Starting phenix.real_space_refine (version: dev) on Wed Feb 22 18:15:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyu_0097/02_2023/6gyu_0097.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyu_0097/02_2023/6gyu_0097.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyu_0097/02_2023/6gyu_0097.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyu_0097/02_2023/6gyu_0097.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyu_0097/02_2023/6gyu_0097.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyu_0097/02_2023/6gyu_0097.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.013 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 Process input model Symmetric amino acids flipped Residue "B PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 26": "NH1" <-> "NH2" Residue "B TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 295": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 397": "NH1" <-> "NH2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "A ARG 17": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ARG 468": "NH1" <-> "NH2" Residue "C TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ARG 25": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D ARG 168": "NH1" <-> "NH2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D ARG 186": "NH1" <-> "NH2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 18159 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 4778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4778 Classifications: {'peptide': 579} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 559} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3526 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 4362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4362 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 510} Unresolved chain links: 1 Chain breaks: 2 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1226 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 4265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4265 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 35, 'TRANS': 476} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 113 SG CYS B 14 114.872 51.167 83.797 1.00166.54 S ATOM 132 SG CYS B 17 115.332 54.747 84.272 1.00171.67 S ATOM 192 SG CYS B 24 114.285 53.545 80.324 1.00165.03 S ATOM 240 SG CYS B 30 117.693 52.033 81.734 1.00166.33 S ATOM 113 SG CYS B 14 114.872 51.167 83.797 1.00166.54 S ATOM 240 SG CYS B 30 117.693 52.033 81.734 1.00166.33 S ATOM 258 SG CYS B 33 118.325 51.880 85.570 1.00170.01 S ATOM 331 SG CYS B 42 117.527 48.058 83.334 1.00181.10 S Time building chain proxies: 10.41, per 1000 atoms: 0.57 Number of scatterers: 18159 At special positions: 0 Unit cell: (170.66, 140.98, 99.64, 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 2 29.99 S 76 16.00 O 3333 8.00 N 3003 7.00 C 11745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 215 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.79 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 30 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 17 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 24 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 14 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 30 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 42 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 33 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 14 " Number of angles added : 12 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4266 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 11 sheets defined 60.6% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 39 through 44 removed outlier: 4.244A pdb=" N LYS B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 72 removed outlier: 3.526A pdb=" N PHE B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR B 70 " --> pdb=" O GLN B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.903A pdb=" N TYR B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 106 removed outlier: 4.171A pdb=" N MET B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 106 " --> pdb=" O TRP B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 122 Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.737A pdb=" N TYR B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE B 127 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLY B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 135 removed outlier: 3.648A pdb=" N GLU B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 132 through 135' Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 154 through 174 removed outlier: 3.664A pdb=" N TRP B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 183 removed outlier: 3.532A pdb=" N GLU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 182 " --> pdb=" O LYS B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 193 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 204 through 224 Processing helix chain 'B' and resid 230 through 241 removed outlier: 3.858A pdb=" N VAL B 234 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 