Starting phenix.real_space_refine on Sun Feb 18 08:59:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k15_9905/02_2024/6k15_9905.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k15_9905/02_2024/6k15_9905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k15_9905/02_2024/6k15_9905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k15_9905/02_2024/6k15_9905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k15_9905/02_2024/6k15_9905.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k15_9905/02_2024/6k15_9905.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 84 5.16 5 C 13701 2.51 5 N 3632 2.21 5 O 4068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 338": "NH1" <-> "NH2" Residue "F ARG 350": "NH1" <-> "NH2" Residue "F ARG 372": "NH1" <-> "NH2" Residue "F ARG 373": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 144": "NH1" <-> "NH2" Residue "H ARG 173": "NH1" <-> "NH2" Residue "H ARG 249": "NH1" <-> "NH2" Residue "H ARG 252": "NH1" <-> "NH2" Residue "H PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 84": "NH1" <-> "NH2" Residue "M ARG 136": "NH1" <-> "NH2" Residue "M ARG 268": "NH1" <-> "NH2" Residue "M ARG 272": "NH1" <-> "NH2" Residue "I TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 51": "NH1" <-> "NH2" Residue "I ARG 400": "NH1" <-> "NH2" Residue "I ARG 468": "NH1" <-> "NH2" Residue "G TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 309": "NH1" <-> "NH2" Residue "G ARG 366": "NH1" <-> "NH2" Residue "G ARG 379": "NH1" <-> "NH2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 430": "NH1" <-> "NH2" Residue "A TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "J ARG 88": "NH1" <-> "NH2" Residue "J TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 202": "NH1" <-> "NH2" Residue "J ARG 258": "NH1" <-> "NH2" Residue "J TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 277": "NH1" <-> "NH2" Residue "J ARG 292": "NH1" <-> "NH2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "X PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 605": "NH1" <-> "NH2" Residue "L ARG 764": "NH1" <-> "NH2" Residue "L ARG 793": "NH1" <-> "NH2" Residue "L PHE 864": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21486 Number of models: 1 Model: "" Number of chains: 14 Chain: "F" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 964 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "H" Number of atoms: 3215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3215 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 13, 'TRANS': 379} Chain breaks: 2 Chain: "D" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2510 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain breaks: 4 Chain: "M" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3058 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1944 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain breaks: 3 Chain: "G" Number of atoms: 1991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1991 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 233} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 3007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 3007 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 22, 'TRANS': 342} Chain breaks: 3 Chain: "J" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1814 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 29 Chain: "E" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 477 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "C" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 269 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "K" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 347 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain: "X" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1220 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 5, 'TRANS': 141} Chain breaks: 3 Chain: "L" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 669 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 7, 'TRANS': 77} Chain breaks: 2 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2484 SG CYS H 260 64.277 108.986 63.012 1.00 83.94 S ATOM 2507 SG CYS H 263 61.868 110.525 60.797 1.00 89.19 S ATOM 2693 SG CYS H 286 64.537 113.050 62.273 1.00 78.89 S Time building chain proxies: 11.65, per 1000 atoms: 0.54 Number of scatterers: 21486 At special positions: 0 Unit cell: (136.96, 170.13, 177.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 84 16.00 O 4068 8.00 N 3632 7.00 C 13701 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.71 Conformation dependent library (CDL) restraints added in 4.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 286 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 263 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 260 " 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5154 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 16 sheets defined 50.9% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'F' and resid 319 through 343 removed outlier: 3.831A pdb=" N LYS F 340 " --> pdb=" O TYR F 336 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL F 341 " --> pdb=" O ASP F 337 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU F 342 " --> pdb=" O ARG F 338 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU F 343 " --> pdb=" O VAL F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 364 No H-bonds generated for 'chain 'F' and resid 362 through 364' Processing helix chain 'F' and resid 416 through 430 Processing helix chain 'H' and resid 58 through 71 Processing helix chain 'H' and resid 85 through 87 No H-bonds generated for 'chain 'H' and resid 85 through 87' Processing helix chain 'H' and resid 95 through 102 Processing helix chain 'H' and resid 103 through 106 Processing helix chain 'H' and resid 114 through 131 removed outlier: 3.526A pdb=" N LEU H 131 " --> pdb=" O ASN H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 144 removed outlier: 3.670A pdb=" N VAL H 142 " --> pdb=" O THR H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 163 Processing helix chain 'H' and resid 171 through 175 removed outlier: 3.782A pdb=" N LYS H 175 " --> pdb=" O PRO H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 242 Processing helix chain 'H' and resid 247 through 251 removed outlier: 3.849A pdb=" N ASN H 250 " --> pdb=" O GLU H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 289 removed outlier: 3.562A pdb=" N PHE H 287 " --> pdb=" O CYS H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 331 Processing helix chain 'H' and resid 333 through 342 removed outlier: 3.993A pdb=" N HIS H 340 " --> pdb=" O LYS H 336 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY H 342 " --> pdb=" O ALA H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 356 removed outlier: 4.059A pdb=" N GLU H 352 " --> pdb=" O GLU H 348 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 360 through 368 Processing helix chain 'H' and resid 388 through 401 Processing helix chain 'H' and resid 403 through 405 No H-bonds generated for 'chain 'H' and resid 403 through 405' Processing helix chain 'H' and resid 406 through 483 removed outlier: 4.144A pdb=" N LYS H 413 " --> pdb=" O LYS H 409 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE H 417 " --> pdb=" O LYS H 413 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU H 419 " --> pdb=" O ARG H 415 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA H 427 " --> pdb=" O GLU H 423 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU H 431 " --> pdb=" O ALA H 427 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS H 434 " --> pdb=" O GLN H 430 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET H 437 " --> pdb=" O VAL H 433 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU H 438 " --> pdb=" O LYS H 434 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS H 439 " --> pdb=" O LEU H 435 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS H 446 " --> pdb=" O SER H 442 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP H 449 " --> pdb=" O THR H 445 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU H 450 " --> pdb=" O LYS H 446 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR H 452 " --> pdb=" O CYS H 448 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU H 455 " --> pdb=" O GLU H 451 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL H 462 " --> pdb=" O LYS H 458 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS H 467 " --> pdb=" O LYS H 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 76 removed outlier: 