" C1 NAG A 501 " 0.258 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 149 " 0.178 2.00e-02 2.50e+03 1.90e-01 4.49e+02 pdb=" CG ASN E 149 " -0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN E 149 " -0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN E 149 " -0.293 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " 0.234 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 80 " 0.141 2.00e-02 2.50e+03 1.38e-01 2.37e+02 pdb=" CG ASN C 80 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN C 80 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN C 80 " -0.207 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.165 2.00e-02 2.50e+03 ... (remaining 2527 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 341 2.69 - 3.24: 14249 3.24 - 3.79: 23448 3.79 - 4.35: 32448 4.35 - 4.90: 54385 Nonbonded interactions: 124871 Sorted by model distance: nonbonded pdb=" OG1 THR B 160 " pdb=" OD1 ASP B 162 " model vdw 2.136 3.040 nonbonded pdb=" O THR A 99 " pdb=" OG1 THR E 110 " model vdw 2.149 3.040 nonbonded pdb=" O THR E 233 " pdb=" OG SER E 236 " model vdw 2.168 3.040 nonbonded pdb=" OG SER E 104 " pdb=" O THR E 131 " model vdw 2.169 3.040 nonbonded pdb=" OG1 THR A 113 " pdb=" O THR B 96 " model vdw 2.182 3.040 ... (remaining 124866 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 12 through 416) selection = (chain 'D' and resid 12 through 416) } ncs_group { reference = (chain 'B' and resid 8 through 447) selection = (chain 'C' and resid 8 through 447) selection = (chain 'E' and resid 8 through 450) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 54.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 41.610 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.070 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:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 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 : 0.007 0.319 15216 Z= 0.311 Angle : 1.179 48.872 20676 Z= 0.486 Chirality : 0.121 4.186 2371 Planarity : 0.006 0.143 2522 Dihedral : 15.133 116.681 5826 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.33 (0.20), residues: 1753 helix: 1.56 (0.22), residues: 587 sheet: -0.26 (0.23), residues: 454 loop : -0.49 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 67 HIS 0.006 0.001 HIS E 267 PHE 0.013 0.001 PHE D 298 TYR 0.029 0.001 TYR B 299 ARG 0.032 0.001 ARG E 269 Details of bonding type rmsd link_NAG-ASN : bond 0.19261 ( 8) link_NAG-ASN : angle 12.21269 ( 24) link_ALPHA1-6 : bond 0.01066 ( 3) link_ALPHA1-6 : angle 19.35336 ( 9) link_BETA1-4 : bond 0.02429 ( 9) link_BETA1-4 : angle 18.48013 ( 27) link_ALPHA1-3 : bond 0.01180 ( 2) link_ALPHA1-3 : angle 7.40175 ( 6) hydrogen bonds : bond 0.12188 ( 593) hydrogen bonds : angle 5.37577 ( 1671) metal coordination : bond 0.22970 ( 3) SS BOND : bond 0.00407 ( 6) SS BOND : angle 1.24426 ( 12) covalent geometry : bond 0.00418 (15185) covalent geometry : angle 0.77103 (20598) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.960 Fit side-chains revert: symmetry clash REVERT: F 454 ARG cc_start: 0.8201 (mtm110) cc_final: 0.7910 (mtp180) REVERT: F 465 THR cc_start: 0.8003 (p) cc_final: 0.7645 (p) REVERT: F 468 LEU cc_start: 0.7691 (tt) cc_final: 0.7317 (tt) REVERT: F 477 ASP cc_start: 0.7562 (m-30) cc_final: 0.6940 (m-30) REVERT: A 248 ASN cc_start: 0.8314 (t0) cc_final: 0.7160 (p0) REVERT: B 153 GLU cc_start: 0.8513 (mm-30) cc_final: 0.7715 (mm-30) REVERT: B 224 GLN cc_start: 0.8533 (mm110) cc_final: 0.8255 (mm110) REVERT: C 95 ASP cc_start: 0.7790 (t70) cc_final: 0.7423 (t0) REVERT: C 137 MET cc_start: 0.8296 (mmp) cc_final: 0.7988 (tpp) REVERT: C 283 MET cc_start: 0.8222 (mmt) cc_final: 0.8020 (mmt) REVERT: C 426 TRP cc_start: 0.7877 (t60) cc_final: 0.7429 (t60) REVERT: E 224 GLN cc_start: 0.8432 (tp40) cc_final: 0.7087 (tm-30) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 1.7785 time to fit residues: 458.2401 Evaluate side-chains 163 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.8980 