Starting phenix.real_space_refine on Mon Jul 6 08:20:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jrg_22445/07_2026/7jrg_22445.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jrg_22445/07_2026/7jrg_22445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jrg_22445/07_2026/7jrg_22445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jrg_22445/07_2026/7jrg_22445.map" model { file = "/net/cci-nas-00/data/ceres_data/7jrg_22445/07_2026/7jrg_22445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jrg_22445/07_2026/7jrg_22445.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jrg_22445/07_2026/7jrg_22445.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jrg_22445/07_2026/7jrg_22445.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 6 7.16 5 Zn 2 6.06 5 P 38 5.49 5 S 132 5.16 5 C 21324 2.51 5 N 5352 2.21 5 O 6076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 207 residue(s): 0.20s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32930 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3838 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 464} Chain: "B" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3471 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 428} Chain: "C" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3104 Classifications: {'peptide': 388} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 362} Chain: "D" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1910 Classifications: {'peptide': 244} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 227} Chain: "E" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 597 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 6, 'TRANS': 70} Chain: "F" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 965 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 108} Chain: "G" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 578 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 65} Chain: "H" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "J" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 480 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "K" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 218 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "M" Number of atoms: 3838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3838 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 464} Chain: "N" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3456 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 28, 'TRANS': 426} Chain: "O" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3104 Classifications: {'peptide': 388} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 362} Chain: "P" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1910 Classifications: {'peptide': 244} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 227} Chain: "Q" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 574 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "R" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 959 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "S" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 578 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 65} Chain: "T" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 527 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 60} Chain: "V" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 476 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "W" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 226 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 108 Unusual residues: {' ZN': 1, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "C" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 415 Unusual residues: {'3PE': 6, 'CDL': 2, 'HEM': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 177 Chain: "D" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "G" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "M" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 156 Unusual residues: {' ZN': 1, '3PE': 1, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Chain: "O" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 420 Unusual residues: {'3PE': 5, 'CDL': 2, 'HEM': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 121 Chain: "P" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "S" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "W" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 46 Time building chain proxies: 6.58, per 1000 atoms: 0.20 Number of scatterers: 32930 At special positions: 0 Unit cell: (129.146, 151.642, 167.473, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Fe 6 26.01 S 132 16.00 P 38 15.00 O 6076 8.00 N 5352 7.00 C 21324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 17 " - pdb=" SG CYS H 59 " distance=2.03 Simple disulfide: pdb=" SG CYS H 31 " - pdb=" SG CYS H 45 " distance=2.02 Simple disulfide: pdb=" SG CYS T 17 " - pdb=" SG CYS T 59 " distance=2.02 Simple disulfide: pdb=" SG CYS T 21 " - pdb=" SG CYS T 55 " distance=2.03 Simple disulfide: pdb=" SG CYS T 31 " - pdb=" SG CYS T 45 " 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 137 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 141 " pdb=" ZN M 601 " pdb="ZN ZN M 601 " - pdb=" NE2 HIS M 137 " pdb="ZN ZN M 601 " - pdb=" NE2 HIS M 141 " 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7432 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 17 sheets defined 59.6% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 49 through 64 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 134 through 144 Processing helix chain 'A' and resid 151 through 162 Processing helix chain 'A' and resid 185 through 199 Processing helix chain 'A' and resid 203 through 221 Processing helix chain 'A' and resid 225 through 238 Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.583A pdb=" N ARG A 245 " --> pdb=" O PRO A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 258 through 270 removed outlier: 3.584A pdb=" N LEU A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 373 through 383 Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 411 through 429 removed outlier: 3.917A pdb=" N VAL A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 450 Processing helix chain 'A' and resid 452 through 467 Processing helix chain 'A' and resid 472 through 482 Processing helix chain 'A' and resid 484 through 496 Processing helix chain 'A' and resid 514 through 522 removed outlier: 3.537A pdb=" N PHE A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 117 through 125 Processing helix chain 'B' and resid 134 through 145 Processing helix chain 'B' and resid 168 through 182 Processing helix chain 'B' and resid 186 through 203 Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 240 through 252 Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 265 through 274 Processing helix chain 'B' and resid 321 through 335 Processing helix chain 'B' and resid 352 through 360 Processing helix chain 'B' and resid 391 through 408 Processing helix chain 'B' and resid 413 through 432 Processing helix chain 'B' and resid 434 through 450 Processing helix chain 'B' and resid 454 through 465 removed outlier: 3.980A pdb=" N PHE B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 478 Processing helix chain 'B' and resid 490 through 493 Processing helix chain 'B' and resid 495 through 502 removed outlier: 3.576A pdb=" N LYS B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 25 removed outlier: 4.676A pdb=" N THR C 18 " --> pdb=" O PRO C 14 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 58 removed outlier: 4.106A pdb=" N GLY C 43 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE C 44 " --> pdb=" O SER C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 80 