Processing helix chain 'B' and resid 251 through 266 Processing helix chain 'B' and resid 279 through 302 removed outlier: 3.668A pdb=" N ILE B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.537A pdb=" N ILE B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 357 removed outlier: 3.986A pdb=" N LEU B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 386 Processing helix chain 'B' and resid 394 through 422 removed outlier: 3.527A pdb=" N PHE B 398 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 443 Processing helix chain 'B' and resid 444 through 447 removed outlier: 3.871A pdb=" N HIS B 447 " --> pdb=" O ASN B 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 444 through 447' Processing helix chain 'B' and resid 450 through 455 removed outlier: 3.744A pdb=" N ASN B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 477 removed outlier: 3.869A pdb=" N MET B 460 " --> pdb=" O HIS B 456 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE B 476 " --> pdb=" O PHE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 495 Processing helix chain 'B' and resid 501 through 522 Processing helix chain 'B' and resid 535 through 552 removed outlier: 3.887A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B 546 " --> pdb=" O GLN B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 562 Processing helix chain 'B' and resid 589 through 601 removed outlier: 3.978A pdb=" N ILE B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 607 removed outlier: 3.621A pdb=" N ASP B 605 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 606 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 607 " --> pdb=" O SER B 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 602 through 607' Processing helix chain 'A' and resid 5 through 12 removed outlier: 3.673A pdb=" N PHE A 9 " --> pdb=" O ASN A 5 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 24 removed outlier: 3.501A pdb=" N HIS A 23 " --> pdb=" O GLU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.543A pdb=" N LEU A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 81 through 94 removed outlier: 4.509A pdb=" N GLU A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TRP A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 143 through 151 removed outlier: 3.900A pdb=" N VAL A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.557A pdb=" N VAL A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 257 through 266 removed outlier: 3.753A pdb=" N SER A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 removed outlier: 3.771A pdb=" N ILE A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.883A pdb=" N ILE A 350 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 380 removed outlier: 3.830A pdb=" N ASN A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.797A pdb=" N VAL A 430 " --> pdb=" O CYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 460 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'C' and resid 56 through 72 removed outlier: 4.022A pdb=" N ASP C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 63 " --> pdb=" O PRO C 59 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR C 70 " --> pdb=" O GLN C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 106 removed outlier: 3.902A pdb=" N LEU C 106 " --> pdb=" O TRP C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 122 removed outlier: 3.540A pdb=" N PHE C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 113 " --> pdb=" O ASP C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.802A pdb=" N TYR C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE C 127 " --> pdb=" O GLY C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 127' Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 153 through 173 Processing helix chain 'C' and resid 175 through 183 removed outlier: 3.998A pdb=" N GLU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 193 Processing helix chain 'C' and resid 204 through 224 Processing helix chain 'C' and resid 230 through 241 removed outlier: 4.090A pdb=" N VAL C 234 " --> pdb=" O ASP C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 249 Processing helix chain 'C' and resid 249 through 266 Processing helix chain 'C' and resid 279 through 303 removed outlier: 3.792A pdb=" N ILE C 284 " --> pdb=" O PRO C 280 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG C 295 " --> pdb=" O ARG C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 341 through 356 removed outlier: 3.687A pdb=" N TYR C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP C 346 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 359 No H-bonds generated for 'chain 'C' and resid 357 through 359' Processing helix chain 'C' and resid 366 through 386 Processing helix chain 'C' and resid 393 through 422 Processing helix chain 'C' and resid 427 through 443 Processing helix chain 'C' and resid 443 through 448 removed outlier: 3.838A pdb=" N HIS C 447 " --> pdb=" O VAL C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 456 removed outlier: 3.601A pdb=" N HIS C 456 " --> pdb=" O PHE