chunk 133 optimal weight: 0.0060 chunk 74 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 464 ASN F 504 GLN B 64 GLN C 113 ASN C 148 GLN E 191 HIS D 116 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.079622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.061673 restraints weight = 32675.071| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.83 r_work: 0.2772 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15216 Z= 0.202 Angle : 0.684 15.656 20676 Z= 0.334 Chirality : 0.046 0.343 2371 Planarity : 0.004 0.073 2522 Dihedral : 10.943 100.265 2500 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.46 % Allowed : 8.27 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.57 (0.20), residues: 1753 helix: 1.78 (0.21), residues: 590 sheet: -0.05 (0.23), residues: 465 loop : -0.45 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 429 HIS 0.004 0.001 HIS C 267 PHE 0.018 0.002 PHE B 293 TYR 0.021 0.002 TYR B 299 ARG 0.006 0.001 ARG A 221 Details of bonding type rmsd link_NAG-ASN : bond 0.00738 ( 8) link_NAG-ASN : angle 5.18793 ( 24) link_ALPHA1-6 : bond 0.00512 ( 3) link_ALPHA1-6 : angle 2.79989 ( 9) link_BETA1-4 : bond 0.00636 ( 9) link_BETA1-4 : angle 3.27754 ( 27) link_ALPHA1-3 : bond 0.00670 ( 2) link_ALPHA1-3 : angle 1.66261 ( 6) hydrogen bonds : bond 0.04200 ( 593) hydrogen bonds : angle 4.50267 ( 1671) metal coordination : bond 0.00797 ( 3) SS BOND : bond 0.00294 ( 6) SS BOND : angle 1.10357 ( 12) covalent geometry : bond 0.00469 (15185) covalent geometry : angle 0.64774 (20598) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 1.665 Fit side-chains REVERT: F 406 ARG cc_start: 0.7979 (tpp80) cc_final: 0.7779 (tpt-90) REVERT: F 465 THR cc_start: 0.8288 (p) cc_final: 0.7814 (p) REVERT: F 467 TYR cc_start: 0.7320 (m-10) cc_final: 0.6949 (m-80) REVERT: F 477 ASP cc_start: 0.7684 (m-30) cc_final: 0.7164 (m-30) REVERT: F 504 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7321 (pm20) REVERT: A 213 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8090 (mmp) REVERT: B 9 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8318 (tpp) REVERT: B 224 GLN cc_start: 0.8838 (mm110) cc_final: 0.8554 (mm110) REVERT: C 95 ASP cc_start: 0.8484 (t70) cc_final: 0.7800 (t0) REVERT: C 138 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8042 (mtt) REVERT: C 275 ILE cc_start: 0.8646 (tp) cc_final: 0.8210 (pp) REVERT: C 426 TRP cc_start: 0.7781 (t60) cc_final: 0.7367 (t60) REVERT: E 190 GLU cc_start: 0.8628 (tt0) cc_final: 0.8355 (tt0) REVERT: E 224 GLN cc_start: 0.8754 (tp40) cc_final: 0.7824 (tm-30) REVERT: D 63 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8328 (t70) REVERT: D 274 ARG cc_start: 0.8504 (mpt-90) cc_final: 0.8278 (mpt-90) outliers start: 23 outliers final: 8 residues processed: 181 average time/residue: 1.5130 time to fit residues: 298.9134 Evaluate side-chains 166 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 173 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 112 optimal weight: 0.0570 chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 168 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 308 ASN B 224 GLN C 85 ASN ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.080708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.062658 restraints weight = 32477.110| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.84 r_work: 0.2780 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15216 Z= 0.127 Angle : 0.593 12.710 20676 Z= 0.293 Chirality : 0.044 0.293 2371 Planarity : 0.004 0.063 2522 Dihedral : 9.373 90.302 2500 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.85 % Allowed : 9.68 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.73 (0.20), residues: 1753 helix: 1.96 (0.21), residues: 591 sheet: 0.06 (0.23), residues: 464 loop : -0.43 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 168 HIS 0.003 0.001 HIS C 267 PHE 0.014 0.001 PHE B 293 TYR 0.025 0.001 TYR B 299 ARG 0.020 0.000 ARG A 