through 110 Processing helix chain 'C' and resid 116 through 139 Processing helix chain 'C' and resid 143 through 156 Processing helix chain 'C' and resid 164 through 173 Processing helix chain 'C' and resid 178 through 211 Proline residue: C 193 - end of helix Processing helix chain 'C' and resid 229 through 252 removed outlier: 3.977A pdb=" N LYS C 234 " --> pdb=" O TYR C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 293 through 311 removed outlier: 3.572A pdb=" N GLY C 297 " --> pdb=" O ASP C 293 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 314 No H-bonds generated for 'chain 'C' and resid 312 through 314' Processing helix chain 'C' and resid 321 through 324 removed outlier: 3.506A pdb=" N PHE C 324 " --> pdb=" O SER C 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 321 through 324' Processing helix chain 'C' and resid 325 through 348 removed outlier: 3.977A pdb=" N CYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN C 348 " --> pdb=" O TRP C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 380 removed outlier: 3.892A pdb=" N PHE C 369 " --> pdb=" O PHE C 365 " (cutoff:3.500A) Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 382 through 387 Processing helix chain 'D' and resid 64 through 69 Processing helix chain 'D' and resid 87 through 101 Processing helix chain 'D' and resid 102 through 105 Processing helix chain 'D' and resid 112 through 117 removed outlier: 3.614A pdb=" N VAL D 117 " --> pdb=" O ARG D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 133 removed outlier: 3.947A pdb=" N ILE D 133 " --> pdb=" O MET D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 170 Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 187 through 198 Processing helix chain 'D' and resid 243 through 260 Processing helix chain 'D' and resid 262 through 292 Processing helix chain 'E' and resid 77 through 85 Processing helix chain 'E' and resid 107 through 137 removed outlier: 4.220A pdb=" N ALA E 111 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR E 112 " --> pdb=" O ARG E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 147 Processing helix chain 'F' and resid 14 through 32 Processing helix chain 'F' and resid 34 through 39 Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.804A pdb=" N ASP F 44 " --> pdb=" O ASP F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 54 removed outlier: 3.570A pdb=" N GLU F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 76 Processing helix chain 'F' and resid 80 through 86 Processing helix chain 'F' and resid 94 through 111 Processing helix chain 'G' and resid 23 through 27 removed outlier: 3.581A pdb=" N LEU G 26 " --> pdb=" O MET G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 40 Processing helix chain 'G' and resid 41 through 71 Proline residue: G 51 - end of helix Processing helix chain 'H' and resid 8 through 18 Processing helix chain 'H' and resid 21 through 39 Processing helix chain 'H' and resid 45 through 68 removed outlier: 3.838A pdb=" N TYR H 49 " --> pdb=" O CYS H 45 " (cutoff:3.500A) Proline residue: H 62 - end of helix removed outlier: 3.775A pdb=" N PHE H 65 " --> pdb=" O ALA H 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 21 Processing helix chain 'J' and resid 23 through 54 Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.567A pdb=" N ILE J 62 " --> pdb=" O TYR J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 39 Processing helix chain 'M' and resid 48 through 64 Processing helix chain 'M' and resid 83 through 87 removed outlier: 4.494A pdb=" N ARG M 86 " --> pdb=" O ASP M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 124 through 128 removed outlier: 3.882A pdb=" N GLU M 128 " --> pdb=" O SER M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 144 Processing helix chain 'M' and resid 151 through 163 Processing helix chain 'M' and resid 185 through 199 removed outlier: 3.690A pdb=" N ALA M 189 " --> pdb=" O ASP M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 220 Processing helix chain 'M' and resid 224 through 238 Processing helix chain 'M' and resid 250 through 255 Processing helix chain 'M' and resid 259 through 270 Processing helix chain 'M' and resid 271 through 273 No H-bonds generated for 'chain 'M' and resid 271 through 273' Processing helix chain 'M' and resid 284 through 296 Processing helix chain 'M' and resid 305 through 312 Processing helix chain 'M' and resid 347 through 357 Processing helix chain 'M' and resid 373 through 383 Processing helix chain 'M' and resid 411 through 429 Processing helix chain 'M' and resid 431 through 450 Processing helix chain 'M' and resid 453 through 467 Processing helix chain 'M' and resid 472 through 482 Processing helix chain 'M' and resid 484 through 496 Processing helix chain 'M' and resid 514 through 522 removed outlier: 3.596A pdb=" N PHE M 518 " --> pdb=" O ASP M 514 " (cutoff:3.500A) Processing helix chain 'N' and resid 117 through 125 Processing helix chain 'N' and resid 134 through 146 Processing helix chain 'N' and resid 168 through 182 Processing helix chain 'N' and resid 186 through 203 Processing helix chain 'N' and resid 207 through 220 removed outlier: 3.627A pdb=" N LEU N 211 " --> pdb=" O ASN N 207 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 239 Processing helix chain 'N' and resid 240 through 252 Processing helix chain 'N' and resid 253 through 255 No H-bonds generated for 'chain 'N' and resid 253 through 255' Processing helix chain 'N' and resid 265 through 278 Proline residue: N 275 - end of helix Processing helix chain 'N' and resid 321 through 335 Processing helix chain 'N' and resid 352 through 362 Processing helix chain 'N' and resid 391 through 408 removed outlier: 3.756A pdb=" N ALA N 407 " --> pdb=" O LEU N 403 " (cutoff:3.500A) Processing helix chain 'N' and resid 413 through 432 Processing helix chain 'N' and resid 434 through 450 removed outlier: 3.603A pdb=" N ALA N 438 " --> pdb=" O SER N 434 " (cutoff:3.500A) Processing helix chain 'N' and resid 454 through 465 removed outlier: 3.940A pdb=" N PHE N 458 " --> pdb=" O PRO N 454 " (cutoff:3.500A) Processing helix chain 'N' and resid 466 through 480 removed outlier: 3.849A pdb=" N SER N 480 " --> pdb=" O LYS N 476 " (cutoff:3.500A) Processing helix chain 'N' and resid 490 through 493 Processing helix chain 'N' and resid 495 through 501 Processing helix chain 'O' and resid 9 through 13 Processing helix chain 'O' and resid 16 through 24 Processing helix chain 'O' and resid 34 through 58 Processing helix chain 'O' and resid 66 through 77 Processing helix chain 'O' and resid 80 through 109 removed outlier: 3.855A pdb=" N LEU O 84 " --> pdb=" O GLY O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 116 through 140 removed outlier: 3.617A pdb=" N LEU O 140 " --> pdb=" O THR O 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 156 Processing helix chain 'O' and resid 157 through 160 removed outlier: 3.694A pdb=" N ILE O 160 " --> pdb=" O ALA O 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 157 through 160' Processing helix chain 'O' and resid 163 through 173 Processing helix chain 'O' and resid 178 through 210 Proline residue: O 193 - end of helix Processing helix chain 'O' and resid 229 through 252 removed outlier: 3.879A pdb=" N LYS O 234 " --> pdb=" O TYR O 230 " (cutoff:3.500A) Processing helix chain 'O' and resid 259 through 264 removed outlier: 3.526A pdb=" N ILE O 264 " --> pdb=" O ASP O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 278 through 280 No H-bonds generated for 'chain 'O' and resid 278 through 280' Processing helix chain 'O' and resid 281 through 291 Processing helix chain 'O' and resid 293 through 311 Processing helix chain 'O' and resid 321 through 324 removed outlier: 