4.136A pdb=" N PHE D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN D 76 " --> pdb=" O PHE D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 95 through 102 removed outlier: 3.855A pdb=" N ASN D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 106 Processing helix chain 'D' and resid 114 through 131 removed outlier: 3.648A pdb=" N TYR D 118 " --> pdb=" O THR D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 144 removed outlier: 3.668A pdb=" N VAL D 142 " --> pdb=" O THR D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 163 removed outlier: 4.085A pdb=" N LYS D 155 " --> pdb=" O ALA D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 331 removed outlier: 3.542A pdb=" N MET D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU D 331 " --> pdb=" O ILE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 341 Processing helix chain 'D' and resid 346 through 355 Processing helix chain 'D' and resid 360 through 368 removed outlier: 3.918A pdb=" N GLU D 366 " --> pdb=" O ASN D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 399 removed outlier: 4.480A pdb=" N ASP D 395 " --> pdb=" O GLU D 391 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN D 398 " --> pdb=" O ASN D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 424 removed outlier: 3.616A pdb=" N GLU D 424 " --> pdb=" O LYS D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 483 removed outlier: 3.884A pdb=" N ILE D 428 " --> pdb=" O GLU D 424 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS D 434 " --> pdb=" O GLN D 430 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP D 449 " --> pdb=" O THR D 445 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR D 452 " --> pdb=" O CYS D 448 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN D 453 " --> pdb=" O ASP D 449 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU D 457 " --> pdb=" O GLN D 453 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU D 464 " --> pdb=" O LYS D 460 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS D 467 " --> pdb=" O LYS D 463 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER D 476 " --> pdb=" O ARG D 472 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP D 481 " --> pdb=" O LYS D 477 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU D 482 " --> pdb=" O GLN D 478 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 47 removed outlier: 3.814A pdb=" N SER M 44 " --> pdb=" O SER M 40 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY M 46 " --> pdb=" O LEU M 42 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL M 47 " --> pdb=" O GLN M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 70 removed outlier: 3.534A pdb=" N GLN M 69 " --> pdb=" O ASN M 66 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER M 70 " --> pdb=" O VAL M 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 66 through 70' Processing helix chain 'M' and resid 80 through 91 removed outlier: 3.548A pdb=" N LEU M 89 " --> pdb=" O MET M 85 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU M 90 " --> pdb=" O GLU M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 93 through 111 Processing helix chain 'M' and resid 112 through 116 Processing helix chain 'M' and resid 123 through 132 removed outlier: 4.433A pdb=" N PHE M 130 " --> pdb=" O LEU M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 141 removed outlier: 4.162A pdb=" N ILE M 137 " --> pdb=" O PRO M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 168 removed outlier: 3.663A pdb=" N SER M 154 " --> pdb=" O LYS M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 181 Processing helix chain 'M' and resid 183 through 201 removed outlier: 3.551A pdb=" N GLY M 201 " --> pdb=" O CYS M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 208 through 210 No H-bonds generated for 'chain 'M' and resid 208 through 210' Processing helix chain 'M' and resid 211 through 230 removed outlier: 4.165A pdb=" N GLU M 217 " --> pdb=" O THR M 213 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU M 218 " --> pdb=" O PHE M 214 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR M 221 " --> pdb=" O GLU M 217 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR M 222 " --> pdb=" O LEU M 218 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU M 223 " --> pdb=" O THR M 219 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP M 224 " --> pdb=" O HIS M 220 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU M 225 " --> pdb=" O TYR M 221 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA M 228 " --> pdb=" O ASP M 224 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER M 230 " --> pdb=" O MET M 226 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 233 No H-bonds generated for 'chain 'M' and resid 231 through 233' Processing helix chain 'M' and resid 240 through 250 removed outlier: 3.714A pdb=" N GLN M 244 " --> pdb=" O ASP M 240 " (cutoff:3.500A) Processing helix chain 'M' and resid 255 through 270 removed outlier: 3.741A pdb=" N LEU M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) Processing helix chain 'M' and resid 278 through 282 Processing helix chain 'M' and resid 288 through 293 removed outlier: 3.609A pdb=" N VAL M 293 " --> pdb=" O LEU M 289 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 298 removed outlier: 3.512A pdb=" N LEU M 298 " --> pdb=" O PHE M 295 " (cutoff:3.500A) Processing helix chain 'M' and resid 302 through 317 Processing helix chain 'M' and resid 322 through 327 Processing helix chain 'M' and resid 331 through 340 removed outlier: 3.601A pdb=" N ILE M 335 " --> pdb=" O GLU M 331 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU M 336 " --> pdb=" O CYS M 332 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU M 337 " --> pdb=" O SER M 333 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA M 338 " --> pdb=" O LEU M 334 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU M 340 " --> pdb=" O LEU M 336 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 358 Processing helix chain 'M' and resid 524 through 538 removed outlier: 3.944A pdb=" N LYS M 528 " --> pdb=" O SER M 524 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL M 529 " --> pdb=" O ASP M 525 " (cutoff:3.500A) Processing helix chain 'M' and resid 545 through 551 Processing helix chain 'M' and resid 553 through 562 removed outlier: 4.282A pdb=" N HIS M 559 " --> pdb=" O PRO M 555 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS M 560 " --> pdb=" O LEU M 556 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA M 562 " --> pdb=" O LEU M 558 " (cutoff:3.500A) Processing helix chain 'M' and resid 565 through 570 removed outlier: 4.164A pdb=" N LEU M 569 " --> pdb=" O PRO M 565 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA M 570 " --> pdb=" O PRO M 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 565 through 570' Processing helix chain 'M' and resid 572 through 578 Processing helix chain 'I' and resid 29 through 54 Processing helix chain 'I' and resid 235 through 243 Processing helix chain 'I' and resid 249 through 263 Processing helix chain 'I' and resid 316 through 324 Processing helix chain 'I' and resid 331 through 342 removed outlier: 3.614A pdb=" N VAL I 339 " --> pdb=" O VAL I 335 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN I 340 " --> pdb=" O VAL I 336 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS I 341 " --> pdb=" O GLN I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 425 removed outlier: 3.728A pdb=" N PHE I 419 " --> pdb=" O LYS I 415 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS I 425 " --> pdb=" O GLU I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 426 through 445 removed outlier: 4.333A pdb=" N HIS I 432 " --> pdb=" O GLU I 428 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS I 438 " --> pdb=" O LEU I 434 " (cutoff:3.500A) Processing helix chain 'I' and resid 473 through 478 removed outlier: 3.575A pdb=" N TYR I 478 " --> pdb=" O ILE I 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 161 through 168 Processing helix chain 'G' and resid 171 through 177 Processing helix chain 'G' and resid 231 through 243 removed outlier: 3.509A pdb=" N LYS G 241 " --> pdb=" O SER G 237 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU G 243 " --> pdb=" O TYR G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 264 Processing helix chain 'G' and resid 306 through 319 removed outlier: 3.567A pdb=" N ASP G 317 " --> pdb=" O SER G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 345 removed outlier: 3.892A