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00673 ( 8) link_NAG-ASN : angle 3.83356 ( 24) link_ALPHA1-6 : bond 0.00791 ( 3) link_ALPHA1-6 : angle 1.86740 ( 9) link_BETA1-4 : bond 0.00401 ( 9) link_BETA1-4 : angle 2.75050 ( 27) link_ALPHA1-3 : bond 0.00922 ( 2) link_ALPHA1-3 : angle 1.62340 ( 6) hydrogen bonds : bond 0.03662 ( 593) hydrogen bonds : angle 4.26968 ( 1671) metal coordination : bond 0.00843 ( 3) SS BOND : bond 0.00286 ( 6) SS BOND : angle 0.87189 ( 12) covalent geometry : bond 0.00286 (15185) covalent geometry : angle 0.56832 (20598) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 1.942 Fit side-chains REVERT: F 465 THR cc_start: 0.8205 (p) cc_final: 0.7930 (p) REVERT: F 467 TYR cc_start: 0.7419 (m-10) cc_final: 0.7013 (m-80) REVERT: F 504 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7495 (pm20) REVERT: A 242 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8622 (mt0) REVERT: B 224 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8509 (mm110) REVERT: C 95 ASP cc_start: 0.8499 (t70) cc_final: 0.7809 (t0) REVERT: C 275 ILE cc_start: 0.8572 (tp) cc_final: 0.8241 (pp) REVERT: C 426 TRP cc_start: 0.7743 (t60) cc_final: 0.7350 (t60) REVERT: E 224 GLN cc_start: 0.8868 (tp40) cc_final: 0.8025 (tm-30) REVERT: D 274 ARG cc_start: 0.8563 (mpt-90) cc_final: 0.8143 (mpt-90) outliers start: 29 outliers final: 10 residues processed: 178 average time/residue: 1.5393 time to fit residues: 300.2746 Evaluate side-chains 165 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 446 SER Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 125 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 471 ASN F 504 GLN A 116 ASN E 224 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.078188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.060175 restraints weight = 32680.141| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.83 r_work: 0.2740 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15216 Z= 0.220 Angle : 0.621 11.037 20676 Z= 0.310 Chirality : 0.046 0.328 2371 Planarity : 0.004 0.058 2522 Dihedral : 9.014 91.773 2500 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.29 % Allowed : 12.09 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.73 (0.20), residues: 1753 helix: 1.99 (0.21), residues: 593 sheet: -0.01 (0.23), residues: 469 loop : -0.42 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 412 HIS 0.004 0.001 HIS C 267 PHE 0.016 0.002 PHE B 293 TYR 0.026 0.002 TYR B 299 ARG 0.014 0.000 ARG A 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 8) link_NAG-ASN : angle 3.29687 ( 24) link_ALPHA1-6 : bond 0.00851 ( 3) link_ALPHA1-6 : angle 2.10597 ( 9) link_BETA1-4 : bond 0.00364 ( 9) link_BETA1-4 : angle 2.73816 ( 27) link_ALPHA1-3 : bond 0.00867 ( 2) link_ALPHA1-3 : angle 1.97328 ( 6) hydrogen bonds : bond 0.04076 ( 593) hydrogen bonds : angle 4.30312 ( 1671) metal coordination : bond 0.00477 ( 3) SS BOND : bond 0.00372 ( 6) SS BOND : angle 1.38520 ( 12) covalent geometry : bond 0.00515 (15185) covalent geometry : angle 0.60001 (20598) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 1.775 Fit side-chains revert: symmetry clash REVERT: F 432 ARG cc_start: 0.7294 (ttp-170) cc_final: 0.6996 (ttm170) REVERT: F 463 LYS cc_start: 0.8716 (tptp) cc_final: 0.8458 (tptp) REVERT: F 465 THR cc_start: 0.8296 (p) cc_final: 0.7893 (p) REVERT: F 504 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7515 (pm20) REVERT: A 274 ARG cc_start: 0.8160 (tpp-160) cc_final: 0.7881 (tpp-160) REVERT: B 9 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8267 (tpp) REVERT: B 14 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8513 (mp0) REVERT: B 224 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8588 (mm110) REVERT: C 95 ASP cc_start: 0.8530 (t70) cc_final: 0.7769 (t0) REVERT: C 227 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7402 (ttt) REVERT: C 275 ILE cc_start: 0.8629 (tp) cc_final: 0.8265 (pp) REVERT: C 426 TRP cc_start: 0.7734 (t60) cc_final: 0.7358 (t60) REVERT: