Starting phenix.real_space_refine on Thu Jan 23 01:29:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xn9_38499/01_2025/8xn9_38499.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xn9_38499/01_2025/8xn9_38499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xn9_38499/01_2025/8xn9_38499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xn9_38499/01_2025/8xn9_38499.map" model { file = "/net/cci-nas-00/data/ceres_data/8xn9_38499/01_2025/8xn9_38499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xn9_38499/01_2025/8xn9_38499.cif" } resolution = 1.99 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= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 12301 2.51 5 N 3208 2.21 5 O 3877 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 19473 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3413 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 1 Chain: "B" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3413 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 1 Chain: "C" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3413 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 1 Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1552 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 197} Chain: "E" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1540 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 196} Chain: "G" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1489 Classifications: {'peptide': 196} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 181} Chain breaks: 2 Chain: "H" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1502 Classifications: {'peptide': 197} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 183} Chain breaks: 2 Chain: "F" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1552 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 197} Chain: "I" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1515 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 184} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "A" 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: "B" 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: "C" 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 Time building chain proxies: 13.11, per 1000 atoms: 0.67 Number of scatterers: 19473 At special positions: 0 Unit cell: (165.02, 159.84, 154.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 3877 8.00 N 3208 7.00 C 12301 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.04 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.04 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.04 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.04 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.04 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.04 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS C 192 " distance=2.06 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.04 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.05 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 197 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.06 Simple disulfide: pdb=" SG CYS G 153 " - pdb=" SG CYS G 209 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.06 Simple disulfide: pdb=" SG CYS H 153 " - pdb=" SG CYS H 209 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.06 Simple disulfide: pdb=" SG CYS I 153 " - pdb=" SG CYS I 209 " 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 NAG-ASN " NAG A 601 " - " ASN A 99 " " NAG A 602 " - " ASN A 414 " " NAG B 601 " - " ASN B 99 " " NAG B 602 " - " ASN B 414 " " NAG C 601 " - " ASN C 99 " " NAG C 602 " - " ASN C 414 " Time building additional restraints: 4.32 Conformation dependent library (CDL) restraints added in 2.7 seconds 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4776 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 54 sheets defined 26.4% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'A' and resid 29 through 36 removed outlier: 3.566A pdb=" N ILE A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.708A pdb=" N SER A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 Proline residue: A 89 - end of helix removed outlier: 4.093A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 145 removed outlier: 4.538A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 191 through 215 removed outlier: 4.629A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.640A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'A' and resid 452 through 476 removed outlier: 3.575A pdb=" N SER A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.752A pdb=" N LYS B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 removed outlier: 3.623A pdb=" N SER B 69 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLN B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 72 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 100 Proline residue: B 89 - end of helix removed outlier: 3.571A pdb=" N ILE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN B 100 " --> pdb=" O ILE B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 125 through 146 removed outlier: 4.378A pdb=" N LYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASN B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 191 through 215 removed outlier: 4.662A pdb=" N PHE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.732A pdb=" N LEU B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 349 through 357 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 452 through 476 removed outlier: 3.620A pdb=" N SER B 457 " --> pdb=" O LYS B 453 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 