pdb=" N LEU G 327 " --> pdb=" O GLU G 323 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER G 329 " --> pdb=" O ILE G 325 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU G 334 " --> pdb=" O GLN G 330 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR G 335 " --> pdb=" O SER G 331 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS G 341 " --> pdb=" O LEU G 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 24 removed outlier: 3.828A pdb=" N VAL A 15 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL A 17 " --> pdb=" O PHE A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 75 through 82 removed outlier: 4.011A pdb=" N PHE A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 110 removed outlier: 4.605A pdb=" N LEU A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 133 removed outlier: 3.578A pdb=" N GLN A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 180 removed outlier: 3.819A pdb=" N TYR A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 removed outlier: 3.516A pdb=" N ARG A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 395 removed outlier: 3.947A pdb=" N ASN A 395 " --> pdb=" O GLN A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 412 removed outlier: 3.951A pdb=" N ASN A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 removed outlier: 3.527A pdb=" N SER A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS A 425 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 463 removed outlier: 4.037A pdb=" N LYS A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 14 removed outlier: 4.459A pdb=" N MET J 9 " --> pdb=" O GLN J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 24 removed outlier: 3.631A pdb=" N LEU J 23 " --> pdb=" O VAL J 20 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA J 24 " --> pdb=" O ALA J 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 20 through 24' Processing helix chain 'J' and resid 56 through 66 Processing helix chain 'J' and resid 75 through 101 removed outlier: 3.538A pdb=" N ILE J 79 " --> pdb=" O GLU J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 127 removed outlier: 4.256A pdb=" N LYS J 117 " --> pdb=" O ASP J 113 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS J 127 " --> pdb=" O GLN J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 197 removed outlier: 3.802A pdb=" N ILE J 193 " --> pdb=" O PRO J 189 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG J 194 " --> pdb=" O ASP J 190 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE J 195 " --> pdb=" O THR J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 207 Processing helix chain 'J' and resid 239 through 248 removed outlier: 3.673A pdb=" N GLU J 244 " --> pdb=" O LYS J 240 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU J 245 " --> pdb=" O ALA J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 266 removed outlier: 3.524A pdb=" N GLN J 254 " --> pdb=" O LEU J 250 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N SER J 256 " --> pdb=" O THR J 252 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS J 260 " --> pdb=" O SER J 256 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN J 264 " --> pdb=" O LYS J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 290 removed outlier: 3.522A pdb=" N ALA J 283 " --> pdb=" O SER J 279 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN J 290 " --> pdb=" O GLN J 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 37 removed outlier: 3.677A pdb=" N ASN E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 removed outlier: 3.523A pdb=" N HIS E 49 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 72 Processing helix chain 'C' and resid 204 through 226 removed outlier: 3.861A pdb=" N ASN C 218 " --> pdb=" O ASP C 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 176 removed outlier: 3.552A pdb=" N GLU K 176 " --> pdb=" O THR K 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 173 through 176' Processing helix chain 'K' and resid 177 through 194 removed outlier: 4.165A pdb=" N GLU K 191 " --> pdb=" O GLY K 187 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU K 194 " --> pdb=" O LEU K 190 " (cutoff:3.500A) Processing helix chain 'X' and resid 365 through 369 Processing helix chain 'X' and resid 381 through 390 removed outlier: 3.859A pdb=" N LYS X 385 " --> pdb=" O PRO X 381 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE X 388 " --> pdb=" O PHE X 384 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS X 390 " --> pdb=" O LYS X 386 " (cutoff:3.500A) Processing helix chain 'X' and resid 489 through 491 No H-bonds generated for 'chain 'X' and resid 489 through 491' Processing helix chain 'L' and resid 863 through 867 removed outlier: 3.860A pdb=" N GLY L 867 " --> pdb=" O PHE L 864 " (cutoff:3.500A) Processing helix chain 'L' and resid 871 through 883 removed outlier: 3.600A pdb=" N THR L 875 " --> pdb=" O SER L 871 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG L 883 " --> pdb=" O LEU L 879 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 359 through 360 Processing sheet with id=AA2, first strand: chain 'H' and resid 186 through 190 Processing sheet with id=AA3, first strand: chain 'H' and resid 80 through 83 removed outlier: 6.334A pdb=" N VAL H 80 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP D 192 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE H 82 " --> pdb=" O ASP D 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'H' and resid 270 through 274 Processing sheet with id=AA5, first strand: chain 'M' and resid 35 through 36 Processing sheet with id=AA6, first strand: chain 'I' and resid 8 through 9 Processing sheet with id=AA7, first strand: chain 'I' and resid 219 through 222 removed outlier: 3.516A pdb=" N ILE I 222 " --> pdb=" O ILE I 349 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE I 349 " --> pdb=" O ILE I 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 233 through 234 Processing sheet with id=AA9, first strand: chain 'G' and resid 203 through 212 removed outlier: 3.717A pdb=" N HIS G 215 " --> pdb=" O HIS G 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 279 through 285 removed outlier: 3.521A pdb=" N GLU G 293 " --> pdb=" O ARG G 379 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 188 through 189 removed outlier: 3.618A pdb=" N VAL A 189 " --> pdb=" O GLN X 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 192 through 196 removed outlier: 4.253A pdb=" N SER A 192 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE A 228 " --> pdb=" O ALA X 497 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N SER X 499 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASN A 230 " --> pdb=" O SER X 499 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N MET X 501 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE X 498 " --> pdb=" O TRP X 620 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASN X 622 " --> pdb=" O PHE X 498 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE X 500 " --> pdb=" O ASN X 622 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG X 605 " --> pdb=" O LEU X 525 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU X 525 " --> pdb=" O ARG X 605 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 478 through 479 Processing sheet with id=AB5, first strand: chain 'C' and resid 198 through 200 Processing sheet with id=AB6, first strand: chain 'X' and resid 443 through 444 removed outlier: 3.537A pdb=" N SER X 513 " --> pdb=" O GLU X 589 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU X 589 " --> pdb=" O SER X 513 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 508 through 510 851 hydrogen bonds defined for protein. 2445 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.86 Time building geometry restraints manager: 8.