3.770A pdb=" N PHE O 324 " --> pdb=" O SER O 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 321 through 324' Processing helix chain 'O' and resid 325 through 347 removed outlier: 4.043A pdb=" N CYS O 347 " --> pdb=" O GLY O 343 " (cutoff:3.500A) Processing helix chain 'O' and resid 353 through 371 removed outlier: 3.823A pdb=" N PHE O 363 " --> pdb=" O GLN O 359 " (cutoff:3.500A) Processing helix chain 'O' and resid 371 through 382 removed outlier: 3.624A pdb=" N LEU O 375 " --> pdb=" O ILE O 371 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 69 Processing helix chain 'P' and resid 87 through 102 Processing helix chain 'P' and resid 112 through 117 Processing helix chain 'P' and resid 122 through 133 removed outlier: 3.915A pdb=" N ILE P 133 " --> pdb=" O MET P 129 " (cutoff:3.500A) Processing helix chain 'P' and resid 162 through 170 Processing helix chain 'P' and resid 187 through 198 Processing helix chain 'P' and resid 243 through 260 Processing helix chain 'P' and resid 262 through 297 removed outlier: 4.587A pdb=" N VAL P 294 " --> pdb=" O LEU P 290 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LEU P 295 " --> pdb=" O ARG P 291 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 85 Processing helix chain 'Q' and resid 109 through 138 Processing helix chain 'Q' and resid 140 through 147 Processing helix chain 'R' and resid 14 through 32 Processing helix chain 'R' and resid 35 through 39 Processing helix chain 'R' and resid 40 through 45 removed outlier: 3.868A pdb=" N ASP R 44 " --> pdb=" O ASP R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 54 removed outlier: 3.851A pdb=" N GLU R 49 " --> pdb=" O LEU R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 76 Processing helix chain 'R' and resid 80 through 86 Processing helix chain 'R' and resid 94 through 111 Processing helix chain 'S' and resid 17 through 20 removed outlier: 3.840A pdb=" N GLN S 20 " --> pdb=" O PRO S 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 17 through 20' Processing helix chain 'S' and resid 29 through 71 removed outlier: 6.232A pdb=" N ILE S 43 " --> pdb=" O SER S 39 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N SER S 44 " --> pdb=" O GLU S 40 " (cutoff:3.500A) Proline residue: S 51 - end of helix Processing helix chain 'T' and resid 8 through 18 Processing helix chain 'T' and resid 21 through 39 removed outlier: 4.075A pdb=" N LEU T 25 " --> pdb=" O CYS T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 60 removed outlier: 4.065A pdb=" N TYR T 49 " --> pdb=" O CYS T 45 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 68 removed outlier: 3.643A pdb=" N LEU T 64 " --> pdb=" O VAL T 60 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE T 65 " --> pdb=" O ALA T 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 12 through 21 Processing helix chain 'V' and resid 23 through 54 Processing helix chain 'W' and resid 16 through 38 Processing helix chain 'W' and resid 40 through 45 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 98 removed outlier: 3.651A pdb=" N ARG A 103 " --> pdb=" O MET A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.518A pdb=" N PHE A 401 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 362 Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 82 removed outlier: 6.860A pdb=" N LYS B 87 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ALA B 261 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA B 89 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 221 through 223 removed outlier: 3.760A pdb=" N VAL B 292 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 296 through 301 Processing sheet with id=AA7, first strand: chain 'C' and resid 27 through 29 Processing sheet with id=AA8, first strand: chain 'D' and resid 134 through 139 removed outlier: 3.673A pdb=" N PHE D 146 " --> pdb=" O ASP D 137 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 213 through 214 Processing sheet with id=AB1, first strand: chain 'M' and resid 94 through 98 removed outlier: 3.786A pdb=" N ARG M 103 " --> pdb=" O MET M 275 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY M 281 " --> pdb=" O GLU M 107 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR M 116 " --> pdb=" O SER M 280 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 361 through 362 Processing sheet with id=AB3, first strand: chain 'M' and resid 361 through 362 Processing sheet with id=AB4, first strand: chain 'N' and resid 78 through 82 removed outlier: 6.756A pdb=" N LYS N 87 " --> pdb=" O LEU N 259 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ALA N 261 " --> pdb=" O LYS N 87 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA N 89 " --> pdb=" O ALA N 261 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 297 through 301 removed outlier: 3.562A pdb=" N PHE N 381 " --> pdb=" O PHE N 313 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 27 through 29 Processing sheet with id=AB7, first strand: chain 'P' and resid 134 through 137 removed outlier: 3.768A pdb=" N PHE P 146 " --> pdb=" O ASP P 137 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 213 through 214 1892 hydrogen bonds defined for protein. 5439 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: 6.11 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.36: 10525 1.36 - 1.53: 20243 1.53 - 1.69: 2710 1.69 - 1.85: 228 1.85 - 2.02: 24 Bond restraints: 33730 Sorted by residual: bond pdb=" C2D HEC P 501 " pdb=" C3D HEC P 501 " ideal model delta sigma weight residual 1.544 1.324 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C2D HEC D 501 " pdb=" C3D HEC D 501 " ideal model delta sigma weight residual 1.544 1.324 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CAC HEC P 501 " pdb=" CBC HEC P 501 " ideal model delta sigma weight residual 1.544 1.361 0.183 2.00e-02 2.50e+03 8.39e+01 bond pdb=" CAC HEC D 501 " pdb=" CBC HEC D 501 " ideal model delta sigma weight residual 1.544 1.362 0.182 2.00e-02 2.50e+03 8.26e+01 bond pdb=" CAB HEC D 501 " pdb=" CBB HEC D 501 " ideal model delta sigma weight residual 1.544 1.402 0.142 2.00e-02 2.50e+03 5.01e+01 ... (remaining 33725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 44600 2.32 - 4.64: 897 4.64 - 6.97: 150 6.97 - 9.29: 15 9.29 - 11.61: 6 Bond angle restraints: 45668 Sorted by residual: angle pdb=" N GLY B 107 " pdb=" CA GLY B 107 " pdb=" C GLY B 107 " ideal model delta sigma weight residual 110.29 117.62 -7.33 1.28e+00 6.10e-01 3.28e+01 angle pdb=" CG MET D 225 " pdb=" SD MET D 225 " pdb=" CE MET D 225 " ideal model delta sigma weight residual 100.90 92.70 8.20 2.20e+00 2.07e-01 1.39e+01 angle pdb=" CB LYS B 472 " pdb=" CG LYS B 472 " pdb=" CD LYS B 472 " ideal model delta sigma weight residual 111.30 119.84 -8.54 2.30e+00 1.89e-01 1.38e+01 angle pdb=" C ARG Q 119 " pdb=" N PHE Q 120 " pdb=" CA PHE Q 120 " ideal model delta sigma weight residual 121.14 114.84 6.30 1.75e+00 3.27e-01 1.30e+01 angle pdb=" C ALA N 370 " pdb=" N PHE N 371 " pdb=" CA PHE N 371 " ideal model delta sigma weight residual 122.82 128.79 -5.97 1.68e+00 3.54e-01 1.26e+01 ... (remaining 45663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 17797 17.96 - 35.92: 1691 35.92 - 53.88: 403 53.88 - 71.83: 99 71.83 - 89.79: 44 Dihedral angle restraints: 20034 sinusoidal: 8459 harmonic: 11575 Sorted by residual: dihedral pdb=" C2C HEM O 403 " pdb=" C3C HEM O 403 " pdb=" CAC HEM O 403 " pdb=" CBC HEM O 403 " ideal model delta sinusoidal sigma weight residual -180.00 -104.81 -75.19 2 1.00e+01 1.00e-02 4.49e+01 dihedral pdb=" C2C HEM O 404 " pdb=" C3C HEM O 404 " pdb=" CAC HEM O 404 " pdb=" CBC HEM O 404 " ideal model delta sinusoidal sigma weight residual 0.00 -56.66 56.66 2 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" C2C HEM