473 " --> pdb=" O GLN B 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 35 removed outlier: 3.709A pdb=" N LYS C 35 " --> pdb=" O GLU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 removed outlier: 3.827A pdb=" N SER C 69 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN C 70 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR C 72 " --> pdb=" O SER C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 99 removed outlier: 3.514A pdb=" N GLY C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) Proline residue: C 89 - end of helix removed outlier: 4.063A pdb=" N TYR C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 Processing helix chain 'C' and resid 125 through 146 removed outlier: 4.398A pdb=" N LYS C 139 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN C 143 " --> pdb=" O LYS C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 154 Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'C' and resid 191 through 215 removed outlier: 4.652A pdb=" N PHE C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL C 213 " --> pdb=" O ASP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 233 through 236 Processing helix chain 'C' and resid 238 through 245 removed outlier: 3.696A pdb=" N LEU C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 349 through 357 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 437 through 441 Processing helix chain 'C' and resid 452 through 476 removed outlier: 3.726A pdb=" N SER C 457 " --> pdb=" O LYS C 453 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 125 through 131 Processing helix chain 'D' and resid 185 through 192 removed outlier: 3.690A pdb=" N HIS D 192 " --> pdb=" O GLN D 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 125 through 131 Processing helix chain 'E' and resid 185 through 192 removed outlier: 3.741A pdb=" N TRP E 189 " --> pdb=" O THR E 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.671A pdb=" N TYR G 32 " --> pdb=" O ILE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.508A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 171 No H-bonds generated for 'chain 'G' and resid 169 through 171' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.705A pdb=" N TYR H 32 " --> pdb=" O ILE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.650A pdb=" N ASP F 83 " --> pdb=" O GLN F 80 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU F 84 " --> pdb=" O THR F 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 80 through 84' Processing helix chain 'F' and resid 125 through 131 removed outlier: 3.771A pdb=" N ALA F 131 " --> pdb=" O GLU F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 191 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.880A pdb=" N TYR I 32 " --> pdb=" O ILE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 66 removed outlier: 5.116A pdb=" N SER I 66 " --> pdb=" O SER I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 169 through 171 No H-bonds generated for 'chain 'I' and resid 169 through 171' Processing helix chain 'I' and resid 214 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 162 removed outlier: 12.862A pdb=" N THR A 168 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ASP A 56 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL A 338 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS A 45 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N CYS A 340 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS A 47 " --> pdb=" O CYS A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.159A pdb=" N MET A 226 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE A 284 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ASN A 51 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N THR A 286 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LYS A 49 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLU A 295 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THR A 43 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE A 293 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LYS A 45 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ALA A 291 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE A 315 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE A 326 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 394 removed outlier: 6.841A pdb=" N ILE A 426 " --> pdb=" O MET C 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 158 through 162 removed outlier: 12.905A pdb=" N THR B 168 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASP B 56 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TYR B 170 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N VAL B 338 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS B 45 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N CYS B 340 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS B 47 " --> pdb=" O CYS B 340 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 226 through 227 removed outlier: 4.250A pdb=" N MET B 226 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE B 277 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE B 284 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASN B 51 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR B 286 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LYS B 49 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU B 295 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR B 43 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 293 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LYS B 45 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ALA B 291 