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6811 1.34 - 1.46: 3479 1.46 - 1.57: 11455 1.57 - 1.69: 0 1.69 - 1.81: 137 Bond restraints: 21882 Sorted by residual: bond pdb=" C ILE G 325 " pdb=" N PRO G 326 " ideal model delta sigma weight residual 1.336 1.383 -0.047 1.20e-02 6.94e+03 1.57e+01 bond pdb=" N GLU X 439 " pdb=" CA GLU X 439 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.82e+00 bond pdb=" N ILE A 237 " pdb=" CA ILE A 237 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.27e-02 6.20e+03 7.49e+00 bond pdb=" N GLN X 440 " pdb=" CA GLN X 440 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.45e+00 bond pdb=" N THR A 235 " pdb=" CA THR A 235 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.20e-02 6.94e+03 6.26e+00 ... (remaining 21877 not shown) Histogram of bond angle deviations from ideal: 96.23 - 103.80: 292 103.80 - 111.38: 8747 111.38 - 118.95: 9064 118.95 - 126.52: 11190 126.52 - 134.10: 290 Bond angle restraints: 29583 Sorted by residual: angle pdb=" N PRO J 17 " pdb=" CA PRO J 17 " pdb=" CB PRO J 17 " ideal model delta sigma weight residual 103.25 110.26 -7.01 1.05e+00 9.07e-01 4.45e+01 angle pdb=" N LYS G 338 " pdb=" CA LYS G 338 " pdb=" C LYS G 338 " ideal model delta sigma weight residual 112.04 102.54 9.50 1.44e+00 4.82e-01 4.35e+01 angle pdb=" N ILE M 553 " pdb=" CA ILE M 553 " pdb=" C ILE M 553 " ideal model delta sigma weight residual 113.53 107.52 6.01 9.80e-01 1.04e+00 3.76e+01 angle pdb=" C HIS H 261 " pdb=" N THR H 262 " pdb=" CA THR H 262 " ideal model delta sigma weight residual 121.54 131.77 -10.23 1.91e+00 2.74e-01 2.87e+01 angle pdb=" N LYS G 340 " pdb=" CA LYS G 340 " pdb=" C LYS G 340 " ideal model delta sigma weight residual 111.28 105.88 5.40 1.09e+00 8.42e-01 2.45e+01 ... (remaining 29578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 12742 15.98 - 31.95: 531 31.95 - 47.93: 137 47.93 - 63.90: 8 63.90 - 79.88: 13 Dihedral angle restraints: 13431 sinusoidal: 5563 harmonic: 7868 Sorted by residual: dihedral pdb=" CA THR H 452 " pdb=" C THR H 452 " pdb=" N GLN H 453 " pdb=" CA GLN H 453 " ideal model delta harmonic sigma weight residual -180.00 -151.98 -28.02 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA GLU H 464 " pdb=" C GLU H 464 " pdb=" N SER H 465 " pdb=" CA SER H 465 " ideal model delta harmonic sigma weight residual -180.00 -152.74 -27.26 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA SER G 275 " pdb=" C SER G 275 " pdb=" N ASP G 276 " pdb=" CA ASP G 276 " ideal model delta harmonic sigma weight residual 180.00 153.93 26.07 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 13428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2607 0.060 - 0.119: 661 0.119 - 0.179: 93 0.179 - 0.239: 15 0.239 - 0.298: 5 Chirality restraints: 3381 Sorted by residual: chirality pdb=" CA ILE A 237 " pdb=" N ILE A 237 " pdb=" C ILE A 237 " pdb=" CB ILE A 237 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE M 115 " pdb=" CA ILE M 115 " pdb=" CG1 ILE M 115 " pdb=" CG2 ILE M 115 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA PRO J 17 " pdb=" N PRO J 17 " pdb=" C PRO J 17 " pdb=" CB PRO J 17 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 3378 not shown) Planarity restraints: 3775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 256 " -0.063 5.00e-02 4.00e+02 9.63e-02 1.48e+01 pdb=" N PRO A 257 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 257 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 257 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 270 " -0.060 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO A 271 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY L 862 " -0.048 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO L 863 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO L 863 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO L 863 " -0.040 5.00e-02 4.00e+02 ... (remaining 3772 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 11 2.29 - 2.94: 8647 2.94 - 3.60: 29652 3.60 - 4.25: 45812 4.25 - 4.90: 76680 Nonbonded interactions: 160802 Sorted by model distance: nonbonded pdb=" OE1 GLU X 439 " pdb=" CG GLU X 490 " model vdw 1.639 3.440 nonbonded pdb=" OE2 GLU A 238 " pdb=" ND2 ASN J 212 " model vdw 1.706 2.520 nonbonded pdb=" OE1 GLU X 439 " pdb=" CD GLU X 490 " model vdw 2.087 3.270 nonbonded pdb=" CD GLU A 238 " pdb=" ND2 ASN J 212 " model vdw 2.182 3.350 nonbonded pdb=" OG SER D 316 " pdb=" OE1 GLU D 319 " model vdw 2.225 2.440 ... (remaining 160797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.890 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: 0.020 Extract box with map and model: 10.530 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 58.560 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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 : 0.005 0.071 21882 Z= 0.317 Angle : 0.959 12.252 29583 Z= 0.531 Chirality : 0.054 0.298 3381 Planarity : 0.007 0.096 3775 Dihedral : 10.227 79.881 8277 Min Nonbonded Distance : 1.639 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.60 % Favored : 91.32 % Rotamer: Outliers : 0.33 % Allowed : 3.17 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.13), residues: 2581 helix: -2.49 (0.11), residues: 1286 sheet: -3.31 (0.34), residues: 150 loop : -3.00 (0.16), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP F 371 HIS 0.013 0.002 HIS A 270 PHE 0.034 0.002 PHE J 83 TYR 0.026 0.002 TYR F 410 ARG 0.013 0.001 ARG F 338 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 658 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8121 (mmm160) cc_final: 0.7881 (ttm170) REVERT: F 395 LEU cc_start: 0.8091 (tp) cc_final: 0.7722 (tt) REVERT: F 409 ILE cc_start: 0.8925 (mm) cc_final: 0.8650 (mt) REVERT: H 349 ASP cc_start: 0.8325 (t70) cc_final: 0.7654 (t0) REVERT: D 94 ILE cc_start: 0.7582 (pp) cc_final: 0.7274 (pt) REVERT: D 226 VAL cc_start: 0.7957 (t) cc_final: 0.7449 (m) REVERT: D 438 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8205 (mt-10) REVERT: M 150 LYS cc_start: 0.8616 (tmtp) cc_final: 0.8036 (tptm) REVERT: I 36 LEU cc_start: 0.9219 (mt) cc_final: 0.8980 (mt) REVERT: I 415 LYS cc_start: 0.8831 (mttt) cc_final: 0.8591 (mtpt) REVERT: I 456 ARG cc_start: 0.8714 (mtp85) cc_final: 0.8116 (mtp85) REVERT: G 29 ILE cc_start: 0.7934 (mm) cc_final: 0.7711 (mm) REVERT: G 259 LYS cc_start: 0.8287 (mptm) cc_final: 0.8047 (tptp) REVERT: G 263 LYS cc_start: 0.7992 (tttt) cc_final: 0.7548 (ttpt) REVERT: G 291 PHE cc_start: 0.7745 (m-80) cc_final: 0.7510 (m-10) REVERT: A 470 ILE cc_start: 0.7494 (mt) cc_final: 0.7180 (pt) REVERT: J 100 LEU cc_start: 0.8640 (tm) cc_final: 0.8381 (tp) REVERT: J 223 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7587 (mt-10) REVERT: E 50 ASN cc_start: 0.8409 (t0) cc_final: 0.8071 (t0) REVERT: E 67 LYS cc_start: 0.8628 (tmmm) cc_final: 0.8372 (mmmt) REVERT: C 217 LYS cc_start: 0.6989 (mttt) cc_final: 0.6664 (mtmt) REVERT: K 186 LYS cc_start: 0.7266 (mttt) cc_final: 0.6765 (mmtp) REVERT: X 532 PRO cc_start: 0.7041 (Cg_endo) cc_final: 0.6607 (Cg_exo) REVERT: X 605 ARG cc_start: 0.7170 (ptm160) cc_final: 0.6962 (ptm160) REVERT: L 757 LYS cc_start: 0.8631 (mttp) cc_final: 0.8261 (mtmm) REVERT: L 860 LEU cc_start: 0.7920 (pt) cc_final: 0.7221 (pt) outliers start: 8 outliers final: 2 residues processed: 665 average time/residue: 0.3802 time to fit residues: 368.7220 Evaluate side-chains 310 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 308 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain X residue 438 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 0.1980 chunk 196 optimal weight: 0.3980 chunk 108 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 203 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 123 optimal weight: 0.0870 chunk 151 optimal weight: 2.9990 chunk 235 optimal weight: 0.0770 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN ** F 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 ASN H 167 ASN H 195 GLN H 239 GLN H 250 ASN H 281 ASN H 314 ASN H 318 GLN H 470 ASN D 145 ASN D 167 ASN M 359 HIS I 245 GLN I 432 HIS I 463 ASN I 464 ASN I 465 ASN G 158 GLN G 352 HIS A 112 GLN ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN A 471 ASN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN J 123 GLN J 259 GLN J 263 ASN E 23 ASN K 160 GLN K 174 GLN X 380 ASN X 493 GLN X 494 ASN X 600 ASN L 800 ASN L 810 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21882 Z= 0.154 Angle : 0.605 10.259 29583 Z= 0.312 Chirality : 0.042 0.186 3381 Planarity : 0.005 0.070 3775 Dihedral : 5.305 40.408 2837 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.85 % Allowed : 10.37 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.15), residues: 2581 helix: -0.70 (0.14), residues: 1291 sheet: -2.86 (0.36), residues: 147 loop : -2.66 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 334 HIS 0.006 0.001 HIS A 270 PHE 0.016 0.001 PHE L 864 TYR 0.026 0.001 TYR X 368 ARG 0.010 0.001 ARG L 764 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 380 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8178 (mmm160) cc_final: 0.7791 (ttm170) REVERT: H 328 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7307 (mt-10) REVERT: H 349 ASP cc_start: 0.8214 (t70) cc_final: 0.7851 (t0) REVERT: H 390 MET cc_start: 0.7344 (mpp) cc_final: 0.6676 (mmt) REVERT: H 468 MET cc_start: 0.8653 (tpp) cc_final: 0.8292 (tpp) REVERT: D 94 ILE cc_start: 0.7430 (pp) cc_final: 0.7168 (pt) REVERT: D 420 LYS cc_start: 0.6406 (tmtm) cc_final: 0.6127 (mptt) REVERT: D 437 MET cc_start: 0.7719 (tmm) cc_final: 0.7435 (ppp) REVERT: D 438 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7929 (mm-30) REVERT: G 259 LYS cc_start: 0.8363 (mptm) cc_final: 0.7969 (tptp) REVERT: G 263 LYS cc_start: 0.8080 (tttt) cc_final: 0.7598 (ttpt) REVERT: G 330 GLN cc_start: 0.8278 (mt0) cc_final: 0.7989 (mt0) REVERT: A 101 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7331 (mt) REVERT: A 258 THR cc_start: 0.7259 (OUTLIER) cc_final: 0.6885 (p) REVERT: A 269 LEU cc_start: 0.8822 (mm) cc_final: 0.8622 (mt) REVERT: J 46 ILE cc_start: 0.4597 (OUTLIER) cc_final: 0.4261 (pt) REVERT: E 50 ASN cc_start: 0.8236 (t0) cc_final: 0.7635 (m110) REVERT: C 217 LYS cc_start: 0.7010 (mttt) cc_final: 0.6627 (mtmt) REVERT: K 174 GLN cc_start: 0.8332 (tt0) cc_final: 0.8026 (tm-30) REVERT: K 186 LYS cc_start: 0.7206 (mttt) cc_final: 0.6826 (mmtt) REVERT: X 435 GLN cc_start: 0.8467 (pm20) cc_final: 0.8171 (pm20) REVERT: X 440 GLN cc_start: 0.6760 (OUTLIER) cc_final: 0.6487 (mt0) REVERT: X 481 TRP cc_start: 0.7784 (m-90) cc_final: 0.7533 (m-10) REVERT: L 757 LYS cc_start: 0.8431 (mttp) cc_final: 0.7879 (tptt) outliers start: 45 outliers final: 19 residues processed: 412 average time/residue: 0.3597 time to fit residues: 231.8798 Evaluate side-chains 298 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 275 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain H residue 239 GLN Chi-restraints excluded: chain H residue 257 VAL Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 215 HIS Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 196 THR Chi-restraints excluded: chain X residue 438 SER Chi-restraints excluded: chain X residue 440 GLN Chi-restraints excluded: chain X residue 485 ILE Chi-restraints excluded: chain X residue 507 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 195 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 chunk 254 optimal weight: 3.9990 chunk 209 optimal weight: 0.9990 chunk 233 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 189 optimal weight: 0.6980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 239 GLN ** H 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN D 145 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 480 GLN ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 271 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21882 Z= 0.203 Angle : 0.586 12.705 29583 Z= 0.299 Chirality : 0.042 0.182 3381 Planarity : 0.004 0.060 3775 Dihedral : 4.885 26.768 2836 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 2.76 % Allowed : 12.09 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.16), residues: 2581 helix: 0.12 (0.15), residues: 1288 sheet: -2.69 (0.36), residues: 150 loop : -2.43 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 791 HIS 0.005 0.001 HIS A 270 PHE 0.013 0.001 PHE A 450 TYR 0.018 0.001 TYR H 272 ARG 0.006 0.000 ARG M 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 293 time to evaluate : 2.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8167 (mmm160) cc_final: 0.7762 (ttm170) REVERT: H 349 ASP cc_start: 0.8257 (t70) cc_final: 0.7810 (t0) REVERT: H 468 MET cc_start: 0.8588 (tpp) cc_final: 0.8285 (tpp) REVERT: D 168 TYR cc_start: 0.8484 (t80) cc_final: 0.8091 (t80) REVERT: D 437 MET cc_start: 0.7824 (tmm) cc_final: 0.7580 (ppp) REVERT: D 438 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7978 (mm-30) REVERT: D 456 MET cc_start: 0.8467 (ppp) cc_final: 0.7768 (ppp) REVERT: I 333 MET cc_start: 0.8265 (tmm) cc_final: 0.7811 (tmm) REVERT: G 259 LYS cc_start: 0.8350 (mptm) cc_final: 0.7980 (tptp) REVERT: G 263 LYS cc_start: 0.8056 (tttt) cc_final: 0.7255 (ttpt) REVERT: G 330 GLN cc_start: 0.8191 (mt0) cc_final: 0.7813 (mt0) REVERT: G 379 ARG cc_start: 0.7481 (ptp-170) cc_final: 0.7184 (ptp-170) REVERT: A 132 LEU cc_start: 0.8414 (tp) cc_final: 0.8176 (tp) REVERT: A 258 THR cc_start: 0.7402 (OUTLIER) cc_final: 0.7000 (p) REVERT: J 204 ASN cc_start: 0.8577 (t0) cc_final: 0.8343 (t0) REVERT: E 50 ASN cc_start: 0.8213 (t0) cc_final: 0.7621 (m110) REVERT: E 67 LYS cc_start: 0.8668 (tmtt) cc_final: 0.8240 (mmmm) REVERT: K 174 GLN cc_start: 0.8324 (tt0) cc_final: 0.8089 (tm-30) REVERT: K 186 LYS cc_start: 0.7328 (mttt) cc_final: 0.6999 (mmtt) REVERT: X 435 GLN cc_start: 0.8315 (pm20) cc_final: 0.8009 (pm20) REVERT: X 440 GLN cc_start: 0.6602 (OUTLIER) cc_final: 0.6379 (mt0) REVERT: X 481 TRP cc_start: 0.7684 (m-10) cc_final: 0.7373 (m-10) REVERT: L 757 LYS cc_start: 0.8457 (mttp) cc_final: 0.7909 (tptt) REVERT: L 877 HIS cc_start: 0.7506 (t-90) cc_final: 0.7224 (t-90) outliers start: 67 outliers final: 38 residues processed: 344 average time/residue: 0.3337 time to fit residues: 177.2203 Evaluate side-chains 302 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 262 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 435 LEU Chi-restraints excluded: chain H residue 454 LEU Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 104 TYR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 473 ASN Chi-restraints excluded: chain I residue 483 LEU Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 215 HIS Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 259 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 191 GLU Chi-restraints excluded: chain X residue 440 GLN Chi-restraints excluded: chain X residue 485 ILE Chi-restraints excluded: chain X residue 507 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 236 optimal weight: 7.9990 chunk 250 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 224 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 ASN H 233 ASN H 470 ASN D 145 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 334 ASN G 256 ASN ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 ASN J 254 GLN E 23 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21882 Z= 0.309 Angle : 0.632 15.210 29583 Z= 0.323 Chirality : 0.043 0.204 3381 Planarity : 0.005 0.060 3775 Dihedral : 4.926 24.875 2835 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 3.29 % Allowed : 13.33 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2581 helix: 0.48 (0.15), residues: 1276 sheet: -2.44 (0.39), residues: 130 loop : -2.35 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 791 HIS 0.005 0.001 HIS F 358 PHE 0.016 0.002 PHE G 359 TYR 0.042 0.002 TYR X 368 ARG 0.006 0.001 ARG I 482 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 280 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8134 (mmm160) cc_final: 0.7758 (ttm170) REVERT: F 410 TYR cc_start: 0.6130 (p90) cc_final: 0.5911 (p90) REVERT: H 149 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7324 (p0) REVERT: H 297 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: H 349 ASP cc_start: 0.8273 (t70) cc_final: 0.7821 (t0) REVERT: H 468 MET cc_start: 0.8655 (tpp) cc_final: 0.8392 (tpp) REVERT: D 168 TYR cc_start: 0.8569 (t80) cc_final: 0.8142 (t80) REVERT: D 437 MET cc_start: 0.7804 (tmm) cc_final: 0.7561 (tmm) REVERT: D 438 GLU cc_start: 0.8562 (mt-10) cc_final: 0.7938 (mm-30) REVERT: M 32 MET cc_start: 0.6048 (ttt) cc_final: 0.5722 (ttt) REVERT: I 333 MET cc_start: 0.8413 (tmm) cc_final: 0.7884 (tmm) REVERT: I 471 MET cc_start: 0.8413 (mmm) cc_final: 0.8067 (mmm) REVERT: G 259 LYS cc_start: 0.8402 (mptm) cc_final: 0.8020 (tptp) REVERT: G 263 LYS cc_start: 0.7898 (tttt) cc_final: 0.7414 (ttpt) REVERT: G 330 GLN cc_start: 0.8170 (mt0) cc_final: 0.7751 (mt0) REVERT: A 132 LEU cc_start: 0.8510 (tp) cc_final: 0.8227 (tp) REVERT: A 258 THR cc_start: 0.7410 (OUTLIER) cc_final: 0.6986 (p) REVERT: J 204 ASN cc_start: 0.8608 (t0) cc_final: 0.8385 (t0) REVERT: J 205 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7854 (tm-30) REVERT: E 50 ASN cc_start: 0.8337 (t0) cc_final: 0.7660 (m110) REVERT: K 174 GLN cc_start: 0.8381 (tt0) cc_final: 0.8028 (tm-30) REVERT: K 186 LYS cc_start: 0.7441 (mttt) cc_final: 0.7091 (mmtt) REVERT: X 435 GLN cc_start: 0.8469 (pm20) cc_final: 0.8092 (pm20) REVERT: X 440 GLN cc_start: 0.6585 (OUTLIER) cc_final: 0.6356 (mt0) REVERT: X 481 TRP cc_start: 0.7707 (m-10) cc_final: 0.7324 (m-10) REVERT: L 757 LYS cc_start: 0.8451 (mttp) cc_final: 0.7915 (tptt) REVERT: L 808 ASP cc_start: 0.6449 (t0) cc_final: 0.5955 (t0) REVERT: L 869 ARG cc_start: 0.7961 (mpt-90) cc_final: 0.7458 (mtt180) REVERT: L 877 HIS cc_start: 0.7698 (t-90) cc_final: 