C 402 " pdb=" C3C HEM C 402 " pdb=" CAC HEM C 402 " pdb=" CBC HEM C 402 " ideal model delta sinusoidal sigma weight residual -0.00 56.04 -56.04 2 1.00e+01 1.00e-02 3.30e+01 ... (remaining 20031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4272 0.069 - 0.139: 565 0.139 - 0.208: 32 0.208 - 0.277: 4 0.277 - 0.347: 2 Chirality restraints: 4875 Sorted by residual: chirality pdb=" CA4 CDL P 502 " pdb=" CA3 CDL P 502 " pdb=" CA6 CDL P 502 " pdb=" OA6 CDL P 502 " both_signs ideal model delta sigma weight residual False -2.57 -2.23 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C2 3PE F 201 " pdb=" C1 3PE F 201 " pdb=" C3 3PE F 201 " pdb=" O21 3PE F 201 " both_signs ideal model delta sigma weight residual False -2.53 -2.23 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA4 CDL M 603 " pdb=" CA3 CDL M 603 " pdb=" CA6 CDL M 603 " pdb=" OA6 CDL M 603 " both_signs ideal model delta sigma weight residual False -2.57 -2.31 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 4872 not shown) Planarity restraints: 5715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 190 " -0.015 2.00e-02 2.50e+03 2.45e-02 1.20e+01 pdb=" CG TYR C 190 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR C 190 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR C 190 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR C 190 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 190 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 190 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 190 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 246 " 0.025 2.00e-02 2.50e+03 2.49e-02 1.08e+01 pdb=" CG PHE O 246 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE O 246 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE O 246 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE O 246 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE O 246 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE O 246 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 190 " 0.013 2.00e-02 2.50e+03 2.25e-02 1.02e+01 pdb=" CG TYR O 190 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR O 190 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR O 190 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR O 190 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR O 190 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR O 190 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR O 190 " -0.002 2.00e-02 2.50e+03 ... (remaining 5712 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 348 2.62 - 3.19: 29400 3.19 - 3.76: 50372 3.76 - 4.33: 71017 4.33 - 4.90: 119639 Nonbonded interactions: 270776 Sorted by model distance: nonbonded pdb=" NE2 HIS O 88 " pdb="FE HEM O 403 " model vdw 2.045 3.080 nonbonded pdb=" NE2 HIS C 88 " pdb="FE HEM C 402 " model vdw 2.053 3.080 nonbonded pdb=" NE2 HIS O 102 " pdb="FE HEM O 404 " model vdw 2.062 3.080 nonbonded pdb=" NE2 HIS C 203 " pdb="FE HEM C 403 " model vdw 2.079 3.080 nonbonded pdb=" O SER C 316 " pdb=" OH TYR F 43 " model vdw 2.111 3.040 ... (remaining 270771 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 41 through 601 or (resid 603 and (name CB2 or name OB2 or \ name CB3 or name OB3 or name C1 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C51 \ or name C52 or name C53 or name C54 or name C55 or name C56 or name C71 or name \ C72 or name C73 or name C74 or name C75 or name C76 or name CA2 or name CA3 or n \ ame CA4 or name CA5 or name CA6 or name CA7 or name CB4 or name CB5 or name CB6 \ or name CB7 or name O1 or name OA2 or name OA3 or name OA4 or name OA5 or name O \ A6 or name OA7 or name OA8 or name OA9 or name OB4 or name OB5 or name OB6 or na \ me OB7 or name OB8 or name OB9 or name PA1 or name PB2)))) selection = (chain 'M' and (resid 41 through 601 or (resid 603 and (name CB2 or name OB2 or \ name CB3 or name OB3 or name C1 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C51 \ or name C52 or name C53 or name C54 or name C55 or name C56 or name C71 or name \ C72 or name C73 or name C74 or name C75 or name C76 or name CA2 or name CA3 or n \ ame CA4 or name CA5 or name CA6 or name CA7 or name CB4 or name CB5 or name CB6 \ or name CB7 or name O1 or name OA2 or name OA3 or name OA4 or name OA5 or name O \ A6 or name OA7 or name OA8 or name OA9 or name OB4 or name OB5 or name OB6 or na \ me OB7 or name OB8 or name OB9 or name PA1 or name PB2)))) } ncs_group { reference = (chain 'B' and resid 50 through 504) selection = chain 'N' } ncs_group { reference = (chain 'C' and (resid 2 through 389 or resid 403 or (resid 405 and (name N or na \ me C1 or name C11 or name C12 or name C2 or name C21 or name C22 or name C23 or \ name C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name O11 or name O12 or name \ O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or \ (resid 407 and (name N or name C1 or name C11 or name C12 or name C2 or name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name \ C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name O11 or name O12 or name O13 or name O14 \ or name O21 or name O22 or name O31 or name O32 or name P )) or resid 408 throug \ h 409)) selection = (chain 'O' and (resid 2 through 389 or resid 403 or (resid 405 and (name N or na \ me C1 or name C11 or name C12 or name C2 or name C21 or name C22 or name C23 or \ name C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name O11 or name O12 or name \ O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or \ (resid 407 and (name N or name C1 or name C11 or name C12 or name C2 or name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name \ C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name O11 or name O12 or name O13 or name O14 \ or name O21 or name O22 or name O31 or name O32 or name P )) or (resid 408 and ( \ name N or name C1 or name C11 or name C12 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name O11 or name O12 or name \ O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or \ (resid 409 and (name N or name C1 or name C11 or name C12 or name C2 or name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name \ C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C3A or name C3B or name C3C or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P )))) } ncs_group { reference = (chain 'D' and (resid 63 through 501 or (resid 502 and (name CB2 or name OB2 or \ name CB3 or name OB3 or name C1 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C31 or name C32 or name C33 or name C34 or name C51 or name C52 or name C53 or n \ ame C54 or name C55 or name C71 or name C72 or name C73 or name C74 or name C75 \ or name C76 or name CA2 or name CA3 or name CA4 or name CA5 or name CA6 or name \ CA7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or name OA2 or na \ me OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 or name OA9 o \ r name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name OB9 or name P \ A1 or name PB2)))) selection = (chain 'P' and (resid 63 through 501 or (resid 502 and (name CB2 or name OB2 or \ name CB3 or name OB3 or name C1 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C31 or name C32 or name C33 or name C34 or name C51 or name C52 or name C53 or n \ ame C54 or name C55 or name C71 or name C72 or name C73 or name C74 or name C75 \ or name C76 or name CA2 or name CA3 or name CA4 or name CA5 or name CA6 or name \ CA7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or name OA2 or na \ me OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 or name OA9 o \ r name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name OB9 or name P \ A1 or name PB2)))) } ncs_group { reference = (chain 'E' and resid 75 through 148) selection = chain 'Q' } ncs_group { reference = (chain 'F' and resid 8 through 122) selection = chain 'R' } ncs_group { reference = (chain 'G' and resid 3 through 72) selection = (chain 'S' and resid 3 through 72) } ncs_group { reference = (chain 'H' and resid 6 through 69) selection = chain 'T' } ncs_group { reference = (chain 'J' and resid 11 through 69) selection = chain 'V' } ncs_group { reference = chain 'K' selection = (chain 'W' and resid 16 through 46) } 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: 10.650 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: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 32.790 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 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 : 0.009 0.363 33749 Z= 0.382 Angle : 0.785 11.609 45678 Z= 0.392 Chirality : 0.047 0.347 4875 Planarity : 0.005 0.065 5715 Dihedral : 15.564 89.793 12587 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.85 % Favored : 93.10 % Rotamer: Outliers : 0.09 % Allowed : 0.36 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3943 helix: 1.33 (0.11), residues: 2197 sheet: -0.99 (0.27), residues: 361 loop : -1.38 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG M 62 TYR 0.058 0.002 TYR C 190 PHE 0.057 0.002 PHE O 246 TRP 0.021 0.002 TRP P 273 HIS 0.009 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00750 / 0.35 (33730) covalent geometry : angle 0.78430 / 0.39 (45668) SS BOND : bond 0.00654 / 0.28 ( 5) SS BOND : angle 2.60370 / 1.88 ( 10) hydrogen bonds : bond 0.10736 / 7.03 ( 1876) hydrogen bonds : angle 5.32800 / 3.81 ( 5439) metal coordination : bond 0.34367 / 15.77 ( 4) Misc. bond : bond 0.15508 / 15.37 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 333 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: B 335 MET cc_start: 0.8444 (mmm) cc_final: 0.7993 (mmm) REVERT: H 7 VAL cc_start: 0.7111 (p) cc_final: 0.6883 (t) REVERT: H 8 ASP cc_start: 0.8015 (m-30) cc_final: 0.7676 (m-30) REVERT: H 14 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7818 (tm-30) REVERT: H 15 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7684 (mm-30) REVERT: H 51 ASP cc_start: 0.8297 (m-30) cc_final: 0.8047 (m-30) REVERT: N 335 MET cc_start: 0.7990 (tpp) cc_final: 0.7750 (mmm) outliers start: 3 outliers final: 2 residues processed: 335 average time/residue: 0.2121 time to fit residues: 114.1822 Evaluate side-chains 269 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 267 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 306 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN B 206 ASN B 332 GLN C 329 GLN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 306 ASN N 301 HIS ** S 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 36 HIS ** T 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.080550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.063055 restraints weight = 78223.490| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.19 r_work: 0.2820 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.412 33749 Z= 0.161 Angle : 0.646 15.320 45678 Z= 0.316 Chirality : 0.044 0.254 4875 Planarity : 0.005 0.064 5715 Dihedral : 12.436 89.821 5217 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.51 % Allowed : 5.88 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.14), residues: 3943 helix: 1.54 (0.11), residues: 2185 sheet: -0.78 (0.28), residues: 360 loop : -1.27 (0.18), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 62 TYR 0.019 0.001 TYR A 404 PHE 0.037 0.001 PHE O 246 TRP 0.019 0.001 TRP P 273 HIS 0.008 0.001 HIS N 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (33730) covalent geometry : angle 0.64492 / 0.32 (45668) SS BOND : bond 0.00642 / 0.28 ( 5) SS BOND : angle 2.40507 / 2.23 ( 10) hydrogen bonds : bond 0.05236 / 3.51 ( 1876) hydrogen bonds : angle 4.74136 / 3.39 ( 5439) metal coordination : bond 0.00951 / 0.46 ( 4) Misc. bond : bond 0.23199 / 18.86 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 295 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 315 LYS cc_start: 0.7376 (mmtt) cc_final: 0.6598 (mmtt) REVERT: H 7 VAL cc_start: 0.7062 (p) cc_final: 0.6663 (t) REVERT: H 14 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7706 (tm-30) REVERT: H 15 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7895 (mm-30) REVERT: H 51 ASP cc_start: 0.8780 (m-30) cc_final: 0.8229 (m-30) REVERT: H 69 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8005 (ptpt) REVERT: S 61 ASN cc_start: 0.7967 (t0) cc_final: 0.7745 (t0) REVERT: S 65 LYS cc_start: 0.8541 (mttm) cc_final: 0.8139 (mttm) REVERT: S 66 GLU cc_start: 0.8372 (tt0) cc_final: 0.7909 (tp30) outliers start: 17 outliers final: 15 residues processed: 306 average time/residue: 0.2235 time to fit residues: 110.3174 Evaluate side-chains 291 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 275 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 383 GLU Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain T residue 55 CYS Chi-restraints excluded: chain W residue 37 LEU Chi-restraints excluded: chain W residue 40 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 0 optimal weight: 8.9990 chunk 376 optimal weight: 10.0000 chunk 341 optimal weight: 5.9990 chunk 339 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 370 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN M 394 ASN T 29 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.077730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.060182 restraints weight = 78697.200| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.17 r_work: 0.2752 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.390 33749 Z= 0.300 Angle : 0.727 14.912 45678 Z= 0.356 Chirality : 0.047 0.235 4875 Planarity : 0.005 0.068 5715 Dihedral : 12.391 88.378 5215 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 1.02 % Allowed : 8.90 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3943 helix: 1.33 (0.11), residues: 2211 sheet: -0.75 (0.28), residues: 360 loop : -1.40 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 289 TYR 0.021 0.002 TYR A 404 PHE 0.039 0.002 PHE Q 120 TRP 0.020 0.002 TRP P 273 HIS 0.009 0.001 HIS T 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00726 / 0.30 (33730) covalent geometry : angle 0.72630 / 0.36 (45668) SS BOND : bond 0.00753 / 0.35 ( 5) SS BOND : angle 2.56093 / 2.27 ( 10) hydrogen bonds : bond 0.06241 / 4.17 ( 1876) hydrogen bonds : angle 4.87118 / 3.48 ( 5439) metal coordination : bond 0.00917 / 0.41 ( 4) Misc. bond : bond 0.22409 / 18.49 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 277 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 315 LYS cc_start: 0.7475 (mmtt) cc_final: 0.6740 (mmtt) REVERT: H 7 VAL cc_start: 0.7100 (p) cc_final: 0.6676 (t) REVERT: H 14 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7648 (tm-30) REVERT: H 15 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7876 (mm-30) REVERT: H 51 ASP cc_start: 0.8794 (m-30) cc_final: 0.8386 (m-30) REVERT: S 61 ASN cc_start: 0.8002 (t0) cc_final: 0.7668 (t0) REVERT: S 65 LYS cc_start: 0.8553 (mttm) cc_final: 0.8132 (mttm) REVERT: S 66 GLU cc_start: 0.8389 (tt0) cc_final: 0.7954 (tp30) outliers start: 34 outliers final: 23 residues processed: 296 average time/residue: 0.2191 time to fit residues: 104.7938 Evaluate side-chains 292 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 269 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 383 GLU Chi-restraints excluded: chain M residue 506 MET Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain T residue 55 CYS Chi-restraints excluded: chain W residue 37 LEU Chi-restraints excluded: chain W residue 40 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 155 optimal weight: 0.0050 chunk 24 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 280 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 314 optimal weight: 5.9990 chunk 237 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 279 optimal weight: 2.