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE B 315 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE B 326 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 101 through 102 removed outlier: 6.900A pdb=" N MET B 115 " --> pdb=" O SER C 428 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N CYS C 392 " --> pdb=" O ILE C 401 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AB3, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AB4, first strand: chain 'C' and resid 158 through 162 removed outlier: 12.760A pdb=" N THR C 168 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASP C 56 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TYR C 170 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL C 338 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS C 45 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N CYS C 340 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS C 47 " --> pdb=" O CYS C 340 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 226 through 227 removed outlier: 4.200A pdb=" N MET C 226 " --> pdb=" O GLY C 264 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE C 277 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL C 269 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR C 275 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE C 284 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASN C 51 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N THR C 286 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LYS C 49 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLU C 295 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N THR C 43 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE C 293 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LYS C 45 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N ALA C 291 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE C 315 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE C 326 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AB7, first strand: chain 'D' and resid 9 through 13 removed outlier: 6.579A pdb=" N ALA D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU D 110 " --> pdb=" O ALA D 10 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU D 12 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 9 through 13 removed outlier: 6.579A pdb=" N ALA D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU D 110 " --> pdb=" O ALA D 10 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU D 12 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY D 98 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AC1, first strand: chain 'D' and resid 118 through 122 removed outlier: 3.572A pdb=" N VAL D 137 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA D 134 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER D 180 " --> pdb=" O CYS D 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 118 through 122 removed outlier: 3.572A pdb=" N VAL D 137 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA D 134 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER D 180 " --> pdb=" O CYS D 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 157 through 159 removed outlier: 4.551A pdb=" N TRP D 152 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.545A pdb=" N ALA E 10 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU E 110 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU E 12 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA E 85 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL E 34 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.545A pdb=" N ALA E 10 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU E 110 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU E 12 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA E 85 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AC7, first strand: chain 'E' and resid 118 through 122 removed outlier: 3.815A pdb=" N ALA E 134 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU E 184 " --> pdb=" O ALA E 134 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR E 176 " --> pdb=" O ASP E 142 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 118 through 122 removed outlier: 3.815A pdb=" N ALA E 134 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU E 184 " --> pdb=" O ALA E 134 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR E 176 " --> pdb=" O ASP E 142 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 157 through 159 removed outlier: 4.126A pdb=" N TRP E 152 " --> pdb=" O VAL E 159 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'G' and resid 57 through 60 removed outlier: 5.504A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL G 115 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 57 through 60 removed outlier: 5.504A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 101 through 103 Processing sheet with id=AD5, first strand: chain 'G' and resid 133 through 135 removed outlier: 5.711A pdb=" N LEU G 154 " --> pdb=" O SER G 193 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N SER G 193 " --> pdb=" O LEU G 154 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LYS G 156 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU G 191 " --> pdb=" O LYS G 156 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 133 through 135 removed outlier: 5.711A pdb=" N LEU G 154 " --> pdb=" O SER G 193 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N SER G 193 " --> pdb=" O LEU G 154 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LYS G 156 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU G 191 " --> pdb=" O LYS G 156 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 