0.7417 (t-170) outliers start: 80 outliers final: 56 residues processed: 336 average time/residue: 0.3398 time to fit residues: 176.4371 Evaluate side-chains 316 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 256 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 392 CYS Chi-restraints excluded: chain H residue 435 LEU Chi-restraints excluded: chain H residue 454 LEU Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 64 ASN Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 104 TYR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 224 ASP Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 473 ASN Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 215 HIS Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 285 CYS Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 312 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain J residue 226 THR Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 259 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain X residue 440 GLN Chi-restraints excluded: chain X residue 485 ILE Chi-restraints excluded: chain X residue 507 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 186 optimal weight: 0.0370 chunk 103 optimal weight: 0.6980 chunk 213 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 63 optimal weight: 0.3980 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 470 ASN D 102 ASN D 145 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 GLN ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 HIS A 392 ASN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21882 Z= 0.155 Angle : 0.551 11.138 29583 Z= 0.277 Chirality : 0.041 0.281 3381 Planarity : 0.004 0.058 3775 Dihedral : 4.511 26.715 2835 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.84 % Allowed : 14.64 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.17), residues: 2581 helix: 0.98 (0.15), residues: 1265 sheet: -2.34 (0.39), residues: 146 loop : -2.14 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 163 HIS 0.007 0.001 HIS A 270 PHE 0.025 0.001 PHE X 384 TYR 0.021 0.001 TYR G 361 ARG 0.006 0.000 ARG I 482 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 295 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8205 (mmm160) cc_final: 0.7530 (ttm170) REVERT: F 410 TYR cc_start: 0.6038 (p90) cc_final: 0.5767 (p90) REVERT: H 349 ASP cc_start: 0.8124 (t70) cc_final: 0.7713 (t0) REVERT: D 102 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8314 (p0) REVERT: D 168 TYR cc_start: 0.8518 (t80) cc_final: 0.8141 (t80) REVERT: D 438 GLU cc_start: 0.8517 (mt-10) cc_final: 0.7332 (mm-30) REVERT: M 32 MET cc_start: 0.5835 (ttt) cc_final: 0.5491 (ttm) REVERT: I 333 MET cc_start: 0.8401 (tmm) cc_final: 0.7912 (tmm) REVERT: I 461 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.6287 (m-80) REVERT: G 259 LYS cc_start: 0.8383 (mptm) cc_final: 0.8007 (tptp) REVERT: G 263 LYS cc_start: 0.7831 (tttt) cc_final: 0.7385 (ttpt) REVERT: G 330 GLN cc_start: 0.8170 (mt0) cc_final: 0.7749 (mt0) REVERT: G 379 ARG cc_start: 0.7468 (ptp-170) cc_final: 0.6872 (ptp-170) REVERT: A 132 LEU cc_start: 0.8547 (tp) cc_final: 0.8251 (tp) REVERT: A 202 MET cc_start: 0.7288 (tpp) cc_final: 0.7019 (tpp) REVERT: A 258 THR cc_start: 0.7317 (OUTLIER) cc_final: 0.6975 (p) REVERT: A 314 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7885 (mp) REVERT: J 204 ASN cc_start: 0.8524 (t0) cc_final: 0.8314 (t0) REVERT: J 205 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7819 (tm-30) REVERT: J 229 ASP cc_start: 0.7156 (OUTLIER) cc_final: 0.6940 (m-30) REVERT: E 50 ASN cc_start: 0.8296 (t0) cc_final: 0.7744 (m110) REVERT: E 67 LYS cc_start: 0.8785 (tptp) cc_final: 0.8157 (mmmm) REVERT: K 174 GLN cc_start: 0.8363 (tt0) cc_final: 0.7992 (tm-30) REVERT: K 186 LYS cc_start: 0.7437 (mttt) cc_final: 0.6955 (mmtt) REVERT: X 435 GLN cc_start: 0.8515 (pm20) cc_final: 0.8064 (pm20) REVERT: X 481 TRP cc_start: 0.7667 (m-10) cc_final: 0.7278 (m-10) REVERT: L 757 LYS cc_start: 0.8455 (mttp) cc_final: 0.7916 (tptt) REVERT: L 808 ASP cc_start: 0.5987 (t0) cc_final: 0.5544 (t0) REVERT: L 868 LEU cc_start: 0.8252 (mp) cc_final: 0.7718 (tt) outliers start: 69 outliers final: 45 residues processed: 346 average time/residue: 0.3154 time to fit residues: 170.0575 Evaluate side-chains 310 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 260 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain H residue 435 LEU Chi-restraints excluded: chain H residue 454 LEU Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 104 TYR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 461 TYR Chi-restraints excluded: chain I residue 473 ASN Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 215 HIS Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 259 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain X residue 485 ILE Chi-restraints excluded: chain X residue 526 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 4.9990 chunk 225 optimal weight: 0.3980 chunk 49 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 61 optimal weight: 0.0770 chunk 250 optimal weight: 0.9990 chunk 208 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 131 optimal weight: 2.9990 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 470 ASN D 102 ASN D 145 ASN D 242 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 ASN E 58 GLN ** X 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21882 Z= 0.155 Angle : 0.548 9.529 29583 Z= 0.277 Chirality : 0.040 0.256 3381 Planarity : 0.004 0.057 3775 Dihedral : 4.356 27.157 2835 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 2.88 % Allowed : 15.43 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.17), residues: 2581 helix: 1.11 (0.15), residues: 1281 sheet: -2.23 (0.39), residues: 150 loop : -2.02 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 315 HIS 0.011 0.001 HIS L 877 PHE 0.019 0.001 PHE X 384 TYR 0.014 0.001 TYR J 134 ARG 0.006 0.000 ARG I 482 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 277 time to evaluate : 2.756 Fit side-chains revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8037 (mmm160) cc_final: 0.7657 (ttm170) REVERT: F 361 GLU cc_start: 0.7817 (tp30) cc_final: 0.7579 (tp30) REVERT: F 410 TYR cc_start: 0.6117 (p90) cc_final: 0.5852 (p90) REVERT: H 349 ASP cc_start: 0.8107 (t70) cc_final: 0.7710 (t0) REVERT: H 468 MET cc_start: 0.8657 (tpt) cc_final: 0.8375 (tpt) REVERT: D 102 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8276 (p0) REVERT: D 168 TYR cc_start: 0.8400 (t80) cc_final: 0.8096 (t80) REVERT: D 437 MET cc_start: 0.7706 (ppp) cc_final: 0.7468 (ppp) REVERT: D 438 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8010 (mm-30) REVERT: M 32 MET cc_start: 0.6126 (ttt) cc_final: 0.5835 (ttm) REVERT: I 15 ASP cc_start: 0.7858 (t70) cc_final: 0.7544 (t0) REVERT: I 333 MET cc_start: 0.8373 (tmm) cc_final: 0.7852 (tmm) REVERT: I 461 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.6046 (m-80) REVERT: G 184 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.8274 (p90) REVERT: G 259 LYS cc_start: 0.8385 (mptm) cc_final: 0.8010 (tptp) REVERT: G 263 LYS cc_start: 0.7859 (tttt) cc_final: 0.7399 (ttpt) REVERT: G 330 GLN cc_start: 0.8150 (mt0) cc_final: 0.7709 (mt0) REVERT: G 379 ARG cc_start: 0.7494 (ptp-170) cc_final: 0.6899 (ptp-170) REVERT: A 258 THR cc_start: 0.7310 (OUTLIER) cc_final: 0.6970 (p) REVERT: A 314 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7902 (mp) REVERT: J 204 ASN cc_start: 0.8516 (t0) cc_final: 0.8287 (t0) REVERT: J 205 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7786 (tm-30) REVERT: E 50 ASN cc_start: 0.8242 (t0) cc_final: 0.7791 (m-40) REVERT: K 174 GLN cc_start: 0.8352 (tt0) cc_final: 0.7989 (tm-30) REVERT: K 186 LYS cc_start: 0.7433 (mttt) cc_final: 0.7052 (mmtt) REVERT: X 435 GLN cc_start: 0.8497 (pm20) cc_final: 0.8012 (pm20) REVERT: X 481 TRP cc_start: 0.7730 (m-10) cc_final: 0.7389 (m-10) REVERT: L 757 LYS cc_start: 0.8443 (mttp) cc_final: 0.7891 (tptt) REVERT: L 808 ASP cc_start: 0.5934 (t0) cc_final: 0.5525 (t0) REVERT: L 868 LEU cc_start: 0.8223 (mp) cc_final: 0.7826 (tt) outliers start: 70 outliers final: 54 residues processed: 327 average time/residue: 0.3338 time to fit residues: 171.3618 Evaluate side-chains 325 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 266 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 435 LEU Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 104 TYR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain I residue 461 TYR Chi-restraints excluded: chain I residue 473 