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 GLN A 291 GLN B 332 GLN D 306 ASN N 475 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.081437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.064064 restraints weight = 77368.801| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.19 r_work: 0.2842 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.352 33749 Z= 0.126 Angle : 0.587 11.018 45678 Z= 0.289 Chirality : 0.042 0.225 4875 Planarity : 0.004 0.062 5715 Dihedral : 11.782 89.196 5215 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.19 % Allowed : 10.33 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.14), residues: 3943 helix: 1.66 (0.11), residues: 2195 sheet: -0.58 (0.28), residues: 354 loop : -1.15 (0.18), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 85 TYR 0.014 0.001 TYR H 49 PHE 0.032 0.001 PHE Q 120 TRP 0.019 0.001 TRP P 273 HIS 0.003 0.001 HIS V 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (33730) covalent geometry : angle 0.58612 / 0.29 (45668) SS BOND : bond 0.00473 / 0.25 ( 5) SS BOND : angle 2.08687 / 1.87 ( 10) hydrogen bonds : bond 0.04638 / 3.12 ( 1876) hydrogen bonds : angle 4.57817 / 3.28 ( 5439) metal coordination : bond 0.00060 / 0.03 ( 4) Misc. bond : bond 0.20428 / 18.66 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 293 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 210 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.6967 (t80) REVERT: C 315 LYS cc_start: 0.7284 (mmtt) cc_final: 0.6874 (mmtt) REVERT: H 7 VAL cc_start: 0.7064 (p) cc_final: 0.6672 (t) REVERT: H 8 ASP cc_start: 0.7677 (m-30) cc_final: 0.7434 (m-30) REVERT: H 14 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7680 (tm-30) REVERT: H 15 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7945 (mm-30) REVERT: H 51 ASP cc_start: 0.8752 (m-30) cc_final: 0.8157 (m-30) REVERT: H 69 LYS cc_start: 0.8226 (tttp) cc_final: 0.7954 (ptpt) REVERT: P 210 GLU cc_start: 0.8351 (tp30) cc_final: 0.7788 (pt0) REVERT: S 66 GLU cc_start: 0.8336 (tt0) cc_final: 0.7883 (tp30) REVERT: S 72 TYR cc_start: 0.7064 (m-10) cc_final: 0.6856 (m-80) outliers start: 40 outliers final: 21 residues processed: 319 average time/residue: 0.2034 time to fit residues: 105.0720 Evaluate side-chains 294 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 272 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 210 TYR Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain M residue 383 GLU Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain N residue 378 THR Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain T residue 55 CYS Chi-restraints excluded: chain V residue 21 MET Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 40 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 197 optimal weight: 7.9990 chunk 240 optimal weight: 0.9980 chunk 209 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 339 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 280 optimal weight: 8.9990 chunk 193 optimal weight: 5.9990 chunk 298 optimal weight: 0.7980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.079618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.062101 restraints weight = 77953.140| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.18 r_work: 0.2795 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.352 33749 Z= 0.202 Angle : 0.634 13.971 45678 Z= 0.309 Chirality : 0.044 0.221 4875 Planarity : 0.005 0.064 5715 Dihedral : 11.773 89.672 5214 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.13 % Allowed : 11.85 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.14), residues: 3943 helix: 1.64 (0.11), residues: 2192 sheet: -0.61 (0.28), residues: 362 loop : -1.19 (0.18), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 266 TYR 0.018 0.001 TYR N 384 PHE 0.034 0.001 PHE Q 120 TRP 0.018 0.001 TRP P 273 HIS 0.006 0.001 HIS O 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 (33730) covalent geometry : angle 0.63284 / 0.31 (45668) SS BOND : bond 0.00565 / 0.24 ( 5) SS BOND : angle 2.18008 / 1.97 ( 10) hydrogen bonds : bond 0.05228 / 3.50 ( 1876) hydrogen bonds : angle 4.61199 / 3.30 ( 5439) metal coordination : bond 0.00323 / 0.14 ( 4) Misc. bond : bond 0.19022 / 15.98 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 277 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 315 LYS cc_start: 0.7403 (mmtt) cc_final: 0.6708 (mmtt) REVERT: H 7 VAL cc_start: 0.7050 (p) cc_final: 0.6663 (t) REVERT: H 14 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7635 (tm-30) REVERT: H 15 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7866 (mm-30) REVERT: H 51 ASP cc_start: 0.8760 (m-30) cc_final: 0.8178 (m-30) REVERT: M 153 ARG cc_start: 0.8821 (ttp-110) cc_final: 0.8476 (ptm-80) REVERT: S 66 GLU cc_start: 0.8368 (tt0) cc_final: 0.7914 (tp30) outliers start: 38 outliers final: 33 residues processed: 301 average time/residue: 0.2231 time to fit residues: 109.9223 Evaluate side-chains 305 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 272 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 383 GLU Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain T residue 55 CYS Chi-restraints excluded: chain V residue 21 MET Chi-restraints excluded: chain W residue 37 LEU Chi-restraints excluded: chain W residue 40 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 304 optimal weight: 2.9990 chunk 352 optimal weight: 3.9990 chunk 333 optimal weight: 0.9990 chunk 236 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 373 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 287 optimal weight: 10.0000 chunk 36 optimal weight: 0.1980 chunk 67 optimal weight: 0.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.081114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.063705 restraints weight = 77519.713| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.19 r_work: 0.2836 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.339 33749 Z= 0.139 Angle : 0.588 12.742 45678 Z= 0.287 Chirality : 0.042 0.251 4875 Planarity : 0.004 0.062 5715 Dihedral : 11.468 89.052 5214 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.40 % Allowed : 12.00 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.14), residues: 3943 helix: 1.72 (0.11), residues: 2203 sheet: -0.55 (0.28), residues: 362 loop : -1.10 (0.18), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 266 TYR 0.022 0.001 TYR N 384 PHE 0.032 0.001 PHE Q 120 TRP 0.018 0.001 TRP P 273 HIS 0.004 0.001 HIS O 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (33730) covalent geometry : angle 0.58730 / 0.29 (45668) SS BOND : bond 0.00479 / 0.23 ( 5) SS BOND : angle 2.02989 / 1.83 ( 10) hydrogen bonds : bond 0.04668 / 3.14 ( 1876) hydrogen bonds : angle 4.50953 / 3.23 ( 5439) metal coordination : bond 0.00078 / 0.03 ( 4) Misc. bond : bond 0.19937 / 18.37 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 286 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 210 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.6894 (t80) REVERT: C 315 LYS cc_start: 0.7383 (mmtt) cc_final: 0.6691 (mmtt) REVERT: H 7 VAL cc_start: 0.7092 (p) cc_final: 0.6671 (t) REVERT: H 14 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7649 (tm-30) REVERT: H 15 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7947 (mm-30) REVERT: H 51 ASP cc_start: 0.8728 (m-30) cc_final: 0.8161 (m-30) REVERT: H 69 LYS cc_start: 0.8324 (tttp) cc_final: 0.8000 (ptpt) REVERT: M 48 MET cc_start: 0.8130 (mmp) cc_final: 0.7925 (mmp) REVERT: M 153 ARG cc_start: 0.8811 (ttp-110) cc_final: 0.8442 (ptm-80) REVERT: P 210 GLU cc_start: 