C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 477 removed outlier: 3.566A pdb=" N GLN C 461 " --> pdb=" O PRO C 457 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 495 Processing helix chain 'C' and resid 501 through 524 removed outlier: 3.576A pdb=" N ASP C 505 " --> pdb=" O GLY C 501 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS C 518 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 519 " --> pdb=" O SER C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 552 removed outlier: 3.693A pdb=" N ILE C 545 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 548 " --> pdb=" O ASP C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 563 removed outlier: 3.587A pdb=" N GLY C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 601 Processing helix chain 'C' and resid 602 through 606 removed outlier: 3.552A pdb=" N ASP C 605 " --> pdb=" O ASN C 602 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE C 606 " --> pdb=" O ILE C 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 602 through 606' Processing helix chain 'D' and resid 22 through 25 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 83 through 97 Processing helix chain 'D' and resid 108 through 113 removed outlier: 3.827A pdb=" N LYS D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 124 Processing helix chain 'D' and resid 127 through 141 Processing helix chain 'D' and resid 145 through 150 Processing helix chain 'D' and resid 151 through 159 Processing helix chain 'D' and resid 163 through 169 removed outlier: 3.672A pdb=" N THR D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 188 Processing helix chain 'E' and resid 30 through 35 Processing helix chain 'E' and resid 38 through 59 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 81 through 94 Processing helix chain 'E' and resid 107 through 138 removed outlier: 4.012A pdb=" N VAL E 138 " --> pdb=" O LYS E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 170 removed outlier: 4.092A pdb=" N LEU E 151 " --> pdb=" O ASP E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 182 Processing helix chain 'E' and resid 183 through 193 removed outlier: 3.651A pdb=" N LYS E 187 " --> pdb=" O PRO E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 223 Processing helix chain 'E' and resid 227 through 233 removed outlier: 3.513A pdb=" N ARG E 231 " --> pdb=" O SER E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 295 Processing helix chain 'E' and resid 334 through 349 removed outlier: 3.512A pdb=" N PHE E 338 " --> pdb=" O ARG E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 377 Processing helix chain 'E' and resid 379 through 383 removed outlier: 3.658A pdb=" N HIS E 383 " --> pdb=" O GLU E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 399 Processing helix chain 'E' and resid 400 through 408 Processing helix chain 'E' and resid 428 through 433 Processing helix chain 'E' and resid 437 through 444 Processing helix chain 'E' and resid 451 through 479 Proline residue: E 473 - end of helix Processing helix chain 'E' and resid 482 through 486 removed outlier: 3.704A pdb=" N GLN E 486 " --> pdb=" O ASP E 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 504 removed outlier: 3.617A pdb=" N GLN E 496 " --> pdb=" O ASN E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 507 No H-bonds generated for 'chain 'E' and resid 505 through 507' Processing helix chain 'E' and resid 526 through 533 Processing sheet with id=AA1, first strand: chain 'B' and resid 152 through 153 removed outlier: 4.216A pdb=" N HIS B 152 " --> pdb=" O ALA C 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 527 through 528 Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 46 removed outlier: 3.657A pdb=" N VAL E 73 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 120 removed outlier: 3.938A pdb=" N VAL A 140 " --> pdb=" O TYR A 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 168 through 169 removed outlier: 6.084A pdb=" N ILE A 168 " --> pdb=" O GLY A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 278 removed outlier: 6.951A pdb=" N ILE A 276 " --> pdb=" O ARG A 313 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 344 through 345 Processing sheet with id=AA8, first strand: chain 'A' and resid 411 through 412 removed outlier: 6.675A pdb=" N LYS A 411 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE A 452 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE A 478 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL A 454 " --> pdb=" O ILE A 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 50 through 51 Processing sheet with id=AB1, first strand: chain 'D' and resid 15 through 19 removed outlier: 4.111A pdb=" N ILE D 75 " --> pdb=" O ASN D 5 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 239 through 241 removed outlier: 3.735A pdb=" N GLN E 268 " --> pdb=" O LYS E 253 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR E 255 " --> pdb=" O HIS E 266 " (cutoff:3.500A) 835 hydrogen bonds defined for protein. 