164 through 167 Processing sheet with id=AD8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.584A pdb=" N TRP H 34 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.996A pdb=" N VAL H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 101 through 103 Processing sheet with id=AE3, first strand: chain 'H' and resid 155 through 158 removed outlier: 5.359A pdb=" N LYS H 156 " --> pdb=" O LEU H 191 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU H 191 " --> pdb=" O LYS H 156 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER H 190 " --> pdb=" O VAL H 182 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 164 through 167 removed outlier: 3.515A pdb=" N THR H 164 " --> pdb=" O ASN H 212 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN H 212 " --> pdb=" O THR H 164 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS H 222 " --> pdb=" O CYS H 209 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL H 211 " --> pdb=" O VAL H 220 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 176 through 178 Processing sheet with id=AE6, first strand: chain 'F' and resid 9 through 13 removed outlier: 6.416A pdb=" N ALA F 10 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU F 110 " --> pdb=" O ALA F 10 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU F 12 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 9 through 13 removed outlier: 6.416A pdb=" N ALA F 10 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU F 110 " --> pdb=" O ALA F 10 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU F 12 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY F 98 " --> pdb=" O ASP F 93 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 18 through 23 Processing sheet with id=AE9, first strand: chain 'F' and resid 118 through 122 removed outlier: 3.706A pdb=" N SER F 141 " --> pdb=" O SER F 118 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL F 137 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA F 134 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR F 176 " --> pdb=" O ASP F 142 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 118 through 122 removed outlier: 3.706A pdb=" N SER F 141 " --> pdb=" O SER F 118 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL F 137 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA F 134 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR F 176 " --> pdb=" O ASP F 142 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 157 through 159 removed outlier: 4.425A pdb=" N TRP F 152 " --> pdb=" O VAL F 159 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AF4, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.635A pdb=" N TRP I 34 " --> pdb=" O ASP I 50 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 11 through 12 removed outlier: 4.041A pdb=" N VAL I 115 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 101 through 103 Processing sheet with id=AF7, first strand: chain 'I' and resid 133 through 135 removed outlier: 3.565A pdb=" N SER I 133 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS I 156 " --> pdb=" O SER I 133 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N TYR I 189 " --> pdb=" O ASP I 157 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 164 through 167 removed outlier: 3.861A pdb=" N LYS I 222 " --> pdb=" O CYS I 209 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL I 211 " --> pdb=" O VAL I 220 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 176 through 178 942 hydrogen bonds defined for protein. 2385 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: 9.21 Time building geometry restraints manager: 5.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 6226 1.35 - 1.48: 4940 1.48 - 1.62: 8560 1.62 - 1.76: 1 1.76 - 1.90: 119 Bond restraints: 19846 Sorted by residual: bond pdb=" CB CYS C 71 " pdb=" SG CYS C 71 " ideal model delta sigma weight residual 1.808 1.895 -0.087 3.30e-02 9.18e+02 6.96e+00 bond pdb=" C ILE B 36 " pdb=" O ILE B 36 " ideal model delta sigma weight residual 1.236 1.216 0.020 1.19e-02 7.06e+03 2.93e+00 bond pdb=" CA VAL C 373 " pdb=" CB VAL C 373 " ideal model delta sigma weight residual 1.537 1.558 -0.021 1.29e-02 6.01e+03 2.63e+00 bond pdb=" CB CYS C 192 " pdb=" SG CYS C 192 " ideal model delta sigma weight residual 1.808 1.755 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" C2 NAG C 602 " pdb=" N2 NAG C 602 " ideal model delta sigma weight residual 1.439 1.471 -0.032 2.00e-02 2.50e+03 2.49e+00 ... (remaining 19841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 26231 1.89 - 3.79: 659 3.79 - 5.68: 98 5.68 - 7.57: 15 7.57 - 9.47: 7 Bond angle restraints: 27010 Sorted by residual: angle pdb=" N PRO I 136 " pdb=" CA PRO I 136 " pdb=" CB PRO I 136 " ideal model delta sigma weight residual 103.00 110.36 -7.36 1.10e+00 8.26e-01 4.48e+01 angle pdb=" CA VAL A 312 " pdb=" C VAL A 312 " pdb=" N PRO A 313 " ideal model delta sigma weight residual 116.57 120.70 -4.13 9.80e-01 1.04e+00 1.78e+01 angle pdb=" C TYR E 51 " pdb=" N ASN E 52 " pdb=" CA ASN E 52 " ideal model delta sigma weight residual 121.54 129.24 -7.70 1.91e+00 2.74e-01 1.62e+01 angle pdb=" C SER D 156 " pdb=" N SER D 157 " pdb=" CA SER D 157 " ideal model delta sigma weight residual 122.74 113.27 9.47 2.44e+00 1.68e-01 1.51e+01 angle pdb=" N GLU C 136 " pdb=" CA GLU C 136 " pdb=" CB GLU C 136 " ideal model delta sigma weight residual 110.22 116.14 -5.92 1.54e+00 4.22e-01 1.48e+01 ... (remaining 27005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 11342 17.82 - 35.64: 597 35.64 - 53.45: 116 53.45 - 71.27: 45 71.27 - 89.09: 22 Dihedral angle restraints: 