0.8383 (tp30) cc_final: 0.7788 (pt0) REVERT: S 66 GLU cc_start: 0.8364 (tt0) cc_final: 0.7910 (tp30) outliers start: 47 outliers final: 32 residues processed: 316 average time/residue: 0.2232 time to fit residues: 114.9922 Evaluate side-chains 305 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 272 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 210 TYR Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 383 GLU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain N residue 309 VAL Chi-restraints excluded: chain N residue 378 THR Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain T residue 55 CYS Chi-restraints excluded: chain V residue 21 MET Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 40 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 285 optimal weight: 2.9990 chunk 308 optimal weight: 0.0040 chunk 303 optimal weight: 8.9990 chunk 47 optimal weight: 0.4980 chunk 317 optimal weight: 6.9990 chunk 273 optimal weight: 0.0050 chunk 146 optimal weight: 6.9990 chunk 359 optimal weight: 5.9990 chunk 379 optimal weight: 6.9990 chunk 175 optimal weight: 0.6980 chunk 350 optimal weight: 3.9990 overall best weight: 0.8408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 351 HIS T 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.082199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.064829 restraints weight = 77508.155| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.19 r_work: 0.2861 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.327 33749 Z= 0.123 Angle : 0.573 11.816 45678 Z= 0.279 Chirality : 0.041 0.309 4875 Planarity : 0.004 0.060 5715 Dihedral : 11.048 89.878 5214 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.19 % Allowed : 12.51 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.14), residues: 3943 helix: 1.83 (0.11), residues: 2206 sheet: -0.26 (0.29), residues: 324 loop : -1.10 (0.18), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 266 TYR 0.022 0.001 TYR N 384 PHE 0.032 0.001 PHE Q 120 TRP 0.017 0.001 TRP P 273 HIS 0.004 0.001 HIS O 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (33730) covalent geometry : angle 0.57213 / 0.28 (45668) SS BOND : bond 0.00455 / 0.23 ( 5) SS BOND : angle 1.98613 / 1.79 ( 10) hydrogen bonds : bond 0.04334 / 2.92 ( 1876) hydrogen bonds : angle 4.40980 / 3.16 ( 5439) metal coordination : bond 0.00108 / 0.05 ( 4) Misc. bond : bond 0.17802 / 15.53 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 294 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8783 (mmm) cc_final: 0.8397 (mmm) REVERT: C 210 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.6679 (t80) REVERT: C 315 LYS cc_start: 0.7343 (mmtt) cc_final: 0.6615 (mmtt) REVERT: D 223 ILE cc_start: 0.9094 (tt) cc_final: 0.8887 (tt) REVERT: G 64 GLU cc_start: 0.8726 (tp30) cc_final: 0.8239 (tp30) REVERT: H 7 VAL cc_start: 0.7109 (p) cc_final: 0.6692 (t) REVERT: H 11 ARG cc_start: 0.7766 (ptt180) cc_final: 0.7397 (ptt180) REVERT: H 14 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7662 (tm-30) REVERT: H 15 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7976 (mm-30) REVERT: H 51 ASP cc_start: 0.8682 (m-30) cc_final: 0.8114 (m-30) REVERT: H 69 LYS cc_start: 0.8273 (tttp) cc_final: 0.8001 (ptpt) REVERT: M 153 ARG cc_start: 0.8799 (ttp-110) cc_final: 0.8455 (ptm-80) REVERT: P 210 GLU cc_start: 0.8312 (tp30) cc_final: 0.7741 (pt0) REVERT: P 225 MET cc_start: 0.9218 (ttp) cc_final: 0.8924 (ttp) REVERT: S 66 GLU cc_start: 0.8369 (tt0) cc_final: 0.7926 (tp30) outliers start: 40 outliers final: 30 residues processed: 320 average time/residue: 0.2210 time to fit residues: 114.5802 Evaluate side-chains 309 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 278 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 210 TYR Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain G residue 35 HIS Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain M residue 383 GLU Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain N residue 378 THR Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain T residue 55 CYS Chi-restraints excluded: chain V residue 21 MET Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 40 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 354 optimal weight: 0.9990 chunk 184 optimal weight: 4.9990 chunk 369 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 347 optimal weight: 0.8980 chunk 120 optimal weight: 0.0270 chunk 258 optimal weight: 3.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.082798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.065427 restraints weight = 77340.372| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.20 r_work: 0.2874 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.325 33749 Z= 0.118 Angle : 0.573 11.582 45678 Z= 0.278 Chirality : 0.041 0.275 4875 Planarity : 0.004 0.059 5715 Dihedral : 10.731 89.674 5214 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.19 % Allowed : 12.57 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.14), residues: 3943 helix: 1.88 (0.11), residues: 2206 sheet: -0.23 (0.29), residues: 324 loop : -1.03 (0.18), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 266 TYR 0.018 0.001 TYR T 52 PHE 0.032 0.001 PHE Q 120 TRP 0.016 0.001 TRP P 273 HIS 0.004 0.001 HIS O 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (33730) covalent geometry : angle 0.57206 / 0.28 (45668) SS BOND : bond 0.00416 / 0.18 ( 5) SS BOND : angle 2.05049 / 1.83 ( 10) hydrogen bonds : bond 0.04214 / 2.84 ( 1876) hydrogen bonds : angle 4.37200 / 3.13 ( 5439) metal coordination : bond 0.00088 / 0.04 ( 4) Misc. bond : bond 0.16932 / 14.25 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 290 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8834 (mmm) cc_final: 0.8442 (mmm) REVERT: C 156 LEU cc_start: 0.8496 (mp) cc_final: 0.8216 (tt) REVERT: C 210 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.6805 (t80) REVERT: C 315 LYS cc_start: 0.7287 (mmtt) cc_final: 0.6586 (mmtt) REVERT: F 30 LYS cc_start: 0.8439 (mtpt) cc_final: 0.8153 (ttpt) REVERT: G 64 GLU cc_start: 0.8729 (tp30) cc_final: 0.8240 (tp30) REVERT: H 7 VAL cc_start: 0.7174 (p) cc_final: 0.6764 (t) REVERT: H 11 ARG cc_start: 0.7772 (ptt180) cc_final: 0.7407 (ptt180) REVERT: H 14 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7664 (tm-30) REVERT: H 15 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7996 (mm-30) REVERT: H 69 LYS cc_start: 0.8274 (tttp) cc_final: 0.8011 (ptpt) REVERT: J 22 ARG cc_start: 0.8139 (mtm110) cc_final: 0.7793 (mtp85) REVERT: M 48 MET cc_start: 0.8161 (mmp) cc_final: 0.7867 (mmp) REVERT: M 153 ARG cc_start: 0.8826 (ttp-110) cc_final: 0.8476 (ptm-80) REVERT: O 145 MET cc_start: 0.8609 (tpp) cc_final: 0.8353 (mpp) REVERT: P 210 GLU cc_start: 0.8314 (tp30) cc_final: 0.7770 (pt0) REVERT: P 225 MET cc_start: 0.9217 (ttp) cc_final: 0.9012 (ttp) REVERT: S 66 GLU cc_start: 0.8393 (tt0) cc_final: 0.7946 (tp30) REVERT: T 32 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7895 (mp) outliers start: 40 outliers final: 30 residues processed: 318 average time/residue: 0.2196 time to fit residues: 113.1309 Evaluate side-chains 310 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 210 TYR Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain G residue 35 HIS Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain M residue 383 GLU Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain N residue 309 VAL Chi-restraints excluded: chain N residue 378 THR Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 55 CYS Chi-restraints excluded: chain V residue 21 MET Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 40 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 136 optimal weight: 5.9990 chunk 178 