D 274 ARG cc_start: 0.8521 (mpt-90) cc_final: 0.8277 (mpt-90) outliers start: 36 outliers final: 15 residues processed: 176 average time/residue: 1.5206 time to fit residues: 293.4941 Evaluate side-chains 168 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 446 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 105 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 110 optimal weight: 0.0870 chunk 71 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 504 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.078955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.061018 restraints weight = 32748.363| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.83 r_work: 0.2744 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15216 Z= 0.144 Angle : 0.589 10.595 20676 Z= 0.292 Chirality : 0.044 0.305 2371 Planarity : 0.004 0.054 2522 Dihedral : 8.472 87.293 2500 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.10 % Allowed : 13.18 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.82 (0.20), residues: 1753 helix: 2.09 (0.21), residues: 593 sheet: 0.07 (0.23), residues: 464 loop : -0.40 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 412 HIS 0.003 0.001 HIS C 267 PHE 0.014 0.001 PHE B 293 TYR 0.025 0.001 TYR B 299 ARG 0.004 0.000 ARG C 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 8) link_NAG-ASN : angle 3.17560 ( 24) link_ALPHA1-6 : bond 0.00969 ( 3) link_ALPHA1-6 : angle 2.06859 ( 9) link_BETA1-4 : bond 0.00434 ( 9) link_BETA1-4 : angle 2.40502 ( 27) link_ALPHA1-3 : bond 0.00978 ( 2) link_ALPHA1-3 : angle 1.84694 ( 6) hydrogen bonds : bond 0.03666 ( 593) hydrogen bonds : angle 4.18764 ( 1671) metal coordination : bond 0.00432 ( 3) SS BOND : bond 0.00286 ( 6) SS BOND : angle 1.04778 ( 12) covalent geometry : bond 0.00330 (15185) covalent geometry : angle 0.57076 (20598) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 1.784 Fit side-chains revert: symmetry clash REVERT: F 432 ARG cc_start: 0.7234 (ttp-170) cc_final: 0.6989 (ttm170) REVERT: F 463 LYS cc_start: 0.8758 (tptp) cc_final: 0.8504 (tptp) REVERT: F 465 THR cc_start: 0.8305 (p) cc_final: 0.7894 (p) REVERT: F 477 ASP cc_start: 0.7605 (m-30) cc_final: 0.7205 (m-30) REVERT: F 504 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: A 114 MET cc_start: 0.8517 (mmp) cc_final: 0.8237 (mmp) REVERT: B 14 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8497 (mp0) REVERT: B 224 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8563 (mm110) REVERT: C 138 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8349 (mtt) REVERT: C 275 ILE cc_start: 0.8589 (tp) cc_final: 0.8369 (pp) REVERT: E 224 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.7981 (tm-30) outliers start: 33 outliers final: 16 residues processed: 170 average time/residue: 1.5166 time to fit residues: 282.4459 Evaluate side-chains 170 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 446 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 121 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 166 optimal weight: 0.0170 chunk 174 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 131 optimal weight: 0.0270 chunk 168 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.079088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.061397 restraints weight = 32798.389| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.89 r_work: 0.2736 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15216 Z= 0.125 Angle : 0.573 10.319 20676 Z= 0.283 Chirality : 0.044 0.308 2371 Planarity : 0.003 0.051 2522 Dihedral : 8.010 83.981 2500 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.65 % Allowed : 13.69 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.90 (0.20), residues: 1753 helix: 2.17 (0.21), residues: 593 sheet: 0.08 (0.24), residues: 464 loop : -0.35 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 412 HIS 0.003 0.001 HIS E 267 PHE 0.013 0.001 PHE C 293 TYR 0.025 0.001 TYR B 299 ARG 0.008 0.000 ARG A 