12122 sinusoidal: 4699 harmonic: 7423 Sorted by residual: dihedral pdb=" CB CYS C 394 " pdb=" SG CYS C 394 " pdb=" SG CYS C 417 " pdb=" CB CYS C 417 " ideal model delta sinusoidal sigma weight residual 93.00 146.43 -53.43 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS A 71 " pdb=" SG CYS A 71 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -139.24 53.24 1 1.00e+01 1.00e-02 3.85e+01 dihedral pdb=" CB CYS B 71 " pdb=" SG CYS B 71 " pdb=" SG CYS B 192 " pdb=" CB CYS B 192 " ideal model delta sinusoidal sigma weight residual -86.00 -134.98 48.98 1 1.00e+01 1.00e-02 3.30e+01 ... (remaining 12119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.760: 3209 0.760 - 1.521: 0 1.521 - 2.281: 0 2.281 - 3.041: 0 3.041 - 3.801: 1 Chirality restraints: 3210 Sorted by residual: chirality pdb=" C1 NAG C 602 " pdb=" ND2 ASN C 414 " pdb=" C2 NAG C 602 " pdb=" O5 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.40 1.40 -3.80 2.00e-01 2.50e+01 3.61e+02 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 99 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 99 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.30e+01 ... (remaining 3207 not shown) Planarity restraints: 3414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 602 " 0.192 2.00e-02 2.50e+03 1.60e-01 3.19e+02 pdb=" C7 NAG B 602 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG B 602 " 0.137 2.00e-02 2.50e+03 pdb=" N2 NAG B 602 " -0.263 2.00e-02 2.50e+03 pdb=" O7 NAG B 602 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 602 " -0.176 2.00e-02 2.50e+03 1.53e-01 2.93e+02 pdb=" C7 NAG C 602 " 0.038 2.00e-02 2.50e+03 pdb=" C8 NAG C 602 " -0.119 2.00e-02 2.50e+03 pdb=" N2 NAG C 602 " 0.265 2.00e-02 2.50e+03 pdb=" O7 NAG C 602 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " 0.169 2.00e-02 2.50e+03 1.42e-01 2.50e+02 pdb=" C7 NAG A 601 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " 0.120 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " -0.236 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " -0.013 2.00e-02 2.50e+03 ... (remaining 3411 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2013 2.76 - 3.29: 18146 3.29 - 3.83: 30877 3.83 - 4.36: 37381 4.36 - 4.90: 64437 Nonbonded interactions: 152854 Sorted by model distance: nonbonded pdb=" OD1 ASP B 304 " pdb=" N ASN B 305 " model vdw 2.220 3.120 nonbonded pdb=" OD2 ASP I 73 " pdb=" NZ LYS I 76 " model vdw 2.223 3.120 nonbonded pdb=" OD2 ASP G 73 " pdb=" NZ LYS G 76 " model vdw 2.237 3.120 nonbonded pdb=" OD2 ASP H 73 " pdb=" OG SER H 75 " model vdw 2.244 3.040 nonbonded pdb=" OD1 ASN C 414 " pdb=" O LEU C 429 " model vdw 2.246 3.040 ... (remaining 152849 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 2 through 210) selection = chain 'E' selection = (chain 'F' and resid 2 through 210) } ncs_group { reference = (chain 'G' and (resid 1 through 134 or resid 153 through 222)) selection = (chain 'H' and (resid 1 through 196 or resid 208 through 222)) selection = (chain 'I' and (resid 1 through 134 or resid 153 through 196 or resid 208 throug \ h 222)) } 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: 9.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.550 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 49.320 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 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 : 0.004 0.087 19846 Z= 0.281 Angle : 0.760 9.468 27010 Z= 0.430 Chirality : 0.088 3.801 3210 Planarity : 0.009 0.185 3408 Dihedral : 12.682 89.089 7271 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % 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: 0.40 (0.16), residues: 2516 helix: 1.07 (0.23), residues: 488 sheet: 1.13 (0.18), residues: 800 loop : -0.66 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 116 HIS 0.009 0.002 HIS H 111 PHE 0.015 0.002 PHE B 301 TYR 0.026 0.002 TYR I 189 ARG 0.009 0.001 ARG I 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 2.218 Fit side-chains revert: symmetry clash REVERT: F 170 LYS cc_start: 0.7819 (ttmt) cc_final: 0.7586 (ttmt) REVERT: I 133 SER cc_start: 0.7639 (p) cc_final: 0.7413 (p) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 1.6476 time to fit residues: 436.3726 Evaluate side-chains 211 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 211 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 196 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 227 optimal weight: 0.6980 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN B 342 GLN B 395 GLN C 102 HIS C 305 ASN ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN H 111 HIS F 54 GLN I 3 GLN I 111 HIS I 184 GLN I 212 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.187350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.132183 restraints weight = 16076.603| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.77 r_work: 0.3322 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.104 19846 Z= 0.556 Angle : 0.986 13.044 27010 Z= 0.541 Chirality : 0.065 0.725 3210 Planarity : 0.007 0.057 3408 Dihedral : 6.400 59.630 2830 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.22 % Allowed : 5.54 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.03 (0.16), residues: 2516 helix: 0.84 (0.22), residues: 486 sheet: 0.76 (0.18), residues: 806 loop : -0.81 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP I 116 HIS 0.011 0.003 HIS G 111 PHE 0.023 0.004 PHE C 376 TYR 0.032 0.004 TYR I 189 ARG 0.014 0.002 ARG H 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: A 406 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7403 (mm-30) REVERT: E 86 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7916 (m-30) REVERT: F 12 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: F 170 LYS cc_start: 0.7677 (ttmt) cc_final: 0.7376 (ttmt) outliers start: 27 outliers final: 16 residues processed: 231 average time/residue: 1.6047 time to fit residues: 410.5644 Evaluate side-chains 227 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain F residue 2 PRO Chi-restraints excluded: chain F residue 12 GLU Chi-restraints excluded: chain I residue 163 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 244 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN B 342 GLN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS C 305 ASN D 54 GLN H 184 GLN F 54 GLN I 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.190428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.135680 restraints weight = 16128.379| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.77 r_work: 0.3381 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19846 Z= 0.215 Angle : 0.650 11.297 27010 Z= 0.353 Chirality : 0.050 0.619 3210 Planarity : 0.005 0.039 3408 Dihedral : 5.491 52.342 2830 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.99 % Allowed : 7.21 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % 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: 0.45 (0.16), residues: 2516 helix: 1.60 (0.23), residues: 489 sheet: 0.94 (0.18), residues: 820 loop : -0.71 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 116 HIS 0.006 0.001 HIS C 102 PHE 0.014 0.002 PHE B 301 TYR 0.014 0.002 TYR B 274 ARG 0.005 0.001 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 209 time to evaluate : 1.964 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: B 163 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: F 170 LYS cc_start: 0.7634 (ttmt) cc_final: 0.7331 (ttmt) REVERT: I 65 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8098 (tmtp) outliers start: 22 outliers final: 8 residues processed: 216 average time/residue: 1.7180 time to fit residues: 410.1729 Evaluate side-chains 211 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 163 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 64 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 166 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 chunk 156 optimal weight: 8.9990 chunk 235 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 250 optimal weight: 6.9990 chunk 211 optimal weight: 8.9990 chunk 225 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN B 380 ASN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS C 305 ASN D 54 GLN F 80 GLN I 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.188054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.132724 restraints weight = 16197.473| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.75 r_work: 0.3341 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 19846 Z= 0.387 Angle : 0.811 13.471 27010 Z= 0.445 Chirality : 0.056 0.551 3210 Planarity : 0.006 0.043 3408 Dihedral : 5.791 47.447 2830 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.76 % Allowed : 7.61 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % 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: 0.24 (0.16), residues: 2516 helix: 1.20 (0.23), residues: 486 sheet: 0.96 (0.18), residues: 791 loop : -0.79 (0.16), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP I 116 HIS 0.009 0.002 HIS G 111 PHE 0.020 0.003 PHE C 376 TYR 0.023 0.003 TYR B 274 ARG 0.011 0.001 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 2.147 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: A 336 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7569 (pmm-80) REVERT: E 46 LYS cc_start: 0.9013 (ptmt) cc_final: 0.8708 (ptmt) REVERT: E 86 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7902 (m-30) REVERT: F 12 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: F 170 LYS cc_start: 0.7613 (ttmt) cc_final: 0.7294 (ttmt) REVERT: I 65 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8095 (tmtp) outliers start: 39 outliers final: 19 residues processed: 227 average time/residue: 1.5628 time to fit residues: 393.7637 Evaluate side-chains 229 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 393 GLN Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain F residue 12 GLU Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 163 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 241 optimal weight: 6.9990 chunk 166 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 230 optimal weight: 30.0000 chunk 191 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 174 optimal weight: 0.3980 chunk 155 optimal weight: 0.0870 chunk 231 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 214 optimal weight: 7.9990 overall best weight: 1.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN B 380 ASN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS C 305 ASN C 395 GLN D 54 GLN I 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.190296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.134842 restraints weight = 16324.241| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.66 r_work: 0.3377 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19846 Z= 0.212 Angle : 0.629 8.703 27010 Z= 0.343 Chirality : 0.049 0.490 3210 Planarity : 0.005 0.038 3408 Dihedral : 5.310 46.805 2830 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.13 % Allowed : 8.83 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % 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: 0.46 (0.16), residues: 2516 helix: 1.65 (0.23), residues: 489 sheet: 0.96 (0.18), residues: 817 loop : -0.72 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 