ASN Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 215 HIS Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 254 GLN Chi-restraints excluded: chain J residue 259 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain X residue 485 ILE Chi-restraints excluded: chain X residue 507 THR Chi-restraints excluded: chain X residue 526 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 182 optimal weight: 0.5980 chunk 141 optimal weight: 0.9990 chunk 210 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 249 optimal weight: 9.9990 chunk 156 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 470 ASN D 102 ASN D 145 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 758 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21882 Z= 0.191 Angle : 0.562 10.420 29583 Z= 0.282 Chirality : 0.041 0.235 3381 Planarity : 0.004 0.057 3775 Dihedral : 4.329 27.062 2835 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.13 % Allowed : 15.71 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.17), residues: 2581 helix: 1.20 (0.15), residues: 1284 sheet: -2.17 (0.40), residues: 150 loop : -1.96 (0.19), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 315 HIS 0.010 0.001 HIS L 877 PHE 0.028 0.001 PHE F 330 TYR 0.035 0.001 TYR X 368 ARG 0.006 0.000 ARG I 482 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 271 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8082 (mmm160) cc_final: 0.7663 (ttm170) REVERT: F 361 GLU cc_start: 0.7836 (tp30) cc_final: 0.7599 (tp30) REVERT: F 410 TYR cc_start: 0.6198 (p90) cc_final: 0.5957 (p90) REVERT: H 169 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.7907 (mm110) REVERT: H 349 ASP cc_start: 0.8096 (t70) cc_final: 0.7697 (t0) REVERT: D 102 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8184 (p0) REVERT: D 438 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7965 (mm-30) REVERT: I 333 MET cc_start: 0.8448 (tmm) cc_final: 0.7963 (tmm) REVERT: I 461 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.6080 (m-80) REVERT: G 184 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.8503 (p90) REVERT: G 259 LYS cc_start: 0.8412 (mptm) cc_final: 0.8014 (tptp) REVERT: G 263 LYS cc_start: 0.7836 (tttt) cc_final: 0.7370 (ttpt) REVERT: G 330 GLN cc_start: 0.8131 (mt0) cc_final: 0.7714 (mt0) REVERT: G 379 ARG cc_start: 0.7523 (ptp-170) cc_final: 0.6913 (ptp-170) REVERT: A 258 THR cc_start: 0.7305 (OUTLIER) cc_final: 0.6955 (p) REVERT: A 314 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7870 (mp) REVERT: J 204 ASN cc_start: 0.8549 (t0) cc_final: 0.8304 (t0) REVERT: J 205 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7768 (tm-30) REVERT: E 50 ASN cc_start: 0.8255 (t0) cc_final: 0.7804 (m-40) REVERT: K 174 GLN cc_start: 0.8354 (tt0) cc_final: 0.7983 (tm-30) REVERT: K 186 LYS cc_start: 0.7455 (mttt) cc_final: 0.7075 (mmtt) REVERT: X 435 GLN cc_start: 0.8515 (pm20) cc_final: 0.8015 (pm20) REVERT: X 481 TRP cc_start: 0.7807 (m-10) cc_final: 0.7273 (m-10) REVERT: L 757 LYS cc_start: 0.8459 (mttp) cc_final: 0.7888 (tptt) REVERT: L 808 ASP cc_start: 0.6035 (t0) cc_final: 0.5653 (t70) outliers start: 76 outliers final: 59 residues processed: 325 average time/residue: 0.3047 time to fit residues: 155.3505 Evaluate side-chains 323 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 258 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain H residue 169 GLN Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 435 LEU Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 104 TYR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain I residue 461 TYR Chi-restraints excluded: chain I residue 473 ASN Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 215 HIS Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain J residue 201 ASN Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 254 GLN Chi-restraints excluded: chain J residue 259 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain X residue 440 GLN Chi-restraints excluded: chain X residue 485 ILE Chi-restraints excluded: chain X residue 507 THR Chi-restraints excluded: chain X residue 526 LEU Chi-restraints excluded: chain L residue 758 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 196 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 470 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 758 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21882 Z= 0.174 Angle : 0.566 11.850 29583 Z= 0.283 Chirality : 0.041 0.225 3381 Planarity : 0.004 0.056 3775 Dihedral : 4.281 26.821 2835 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 3.04 % Allowed : 15.88 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.17), residues: 2581 helix: 1.28 (0.15), residues: 1283 sheet: -2.14 (0.40), residues: 152 loop : -1.90 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 315 HIS 0.008 0.001 HIS L 877 PHE 0.024 0.001 PHE F 330 TYR 0.024 0.001 TYR G 361 ARG 0.006 0.000 ARG I 482 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 270 time to evaluate : 2.759 Fit side-chains revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8053 (mmm160) cc_final: 0.7780 (ttm170) REVERT: F 361 GLU cc_start: 0.7815 (tp30) cc_final: 0.7598 (tp30) REVERT: H 169 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.7901 (mm110) REVERT: H 349 ASP cc_start: 0.8114 (t70) cc_final: 0.7725 (t0) REVERT: H 390 MET cc_start: 0.8383 (pmm) cc_final: 0.8066 (pmm) REVERT: D 352 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7396 (mm-30) REVERT: D 437 MET cc_start: 0.7765 (ppp) cc_final: 0.7201 (ppp) REVERT: D 438 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8009 (mm-30) REVERT: I 333 MET cc_start: 0.8426 (tmm) cc_final: 0.7948 (tmm) REVERT: I 461 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.6008 (m-80) REVERT: G 184 TYR cc_start: 0.8852 (OUTLIER) cc_final: 0.8499 (p90) REVERT: G 259 LYS cc_start: 0.8383 (mptm) cc_final: 0.8009 (tptp) REVERT: G 263 LYS cc_start: 0.7818 (tttt) cc_final: 0.7364 (ttpt) REVERT: G 330 GLN cc_start: 0.8135 (mt0) cc_final: 0.7720 (mt0) REVERT: A 202 MET cc_start: 0.7414 (tpp) cc_final: 0.7086 (tpp) REVERT: A 258 THR cc_start: 0.7259 (OUTLIER) cc_final: 0.6912 (p) REVERT: A 314 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7854 (mp) REVERT: A 447 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7723 (tm-30) REVERT: J 100 LEU cc_start: 0.8389 (tt) cc_final: 0.8165 (tp) REVERT: J 204 ASN cc_start: 0.8515 (t0) cc_final: 0.8102 (t0) REVERT: J 205 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7767 (tm-30) REVERT: E 50 ASN cc_start: 0.8254 (t0) cc_final: 0.7793 (m-40) REVERT: E 67 LYS cc_start: 0.8788 (tptp) cc_final: 0.8163 (mmmm) REVERT: C 196 PHE cc_start: 0.8522 (m-80) cc_final: 0.8279 (m-80) REVERT: K 174 GLN cc_start: 0.8349 (tt0) cc_final: 0.7982 (tm-30) REVERT: K 186 LYS cc_start: 0.7388 (mttt) cc_final: 0.7031 (mmtt) REVERT: X 435 GLN cc_start: 0.8521 (pm20) cc_final: 0.8016 (pm20) REVERT: X 481 TRP cc_start: 0.7829 (m-10) cc_final: 0.7316 (m-10) REVERT: L 757 LYS cc_start: 0.8373 (mttp) cc_final: 0.7880 (tptt) REVERT: L 808 ASP cc_start: 0.5986 (t0) cc_final: 0.5610 (t70) outliers start: 74 outliers final: 55 residues processed: 323 average time/residue: 0.3243 time to fit residues: 163.2231 Evaluate side-chains 322 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 261 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain H residue 169 GLN Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 435 LEU Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 104 TYR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 224 ASP Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain I residue 461 TYR Chi-restraints excluded: chain I residue 473 ASN Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 215 HIS Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain J residue 201 ASN Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 254 GLN Chi-restraints excluded: chain J residue 259 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain X residue 485 ILE Chi-restraints excluded: chain X residue 507 THR Chi-restraints excluded: chain X residue 526 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 0.1980 chunk 239 optimal weight: 0.9980 chunk 218 optimal weight: 6.9990 chunk 232 optimal weight: 0.9980 chunk 140 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 chunk 220 optimal weight: 0.5980 chunk 231 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 470 ASN D 145 ASN D 340 HIS ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21882 Z= 0.162 Angle : 0.565 11.082 29583 Z= 0.281 