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 8) link_NAG-ASN : angle 2.93752 ( 24) link_ALPHA1-6 : bond 0.01018 ( 3) link_ALPHA1-6 : angle 2.08249 ( 9) link_BETA1-4 : bond 0.00469 ( 9) link_BETA1-4 : angle 2.22611 ( 27) link_ALPHA1-3 : bond 0.01038 ( 2) link_ALPHA1-3 : angle 1.83712 ( 6) hydrogen bonds : bond 0.03438 ( 593) hydrogen bonds : angle 4.10345 ( 1671) metal coordination : bond 0.00434 ( 3) SS BOND : bond 0.00254 ( 6) SS BOND : angle 0.91264 ( 12) covalent geometry : bond 0.00280 (15185) covalent geometry : angle 0.55675 (20598) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 2.828 Fit side-chains revert: symmetry clash REVERT: F 406 ARG cc_start: 0.8340 (tpp80) cc_final: 0.7916 (tpp80) REVERT: F 432 ARG cc_start: 0.7240 (ttp-170) cc_final: 0.7010 (ttm170) REVERT: F 465 THR cc_start: 0.8336 (p) cc_final: 0.7889 (p) REVERT: F 469 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7739 (mm-30) REVERT: F 477 ASP cc_start: 0.7392 (m-30) cc_final: 0.7106 (m-30) REVERT: F 504 GLN cc_start: 0.8064 (pm20) cc_final: 0.7725 (pm20) REVERT: A 242 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8571 (mt0) REVERT: B 14 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8470 (mp0) REVERT: B 224 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8571 (mm110) REVERT: C 138 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8385 (mtt) REVERT: E 40 MET cc_start: 0.9579 (OUTLIER) cc_final: 0.9084 (mtt) REVERT: E 224 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8054 (tm-30) REVERT: D 138 GLU cc_start: 0.8224 (pp20) cc_final: 0.7989 (pp20) outliers start: 26 outliers final: 14 residues processed: 174 average time/residue: 1.6160 time to fit residues: 307.9785 Evaluate side-chains 170 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 446 SER Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 113 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.078461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.060790 restraints weight = 32891.924| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.88 r_work: 0.2728 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15216 Z= 0.154 Angle : 0.591 10.674 20676 Z= 0.292 Chirality : 0.044 0.310 2371 Planarity : 0.004 0.054 2522 Dihedral : 7.739 81.221 2500 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.78 % Allowed : 14.58 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.88 (0.20), residues: 1753 helix: 2.15 (0.21), residues: 594 sheet: 0.07 (0.24), residues: 464 loop : -0.35 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 67 HIS 0.003 0.001 HIS E 267 PHE 0.013 0.001 PHE B 293 TYR 0.026 0.001 TYR B 299 ARG 0.007 0.000 ARG A 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 8) link_NAG-ASN : angle 2.82555 ( 24) link_ALPHA1-6 : bond 0.01025 ( 3) link_ALPHA1-6 : angle 2.12294 ( 9) link_BETA1-4 : bond 0.00442 ( 9) link_BETA1-4 : angle 2.19917 ( 27) link_ALPHA1-3 : bond 0.01014 ( 2) link_ALPHA1-3 : angle 1.90341 ( 6) hydrogen bonds : bond 0.03556 ( 593) hydrogen bonds : angle 4.10220 ( 1671) metal coordination : bond 0.00269 ( 3) SS BOND : bond 0.00346 ( 6) SS BOND : angle 1.02253 ( 12) covalent geometry : bond 0.00355 (15185) covalent geometry : angle 0.57531 (20598) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 1.580 Fit side-chains revert: symmetry clash REVERT: F 432 ARG cc_start: 0.7213 (ttp-170) cc_final: 0.6991 (ttm170) REVERT: F 465 THR cc_start: 0.8286 (p) cc_final: 0.8009 (p) REVERT: F 477 ASP cc_start: 0.7463 (m-30) cc_final: 0.7239 (m-30) REVERT: F 504 GLN cc_start: 0.8048 (pm20) cc_final: 0.7742 (pm20) REVERT: B 14 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8457 (mp0) REVERT: B 40 MET cc_start: 0.9479 (OUTLIER) cc_final: 0.8913 (mtt) REVERT: B 49 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7220 (tmm) REVERT: B 224 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8589 (mm110) REVERT: C 138 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8453 (mtt) REVERT: E 224 