2451 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: 5.59 Time building geometry restraints manager: 7.35 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: 5654 1.34 - 1.46: 4049 1.46 - 1.58: 8779 1.58 - 1.70: 0 1.70 - 1.82: 115 Bond restraints: 18597 Sorted by residual: bond pdb=" C LEU B 58 " pdb=" N PRO B 59 " ideal model delta sigma weight residual 1.335 1.384 -0.049 1.30e-02 5.92e+03 1.41e+01 bond pdb=" CB ASP A 173 " pdb=" CG ASP A 173 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.50e-02 1.60e+03 4.01e+00 bond pdb=" N ASN A 371 " pdb=" CA ASN A 371 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.54e-02 4.22e+03 3.34e+00 bond pdb=" CA LYS A 299 " pdb=" C LYS A 299 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.34e-02 5.57e+03 2.65e+00 bond pdb=" CA LEU B 48 " pdb=" C LEU B 48 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.34e-02 5.57e+03 2.60e+00 ... (remaining 18592 not shown) Histogram of bond angle deviations from ideal: 96.90 - 104.69: 281 104.69 - 112.49: 9151 112.49 - 120.28: 8446 120.28 - 128.08: 7140 128.08 - 135.88: 162 Bond angle restraints: 25180 Sorted by residual: angle pdb=" N ASP A 37 " pdb=" CA ASP A 37 " pdb=" C ASP A 37 " ideal model delta sigma weight residual 114.62 107.54 7.08 1.14e+00 7.69e-01 3.86e+01 angle pdb=" C LYS A 368 " pdb=" N TRP A 369 " pdb=" CA TRP A 369 " ideal model delta sigma weight residual 121.54 133.40 -11.86 1.91e+00 2.74e-01 3.85e+01 angle pdb=" C LEU E 93 " pdb=" N ILE E 94 " pdb=" CA ILE E 94 " ideal model delta sigma weight residual 122.72 115.30 7.42 1.39e+00 5.18e-01 2.85e+01 angle pdb=" C ILE A 172 " pdb=" N ASP A 173 " pdb=" CA ASP A 173 " ideal model delta sigma weight residual 126.45 135.88 -9.43 1.77e+00 3.19e-01 2.84e+01 angle pdb=" C ASP E 245 " pdb=" N ARG E 246 " pdb=" CA ARG E 246 " ideal model delta sigma weight residual 121.54 130.96 -9.42 1.91e+00 2.74e-01 2.43e+01 ... (remaining 25175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.15: 10430 15.15 - 30.30: 583 30.30 - 45.45: 142 45.45 - 60.60: 19 60.60 - 75.75: 15 Dihedral angle restraints: 11189 sinusoidal: 4638 harmonic: 6551 Sorted by residual: dihedral pdb=" CA ALA E 258 " pdb=" C ALA E 258 " pdb=" N GLU E 259 " pdb=" CA GLU E 259 " ideal model delta harmonic sigma weight residual 180.00 142.96 37.04 0 5.00e+00 4.00e-02 5.49e+01 dihedral pdb=" CB CYS B 99 " pdb=" SG CYS B 99 " pdb=" SG CYS B 215 " pdb=" CB CYS B 215 " ideal model delta sinusoidal sigma weight residual 93.00 151.56 -58.56 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CA THR E 263 " pdb=" C THR E 263 " pdb=" N PRO E 264 " pdb=" CA PRO E 264 " ideal model delta harmonic sigma weight residual -180.00 -146.95 -33.05 0 5.00e+00 4.00e-02 4.37e+01 ... (remaining 11186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2134 0.060 - 0.120: 549 0.120 - 0.180: 73 0.180 - 0.240: 13 0.240 - 0.300: 3 Chirality restraints: 2772 Sorted by residual: chirality pdb=" CA LEU B 48 " pdb=" N LEU B 48 " pdb=" C LEU B 48 " pdb=" CB LEU B 48 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CG LEU B 489 " pdb=" CB LEU B 489 " pdb=" CD1 LEU B 489 " pdb=" CD2 LEU B 489 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB ILE A 301 " pdb=" CA ILE A 301 " pdb=" CG1 ILE A 301 " pdb=" CG2 ILE A 301 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2769 not shown) Planarity restraints: 3187 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 443 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.51e+00 pdb=" C GLN A 443 " -0.053 2.00e-02 2.50e+03 pdb=" O GLN A 443 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN A 444 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 90 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.35e+00 pdb=" C LEU E 90 " -0.050 2.00e-02 2.50e+03 pdb=" O LEU E 90 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP E 91 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 110 " 0.007 2.00e-02 2.50e+03 2.03e-02 8.21e+00 pdb=" CG TYR A 110 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A 110 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 110 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 110 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 110 " 0.025 2.00e-02 2.50e+03 pdb=" CZ TYR A 110 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 110 " -0.012 2.00e-02 2.50e+03 ... (remaining 3184 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 2 2.06 - 2.77: 3418 2.77 - 3.48: 24623 3.48 - 4.19: 44184 4.19 - 4.90: 77506 Nonbonded interactions: 149733 Sorted by model distance: nonbonded pdb=" O ILE B 49 " pdb=" O THR B 50 " model vdw 1.349 3.040 nonbonded pdb=" O THR B 46 " pdb=" N LEU B 48 " model vdw 1.902 2.520 nonbonded pdb=" O MET B 43 " pdb=" CD2 LEU B 48 " model vdw 2.086 3.460 nonbonded pdb=" O ILE B 49 " pdb=" C THR B 50 " model vdw 2.168 3.270 nonbonded pdb=" O LEU B 48 " pdb=" N THR B 50 " model vdw 2.172 2.520 ... (remaining 149728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 1 through 2 or (resid 3 and (name N or name CA or name C o \ r name O or name CB )) or resid 49 through 319 or resid 339 through 608)) selection = (chain 'C' and (resid 1 through 3 or resid 49 through 319 or resid 339 through 6 \ 08)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 76 5.16 5 C 11745 2.51 5 N 3003 2.21 5 O 3333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 0.840 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: 4.520 Check model and map are aligned: 0.270 Process input model: 48.120 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.180 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:16.