Chirality : 0.041 0.192 3381 Planarity : 0.004 0.056 3775 Dihedral : 4.210 26.765 2835 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 2.96 % Allowed : 16.25 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.17), residues: 2581 helix: 1.37 (0.15), residues: 1288 sheet: -2.09 (0.41), residues: 153 loop : -1.83 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 315 HIS 0.008 0.001 HIS A 270 PHE 0.032 0.001 PHE X 384 TYR 0.018 0.001 TYR G 361 ARG 0.014 0.000 ARG M 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 277 time to evaluate : 2.744 Fit side-chains revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8032 (mmm160) cc_final: 0.7687 (ttm170) REVERT: F 361 GLU cc_start: 0.7795 (tp30) cc_final: 0.7585 (tp30) REVERT: H 169 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7975 (mm110) REVERT: H 349 ASP cc_start: 0.8105 (t70) cc_final: 0.7727 (t0) REVERT: D 352 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7600 (mm-30) REVERT: D 438 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8196 (mm-30) REVERT: M 32 MET cc_start: 0.6043 (ttm) cc_final: 0.5776 (ttm) REVERT: I 333 MET cc_start: 0.8403 (tmm) cc_final: 0.7931 (tmm) REVERT: I 461 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.5722 (m-80) REVERT: G 32 MET cc_start: 0.6696 (tpp) cc_final: 0.5744 (mtm) REVERT: G 259 LYS cc_start: 0.8380 (mptm) cc_final: 0.8001 (tptp) REVERT: G 330 GLN cc_start: 0.8160 (mt0) cc_final: 0.7742 (mt0) REVERT: G 366 ARG cc_start: 0.7786 (mmm-85) cc_final: 0.6637 (mtp180) REVERT: A 202 MET cc_start: 0.7548 (tpp) cc_final: 0.7191 (tpp) REVERT: A 258 THR cc_start: 0.7280 (OUTLIER) cc_final: 0.6958 (p) REVERT: A 314 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7837 (mp) REVERT: A 447 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: J 100 LEU cc_start: 0.8390 (tt) cc_final: 0.8144 (tp) REVERT: J 204 ASN cc_start: 0.8478 (t0) cc_final: 0.8080 (t0) REVERT: E 50 ASN cc_start: 0.8270 (t0) cc_final: 0.7839 (m110) REVERT: K 186 LYS cc_start: 0.7311 (mttt) cc_final: 0.7012 (mmtt) REVERT: X 481 TRP cc_start: 0.7788 (m-10) cc_final: 0.7128 (m-10) REVERT: X 482 VAL cc_start: 0.8769 (t) cc_final: 0.8444 (p) REVERT: L 757 LYS cc_start: 0.8220 (mttp) cc_final: 0.7741 (tptt) REVERT: L 808 ASP cc_start: 0.6092 (t0) cc_final: 0.5717 (t70) REVERT: L 869 ARG cc_start: 0.7602 (mpt-90) cc_final: 0.7222 (mtt180) outliers start: 72 outliers final: 55 residues processed: 329 average time/residue: 0.3308 time to fit residues: 168.2578 Evaluate side-chains 323 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 263 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain H residue 169 GLN Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 435 LEU Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 104 TYR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 224 ASP Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain I residue 461 TYR Chi-restraints excluded: chain I residue 473 ASN Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 215 HIS Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 201 ASN Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 254 GLN Chi-restraints excluded: chain J residue 259 GLN Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain X residue 485 ILE Chi-restraints excluded: chain X residue 507 THR Chi-restraints excluded: chain X residue 526 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 0.8980 chunk 245 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 116 optimal weight: 0.0980 chunk 171 optimal weight: 0.0010 chunk 258 optimal weight: 0.0670 chunk 237 optimal weight: 0.0470 chunk 205 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 125 optimal weight: 0.4980 overall best weight: 0.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 288 GLN H 470 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 480 GLN ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.197 21882 Z= 0.253 Angle : 0.737 59.192 29583 Z= 0.401 Chirality : 0.042 0.479 3381 Planarity : 0.004 0.071 3775 Dihedral : 4.228 26.744 2835 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.71 % Allowed : 16.54 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.18), residues: 2581 helix: 1.38 (0.15), residues: 1288 sheet: -2.07 (0.41), residues: 153 loop : -1.82 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 315 HIS 0.008 0.001 HIS J 118 PHE 0.072 0.001 PHE D 112 TYR 0.049 0.001 TYR G 361 ARG 0.027 0.000 ARG M 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 263 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8027 (mmm160) cc_final: 0.7683 (ttm170) REVERT: F 361 GLU cc_start: 0.7792 (tp30) cc_final: 0.7582 (tp30) REVERT: H 349 ASP cc_start: 0.8103 (t70) cc_final: 0.7720 (t0) REVERT: D 145 ASN cc_start: 0.7849 (OUTLIER) cc_final: 0.7468 (t0) REVERT: D 352 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7580 (mm-30) REVERT: D 438 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8197 (mm-30) REVERT: M 32 MET cc_start: 0.6039 (ttm) cc_final: 0.5778 (ttm) REVERT: I 333 MET cc_start: 0.8400 (tmm) cc_final: 0.7927 (tmm) REVERT: I 461 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.5718 (m-80) REVERT: G 32 MET cc_start: 0.6686 (tpp) cc_final: 0.5743 (mtm) REVERT: G 259 LYS cc_start: 0.8447 (mptm) cc_final: 0.7999 (tptp) REVERT: G 330 GLN cc_start: 0.8157 (mt0) cc_final: 0.7734 (mt0) REVERT: G 366 ARG cc_start: 0.7786 (mmm-85) cc_final: 0.6636 (mtp180) REVERT: A 202 MET cc_start: 0.7543 (tpp) cc_final: 0.7188 (tpp) REVERT: A 258 THR cc_start: 0.7274 (OUTLIER) cc_final: 0.6955 (p) REVERT: A 314 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7837 (mp) REVERT: J 100 LEU cc_start: 0.8385 (tt) cc_final: 0.8141 (tp) REVERT: J 204 ASN cc_start: 0.8470 (t0) cc_final: 0.8058 (t0) REVERT: J 207 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7311 (tm-30) REVERT: E 50 ASN cc_start: 0.8268 (t0) cc_final: 0.7838 (m110) REVERT: K 186 LYS cc_start: 0.7312 (mttt) cc_final: 0.7007 (mmtt) REVERT: X 481 TRP cc_start: 0.7787 (m-10) cc_final: 0.7157 (m-10) REVERT: X 482 VAL cc_start: 0.8774 (t) cc_final: 0.8439 (p) REVERT: L 757 LYS cc_start: 0.8218 (mttp) cc_final: 0.7738 (tptt) REVERT: L 808 ASP cc_start: 0.6085 (t0) cc_final: 0.5711 (t70) REVERT: L 869 ARG cc_start: 0.7762 (mpt-90) cc_final: 0.7511 (mpt-90) outliers start: 66 outliers final: 53 residues processed: 308 average time/residue: 0.3390 time to fit residues: 161.9418 Evaluate side-chains 319 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 262 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 435 LEU Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 104 TYR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 224 ASP Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain I residue 461 TYR Chi-restraints excluded: chain I residue 473 ASN Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 215 HIS Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 254 GLN Chi-restraints excluded: chain J residue 259 GLN Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain X residue 485 ILE Chi-restraints excluded: chain X residue 507 THR Chi-restraints excluded: chain X residue 526 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 7.9990 chunk 218 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 205 optimal weight: 0.0010 chunk 86 optimal weight: 0.4980 chunk 211 optimal weight: 0.7980 chunk 26 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN H 288 GLN H 470 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 480 GLN ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 600 ASN ** 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 = 0.3908 r_free = 0.3908 target = 0.117253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.089348 restraints weight = 56322.009| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.20 r_work: 0.3288 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.197 21882 Z= 0.253 Angle : 0.737 59.192 29583 Z= 0.401 Chirality : 0.042 0.479 3381 Planarity : 0.004 0.071 3775 Dihedral : 4.228 26.744 2835 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.34 % Allowed : 16.74 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.18), residues: 2581 helix: 1.38 (0.15), residues: 1288 sheet: -2.07 (0.41), residues: 153 loop : -1.82 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 315 HIS 0.008 0.001 HIS J 118 PHE 0.072 0.001 PHE D 112 TYR 0.049 0.001 TYR G 361 ARG 0.027 0.000 ARG M 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5067.43 seconds wall clock time: 92 minutes 19.99 seconds (5539.99 seconds total)