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: D 138 GLU cc_start: 0.8259 (pp20) cc_final: 0.8002 (pp20) outliers start: 28 outliers final: 15 residues processed: 171 average time/residue: 1.6712 time to fit residues: 312.2803 Evaluate side-chains 172 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 446 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 107 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 96 optimal weight: 0.4980 chunk 34 optimal weight: 0.0980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.080063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.062478 restraints weight = 32486.418| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.89 r_work: 0.2778 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15216 Z= 0.106 Angle : 0.572 10.043 20676 Z= 0.282 Chirality : 0.043 0.301 2371 Planarity : 0.003 0.045 2522 Dihedral : 7.368 77.030 2500 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.46 % Allowed : 14.96 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 1.00 (0.21), residues: 1753 helix: 2.23 (0.21), residues: 594 sheet: 0.15 (0.24), residues: 469 loop : -0.28 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 67 HIS 0.003 0.001 HIS E 267 PHE 0.014 0.001 PHE B 301 TYR 0.024 0.001 TYR B 299 ARG 0.011 0.000 ARG A 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 8) link_NAG-ASN : angle 2.61145 ( 24) link_ALPHA1-6 : bond 0.01119 ( 3) link_ALPHA1-6 : angle 2.14743 ( 9) link_BETA1-4 : bond 0.00545 ( 9) link_BETA1-4 : angle 1.94656 ( 27) link_ALPHA1-3 : bond 0.01059 ( 2) link_ALPHA1-3 : angle 1.63622 ( 6) hydrogen bonds : bond 0.03162 ( 593) hydrogen bonds : angle 3.99533 ( 1671) metal coordination : bond 0.00481 ( 3) SS BOND : bond 0.00212 ( 6) SS BOND : angle 0.68894 ( 12) covalent geometry : bond 0.00233 (15185) covalent geometry : angle 0.55923 (20598) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 406 ARG cc_start: 0.8452 (tpp80) cc_final: 0.8246 (tpp80) REVERT: F 444 SER cc_start: 0.8741 (t) cc_final: 0.8058 (p) REVERT: F 463 LYS cc_start: 0.8444 (tptp) cc_final: 0.8176 (tptp) REVERT: F 465 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.7988 (p) REVERT: F 504 GLN cc_start: 0.8150 (pm20) cc_final: 0.7801 (pm20) REVERT: B 14 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8434 (mp0) REVERT: B 49 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7290 (tmm) REVERT: B 163 ASP cc_start: 0.8735 (m-30) cc_final: 0.8426 (m-30) REVERT: B 224 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8545 (mm110) REVERT: C 138 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8332 (mtt) REVERT: C 301 PHE cc_start: 0.7994 (t80) cc_final: 0.7547 (t80) REVERT: E 224 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8122 (tm-30) REVERT: D 138 GLU cc_start: 0.8259 (pp20) cc_final: 0.7976 (pp20) outliers start: 23 outliers final: 10 residues processed: 174 average time/residue: 1.4110 time to fit residues: 268.5420 Evaluate side-chains 169 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 465 THR Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 106 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 146 optimal weight: 0.2980 chunk 51 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.077047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.059258 restraints weight = 32813.994| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.89 r_work: 0.2688 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 15216 Z= 0.251 Angle : 0.646 11.231 20676 Z= 0.322 Chirality : 0.046 0.340 2371 Planarity : 0.004 0.047 2522 Dihedral : 7.542 74.941 2500 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.59 % Allowed : 15.15 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.87 (0.20), residues: 1753 helix: 2.13 (0.21), residues: 594 sheet: 0.01 (0.23), residues: 469 loop : -0.31 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 237 HIS 0.004 0.001 HIS C 267 PHE 0.016 0.002 PHE A 304 TYR 0.027 0.002 TYR B 299 ARG 0.007 0.000 