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 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 0.053 18597 Z= 0.331 Angle : 0.937 14.815 25180 Z= 0.522 Chirality : 0.053 0.300 2772 Planarity : 0.007 0.059 3187 Dihedral : 10.803 75.752 6920 Min Nonbonded Distance : 1.349 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.37 % Favored : 93.35 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.10 % 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: -4.30 (0.13), residues: 2166 helix: -2.48 (0.10), residues: 1276 sheet: -4.11 (0.51), residues: 56 loop : -3.17 (0.17), residues: 834 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 499 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 509 average time/residue: 1.3760 time to fit residues: 778.3696 Evaluate side-chains 217 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 212 time to evaluate : 2.216 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 1 average time/residue: 0.2966 time to fit residues: 3.4850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 103 optimal weight: 0.0370 chunk 126 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 GLN B 254 ASN B 259 GLN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN B 543 ASN B 552 ASN A 108 HIS ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 ASN A 420 GLN A 427 GLN C 82 GLN C 189 HIS C 199 ASN C 394 ASN C 399 GLN C 543 ASN C 552 ASN D 5 ASN E 54 GLN E 68 ASN E 143 ASN E 177 ASN E 191 ASN ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 HIS E 379 ASN E 408 ASN E 471 ASN E 492 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 18597 Z= 0.215 Angle : 0.657 13.683 25180 Z= 0.336 Chirality : 0.042 0.178 2772 Planarity : 0.005 0.055 3187 Dihedral : 5.717 74.974 2395 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.82 % Favored : 94.09 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.53 (0.16), residues: 2166 helix: -0.87 (0.13), residues: 1316 sheet: -3.54 (0.46), residues: 71 loop : -2.81 (0.19), residues: 779 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 245 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 20 residues processed: 290 average time/residue: 1.1078 time to fit residues: 367.0869 Evaluate side-chains 208 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 188 time to evaluate : 2.417 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 6 average time/residue: 0.1969 time to fit residues: 5.2590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 197 optimal weight: 10.0000 chunk 213 optimal weight: 20.0000 chunk 175 optimal weight: 2.9990 chunk 195 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 ASN B 406 GLN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN A 171 ASN C 82 GLN C 399 GLN E 219 GLN E 445 HIS E 492 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 18597 Z= 0.279 Angle : 0.646 14.277 25180 Z= 0.328 Chirality : 0.043 0.175 2772 Planarity : 0.004 0.050 3187 Dihedral : 5.457 74.528 2395 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.96 % Favored : 93.91 % Rotamer Outliers : 3.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.62 (0.17), residues: 2166 helix: -0.11 (0.14), residues: 1313 sheet: -2.72 (0.63), residues: 46 loop : -2.57 (0.19), residues: 807 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 202 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 30 residues processed: 252 average time/residue: 1.0593 time to fit residues: 307.5277 Evaluate side-chains 200 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 170 time to evaluate : 2.203 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 23 residues processed: 7 average time/residue: 0.3811 time to fit residues: 6.6329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 20.0000 chunk 148 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 198 optimal weight: 0.0070 chunk 209 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 303 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 18597 Z= 0.170 Angle : 0.600 16.135 25180 Z= 0.299 Chirality : 0.041 0.166 2772 Planarity : 0.004 0.048 3187 Dihedral : 5.225 75.387 2395 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.45 % Favored : 94.46 % Rotamer Outliers : 3.