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 277 optimal weight: 0.0970 chunk 107 optimal weight: 1.9990 chunk 256 optimal weight: 0.3980 chunk 314 optimal weight: 0.3980 chunk 300 optimal weight: 0.9990 chunk 205 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.083486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.066210 restraints weight = 76940.100| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.18 r_work: 0.2891 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.321 33749 Z= 0.114 Angle : 0.566 12.022 45678 Z= 0.275 Chirality : 0.041 0.307 4875 Planarity : 0.004 0.058 5715 Dihedral : 10.472 89.943 5214 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.05 % Allowed : 13.02 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.14), residues: 3943 helix: 1.97 (0.11), residues: 2202 sheet: -0.22 (0.29), residues: 324 loop : -0.99 (0.18), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 266 TYR 0.017 0.001 TYR T 52 PHE 0.033 0.001 PHE Q 120 TRP 0.016 0.001 TRP P 273 HIS 0.003 0.001 HIS V 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (33730) covalent geometry : angle 0.56545 / 0.27 (45668) SS BOND : bond 0.00422 / 0.24 ( 5) SS BOND : angle 1.95381 / 1.75 ( 10) hydrogen bonds : bond 0.04042 / 2.73 ( 1876) hydrogen bonds : angle 4.31798 / 3.09 ( 5439) metal coordination : bond 0.00070 / 0.03 ( 4) Misc. bond : bond 0.16918 / 14.38 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 289 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8822 (mmm) cc_final: 0.8441 (mmm) REVERT: C 156 LEU cc_start: 0.8452 (mp) cc_final: 0.8226 (tt) REVERT: C 210 TYR cc_start: 0.7638 (OUTLIER) cc_final: 0.6831 (t80) REVERT: C 315 LYS cc_start: 0.7221 (mmtt) cc_final: 0.6518 (mmtt) REVERT: F 30 LYS cc_start: 0.8434 (mtpt) cc_final: 0.8144 (ttpt) REVERT: G 64 GLU cc_start: 0.8712 (tp30) cc_final: 0.8222 (tp30) REVERT: H 7 VAL cc_start: 0.7208 (p) cc_final: 0.6788 (t) REVERT: H 11 ARG cc_start: 0.7788 (ptt180) cc_final: 0.7432 (ptt180) REVERT: H 14 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7656 (tm-30) REVERT: H 15 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8002 (mm-30) REVERT: H 69 LYS cc_start: 0.8198 (tttp) cc_final: 0.7980 (ptpt) REVERT: J 22 ARG cc_start: 0.8105 (mtm110) cc_final: 0.7776 (mtp85) REVERT: M 153 ARG cc_start: 0.8815 (ttp-110) cc_final: 0.8462 (ptm-80) REVERT: O 145 MET cc_start: 0.8651 (tpp) cc_final: 0.8267 (mpp) REVERT: P 210 GLU cc_start: 0.8282 (tp30) cc_final: 0.7751 (pt0) REVERT: P 225 MET cc_start: 0.9247 (ttp) cc_final: 0.8974 (ttp) REVERT: S 66 GLU cc_start: 0.8397 (tt0) cc_final: 0.7947 (tp30) REVERT: T 32 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7759 (mp) outliers start: 35 outliers final: 29 residues processed: 314 average time/residue: 0.2209 time to fit residues: 112.9206 Evaluate side-chains 309 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 278 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 210 TYR Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain G residue 35 HIS Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain M residue 383 GLU Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain N residue 309 VAL Chi-restraints excluded: chain N residue 378 THR Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain V residue 21 MET Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 194 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 304 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 chunk 250 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 241 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.080284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.062708 restraints weight = 77800.091| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.17 r_work: 0.2816 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.336 33749 Z= 0.201 Angle : 0.649 17.899 45678 Z= 0.313 Chirality : 0.044 0.288 4875 Planarity : 0.004 0.060 5715 Dihedral : 10.805 89.267 5214 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.07 % Allowed : 13.32 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.14), residues: 3943 helix: 1.77 (0.11), residues: 2212 sheet: -0.48 (0.27), residues: 360 loop : -0.99 (0.18), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 119 TYR 0.021 0.001 TYR T 52 PHE 0.032 0.002 PHE Q 120 TRP 0.017 0.001 TRP T 53 HIS 0.007 0.001 HIS O 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 (33730) covalent geometry : angle 0.64784 / 0.31 (45668) SS BOND : bond 0.00547 / 0.26 ( 5) SS BOND : angle 2.60720 / 1.61 ( 10) hydrogen bonds : bond 0.05098 / 3.42 ( 1876) hydrogen bonds : angle 4.48835 / 3.21 ( 5439) metal coordination : bond 0.00369 / 0.14 ( 4) Misc. bond : bond 0.18805 / 16.53 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 281 time to evaluate : 1.418 Fit side-chains REVERT: C 315 LYS cc_start: 0.7340 (mmtt) cc_final: 0.6657 (mmtt) REVERT: G 64 GLU cc_start: 0.8754 (tp30) cc_final: 0.8244 (tp30) REVERT: H 7 VAL cc_start: 0.7067 (p) cc_final: 0.6692 (t) REVERT: H 11 ARG cc_start: 0.7784 (ptt180) cc_final: 0.7416 (ptt180) REVERT: H 14 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7565 (tm-30) REVERT: H 15 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7949 (mm-30) REVERT: H 51 ASP cc_start: 0.8675 (m-30) cc_final: 0.8129 (m-30) REVERT: M 48 MET cc_start: 0.8299 (mmp) cc_final: 0.8078 (mmp) REVERT: P 225 MET cc_start: 0.9323 (ttp) cc_final: 0.9009 (ttp) REVERT: S 66 GLU cc_start: 0.8383 (tt0) cc_final: 0.7956 (tp30) REVERT: T 20 LYS cc_start: 0.8281 (tptm) cc_final: 0.7834 (tttt) REVERT: T 32 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7772 (mp) REVERT: V 47 HIS cc_start: 0.8154 (t70) cc_final: 0.7859 (t70) outliers start: 36 outliers final: 30 residues processed: 308 average time/residue: 0.2037 time to fit residues: 100.9940 Evaluate side-chains 305 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 274 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain G residue 35 HIS Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain M residue 383 GLU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain N residue 378 THR Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain V residue 21 MET Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 269 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 249 optimal weight: 5.9990 chunk 306 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 364 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 332 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.079364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.061775 restraints weight = 77776.816| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.17 r_work: 0.2795 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.348 33749 Z= 0.223 Angle : 0.662 17.712 45678 Z= 0.322 Chirality : 0.044 0.280 4875 Planarity : 0.005 0.062 5715 Dihedral : 11.096 86.780 5214 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.02 % Allowed : 13.41 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.14), residues: 3943 helix: 1.67 (0.11), residues: 2194 sheet: -0.51 (0.28), residues: 360 loop : -1.05 (0.18), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 153 TYR 0.019 0.002 TYR T 52 PHE 0.032 0.002 PHE Q 120 TRP 0.017 0.001 TRP C 249 HIS 0.006 0.001 HIS O 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.22 (33730) covalent geometry : angle 0.66143 / 0.32 (45668) SS BOND : bond 0.00593 / 0.26 ( 5) SS BOND : angle 2.33799 / 1.96 ( 10) hydrogen bonds : bond 0.05388 / 3.61 ( 1876) hydrogen bonds : angle 4.60159 / 3.29 ( 5439) metal coordination : bond 0.00393 / 0.16 ( 4) Misc. bond : bond 0.19801 / 17.16 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7874.43 seconds wall clock time: 136 minutes 1.40 seconds (8161.40 seconds total)