116 HIS 0.006 0.001 HIS C 102 PHE 0.013 0.002 PHE C 376 TYR 0.014 0.002 TYR B 274 ARG 0.007 0.001 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 2.199 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: B 163 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6825 (mp0) REVERT: E 86 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7930 (m-30) REVERT: H 93 MET cc_start: 0.8663 (tpt) cc_final: 0.8449 (tpt) REVERT: F 170 LYS cc_start: 0.7632 (ttmt) cc_final: 0.7323 (ttmt) REVERT: I 65 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8090 (tmtp) outliers start: 25 outliers final: 12 residues processed: 214 average time/residue: 1.6662 time to fit residues: 393.8456 Evaluate side-chains 213 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 176 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 18 optimal weight: 0.1980 chunk 197 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 128 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN B 380 ASN B 395 GLN C 102 HIS C 305 ASN C 395 GLN D 54 GLN E 171 GLN G 184 GLN I 3 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.192333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135130 restraints weight = 16538.191| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.70 r_work: 0.3405 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19846 Z= 0.168 Angle : 0.561 7.809 27010 Z= 0.304 Chirality : 0.047 0.437 3210 Planarity : 0.004 0.040 3408 Dihedral : 4.968 47.798 2830 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.04 % Allowed : 9.50 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % 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: 0.63 (0.16), residues: 2516 helix: 1.80 (0.23), residues: 500 sheet: 1.20 (0.18), residues: 789 loop : -0.71 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 33 HIS 0.005 0.001 HIS C 102 PHE 0.012 0.001 PHE H 79 TYR 0.013 0.001 TYR I 189 ARG 0.009 0.000 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 2.388 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: B 138 MET cc_start: 0.8039 (mmm) cc_final: 0.7708 (mmm) REVERT: E 86 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: F 170 LYS cc_start: 0.7572 (ttmt) cc_final: 0.7240 (ttmt) REVERT: I 65 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.8034 (tmtp) outliers start: 23 outliers final: 11 residues processed: 217 average time/residue: 1.6740 time to fit residues: 401.2607 Evaluate side-chains 209 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 176 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 137 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 60 optimal weight: 0.5980 chunk 136 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 223 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN B 380 ASN B 395 GLN C 102 HIS C 219 GLN C 305 ASN D 54 GLN I 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.189920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.134256 restraints weight = 16194.087| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.72 r_work: 0.3373 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 19846 Z= 0.261 Angle : 0.665 8.426 27010 Z= 0.364 Chirality : 0.051 0.472 3210 Planarity : 0.005 0.046 3408 Dihedral : 5.302 49.091 2830 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.26 % Allowed : 9.68 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % 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: 0.53 (0.16), residues: 2516 helix: 1.64 (0.23), residues: 488 sheet: 1.01 (0.18), residues: 815 loop : -0.65 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 116 HIS 0.008 0.001 HIS C 102 PHE 0.014 0.002 PHE C 376 TYR 0.016 0.002 TYR B 274 ARG 0.009 0.001 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 2.132 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: E 86 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7939 (m-30) REVERT: G 3 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7811 (tp40) REVERT: F 170 LYS cc_start: 0.7604 (ttmt) cc_final: 0.7270 (ttmt) REVERT: I 65 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8079 (tmtp) outliers start: 28 outliers final: 17 residues processed: 211 average time/residue: 1.6269 time to fit residues: 379.5977 Evaluate side-chains 217 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 176 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 145 optimal weight: 20.0000 chunk 160 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 107 optimal weight: 0.5980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN B 380 ASN B 395 GLN C 102 HIS C 219 GLN C 305 ASN D 54 GLN F 80 GLN F 192 HIS I 3 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.189295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.133374 restraints weight = 16226.310| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.73 r_work: 0.3367 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 19846 Z= 0.290 Angle : 0.705 8.387 27010 Z= 0.386 Chirality : 0.052 0.496 3210 Planarity : 0.005 0.045 3408 Dihedral : 5.477 50.304 2830 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.71 % Allowed : 9.37 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % 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: 0.43 (0.16), residues: 2516 helix: 1.49 (0.23), residues: 488 sheet: 0.99 (0.18), residues: 812 loop : -0.71 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 116 HIS 0.009 0.002 HIS C 102 PHE 0.015 0.002 PHE C 376 TYR 0.018 0.002 TYR B 274 ARG 0.010 0.001 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 2.158 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: E 86 