ARG E 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 8) link_NAG-ASN : angle 2.83843 ( 24) link_ALPHA1-6 : bond 0.00991 ( 3) link_ALPHA1-6 : angle 2.18830 ( 9) link_BETA1-4 : bond 0.00418 ( 9) link_BETA1-4 : angle 2.29081 ( 27) link_ALPHA1-3 : bond 0.00863 ( 2) link_ALPHA1-3 : angle 1.90931 ( 6) hydrogen bonds : bond 0.03967 ( 593) hydrogen bonds : angle 4.17408 ( 1671) metal coordination : bond 0.00143 ( 3) SS BOND : bond 0.00349 ( 6) SS BOND : angle 1.43947 ( 12) covalent geometry : bond 0.00588 (15185) covalent geometry : angle 0.63135 (20598) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 1.925 Fit side-chains revert: symmetry clash REVERT: F 463 LYS cc_start: 0.8534 (tptp) cc_final: 0.8227 (tptp) REVERT: F 465 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.7949 (p) REVERT: F 504 GLN cc_start: 0.8158 (pm20) cc_final: 0.7843 (pm20) REVERT: B 14 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8471 (mp0) REVERT: B 40 MET cc_start: 0.9502 (OUTLIER) cc_final: 0.8966 (mtt) REVERT: B 49 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7283 (tmm) REVERT: C 49 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7719 (ppp) REVERT: C 301 PHE cc_start: 0.8031 (t80) cc_final: 0.7561 (t80) REVERT: E 224 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8134 (tm-30) REVERT: D 138 GLU cc_start: 0.8319 (pp20) cc_final: 0.8057 (pp20) REVERT: D 203 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8742 (p) REVERT: D 229 GLN cc_start: 0.8579 (tp40) cc_final: 0.8268 (tt0) outliers start: 25 outliers final: 10 residues processed: 168 average time/residue: 1.6847 time to fit residues: 312.5743 Evaluate side-chains 167 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 465 THR Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.3823 > 50: distance: 88 - 96: 4.361 distance: 96 - 97: 4.962 distance: 97 - 98: 7.873 distance: 97 - 100: 6.979 distance: 98 - 99: 13.447 distance: 98 - 104: 16.373 distance: 100 - 101: 9.330 distance: 101 - 102: 10.375 distance: 101 - 103: 3.004 distance: 104 - 105: 10.375 distance: 104 - 153: 35.023 distance: 105 - 106: 5.189 distance: 105 - 108: 13.955 distance: 106 - 107: 3.884 distance: 106 - 111: 4.124 distance: 107 - 150: 39.491 distance: 108 - 109: 9.831 distance: 108 - 110: 21.944 distance: 111 - 112: 16.250 distance: 112 - 113: 11.967 distance: 112 - 115: 3.778 distance: 113 - 114: 12.296 distance: 113 - 118: 4.843 distance: 115 - 116: 16.327 distance: 115 - 117: 11.314 distance: 118 - 119: 10.951 distance: 119 - 120: 10.011 distance: 119 - 122: 16.800 distance: 120 - 121: 8.992 distance: 120 - 129: 8.750 distance: 122 - 123: 12.913 distance: 123 - 124: 7.141 distance: 123 - 125: 11.876 distance: 124 - 126: 8.164 distance: 125 - 127: 9.259 distance: 126 - 128: 15.728 distance: 127 - 128: 14.218 distance: 129 - 130: 13.860 distance: 130 - 131: 19.355 distance: 130 - 133: 16.568 distance: 131 - 132: 16.254 distance: 131 - 134: 30.427 distance: 134 - 135: 23.930 distance: 135 - 136: 24.850 distance: 135 - 138: 18.992 distance: 136 - 137: 12.940 distance: 136 - 141: 12.952 distance: 138 - 139: 9.695 distance: 138 - 140: 23.153 distance: 141 - 142: 12.742 distance: 142 - 143: 7.334 distance: 143 - 144: 14.378 distance: 143 - 145: 16.605 distance: 145 - 146: 44.335 distance: 146 - 147: 19.057 distance: 146 - 149: 6.695 distance: 147 - 148: 37.860 distance: 147 - 150: 8.043 distance: 150 - 151: 11.177 distance: 151 - 152: 19.180 distance: 151 - 154: 16.769 distance: 152 - 153: 12.721 distance: 152 - 162: 18.527 distance: 154 - 155: 8.955 distance: 155 - 156: 29.933 distance: 155 - 157: 13.012 distance: 156 - 158: 25.153 distance: 157 - 159: 18.239 distance: 158 - 160: 18.743 distance: 159 - 160: 32.763 distance: 160 - 161: 17.146 distance: 162 - 163: 28.128 distance: 162 - 168: 19.873 distance: 163 - 164: 9.212 distance: 163 - 166: 24.491 distance: 164 - 165: 24.246 distance: 164 - 169: 11.211 distance: 166 - 167: 35.906 distance: 167 - 168: 42.265