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7923 (m-30) REVERT: G 3 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7778 (tp40) REVERT: I 65 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8104 (tmtp) outliers start: 38 outliers final: 25 residues processed: 222 average time/residue: 1.6388 time to fit residues: 404.3137 Evaluate side-chains 229 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 393 GLN Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 195 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 230 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 145 optimal weight: 20.0000 chunk 234 optimal weight: 6.9990 chunk 233 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 172 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN B 380 ASN B 395 GLN C 102 HIS C 219 GLN C 305 ASN C 395 GLN D 54 GLN D 192 HIS I 3 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.192071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.136243 restraints weight = 16471.838| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.68 r_work: 0.3417 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19846 Z= 0.169 Angle : 0.572 11.547 27010 Z= 0.308 Chirality : 0.047 0.431 3210 Planarity : 0.004 0.046 3408 Dihedral : 5.021 49.299 2830 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.04 % Allowed : 10.36 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % 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: 0.65 (0.16), residues: 2516 helix: 1.80 (0.23), residues: 500 sheet: 1.24 (0.18), residues: 796 loop : -0.72 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 33 HIS 0.007 0.001 HIS C 102 PHE 0.012 0.001 PHE H 79 TYR 0.010 0.001 TYR B 46 ARG 0.011 0.000 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 2.450 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: B 138 MET cc_start: 0.8020 (mmm) cc_final: 0.7674 (mmm) REVERT: E 86 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7849 (m-30) REVERT: H 43 LYS cc_start: 0.7767 (mptm) cc_final: 0.7412 (mmtp) REVERT: H 76 LYS cc_start: 0.6532 (mtmm) cc_final: 0.6309 (pttm) REVERT: I 65 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8030 (tmtp) outliers start: 23 outliers final: 14 residues processed: 217 average time/residue: 1.6334 time to fit residues: 392.3117 Evaluate side-chains 220 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 195 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 239 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 249 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 199 optimal weight: 0.5980 chunk 103 optimal weight: 0.0020 chunk 206 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN B 380 ASN B 395 GLN C 102 HIS C 219 GLN C 305 ASN C 395 GLN D 54 GLN I 3 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.193171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.137031 restraints weight = 16603.587| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.63 r_work: 0.3420 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 19846 Z= 0.155 Angle : 0.549 9.569 27010 Z= 0.294 Chirality : 0.046 0.401 3210 Planarity : 0.004 0.041 3408 Dihedral : 4.800 50.052 2830 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.95 % Allowed : 10.41 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % 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: 0.80 (0.17), residues: 2516 helix: 1.94 (0.24), residues: 500 sheet: 1.33 (0.18), residues: 794 loop : -0.64 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 33 HIS 0.007 0.001 HIS C 102 PHE 0.012 0.001 PHE H 79 TYR 0.017 0.001 TYR I 189 ARG 0.009 0.000 ARG E 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 2.016 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: B 138 MET cc_start: 0.8030 (mmm) cc_final: 0.7689 (mmm) REVERT: C 138 MET cc_start: 0.8072 (mtp) cc_final: 0.7664 (mmm) REVERT: E 86 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: G 67 ARG cc_start: 0.8134 (mtm110) cc_final: 0.7903 (mtm110) REVERT: G 71 SER cc_start: 0.8041 (p) cc_final: 0.7824 (m) REVERT: G 76 LYS cc_start: 0.6809 (pttm) cc_final: 0.6568 (pmtt) REVERT: I 65 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.8017 (tmtp) outliers start: 21 outliers final: 14 residues processed: 215 average time/residue: 1.7089 time to fit residues: 408.2400 Evaluate side-chains 217 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 195 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 245 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 216 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN B 395 GLN C 102 HIS C 305 ASN C 395 GLN D 54 GLN F 54 GLN I 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.190469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.133224 restraints weight = 16360.050| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.64 r_work: 0.3371 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 19846 Z= 0.232 Angle : 0.643 9.509 27010 Z= 0.349 Chirality : 0.050 0.450 3210 Planarity : 0.005 0.041 3408 Dihedral : 5.157 51.157 2830 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.04 % Allowed : 10.45 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % 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: 0.63 (0.16), residues: 2516 helix: 1.77 (0.23), residues: 488 sheet: 1.14 (0.18), residues: 806 loop : -0.64 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 116 HIS 0.008 0.001 HIS C 102 PHE 0.012 0.002 PHE C 376 TYR 0.018 0.002 TYR I 189 ARG 0.015 0.001 ARG A 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28900.77 seconds wall clock time: 506 minutes 46.81 seconds (30406.81 seconds total)