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.04 (0.18), residues: 2166 helix: 0.40 (0.15), residues: 1302 sheet: -2.18 (0.70), residues: 46 loop : -2.44 (0.19), residues: 818 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 209 time to evaluate : 2.251 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 28 residues processed: 263 average time/residue: 0.9608 time to fit residues: 294.9101 Evaluate side-chains 205 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 177 time to evaluate : 2.237 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 25 residues processed: 3 average time/residue: 0.2894 time to fit residues: 4.4223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 0.0570 chunk 119 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 86 optimal weight: 0.0980 chunk 178 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 107 optimal weight: 0.0020 chunk 188 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.4108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN B 542 GLN A 439 HIS C 82 GLN C 303 GLN C 399 GLN D 88 GLN E 219 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 18597 Z= 0.156 Angle : 0.598 15.786 25180 Z= 0.294 Chirality : 0.040 0.155 2772 Planarity : 0.004 0.046 3187 Dihedral : 5.009 76.154 2395 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.72 % Favored : 94.18 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.18), residues: 2166 helix: 0.71 (0.15), residues: 1314 sheet: -1.91 (0.68), residues: 52 loop : -2.29 (0.20), residues: 800 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 207 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 32 residues processed: 253 average time/residue: 1.0193 time to fit residues: 300.9319 Evaluate side-chains 204 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 172 time to evaluate : 2.216 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 28 residues processed: 4 average time/residue: 0.3128 time to fit residues: 5.1303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN B 303 GLN B 542 GLN A 439 HIS C 82 GLN C 235 GLN C 399 GLN C 552 ASN D 88 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 18597 Z= 0.268 Angle : 0.638 15.896 25180 Z= 0.317 Chirality : 0.043 0.166 2772 Planarity : 0.004 0.041 3187 Dihedral : 5.040 74.877 2395 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.91 % Favored : 93.95 % Rotamer Outliers : 3.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.51 (0.18), residues: 2166 helix: 0.82 (0.15), residues: 1300 sheet: -1.66 (0.74), residues: 46 loop : -2.22 (0.20), residues: 820 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 182 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 39 residues processed: 240 average time/residue: 0.9842 time to fit residues: 276.5678 Evaluate side-chains 207 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 168 time to evaluate : 2.197 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 32 residues processed: 7 average time/residue: 0.3814 time to fit residues: 6.7572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 176 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN C 82 GLN C 235 GLN D 101 ASN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 18597 Z= 0.213 Angle : 0.623 14.549 25180 Z= 0.308 Chirality : 0.042 0.188 2772 Planarity : 0.004 0.050 3187 Dihedral : 4.994 74.895 2395 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.86 % Favored : 94.09 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.36 (0.18), residues: 2166 helix: 0.94 (0.15), residues: 1300 sheet: -1.50 (0.76), residues: 46 loop : -2.16 (0.20), residues: 820 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 182 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 38 residues processed: 229 average time/residue: 0.9854 time to fit residues: 263.4920 Evaluate side-chains 204 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 166 time to evaluate : 2.295 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 34 residues processed: 4 average time/residue: 0.2854 time to fit residues: 4.7055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 0.3980 chunk 40 optimal weight: 0.5980 chunk 132 optimal weight: 0.3980 chunk 142 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN C 235 GLN D 101 ASN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 18597 Z= 0.162 Angle : 0.613 14.369 25180 Z= 0.300 Chirality : 0.041 0.166 2772 Planarity : 0.004 0.055 3187 Dihedral : 4.910 75.666 2395 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.72 % Favored : 94.23 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.16 (0.18), residues: 2166 helix: 1.09 (0.15), residues: 1299 sheet: -1.50 (0.66), residues: 56 loop : -2.03 (0.20), residues: 811 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 188 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 38 residues processed: 228 average time/residue: 0.9814 time to fit residues: 262.6366 Evaluate side-chains 202 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 164 time to evaluate : 2.255 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 33 residues processed: 5 average time/residue: 0.2421 time to fit residues: 5.0883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 30.0000 chunk 200 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 153 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 184 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN B 542 GLN C 82 GLN C 235 GLN D 88 GLN D 101 ASN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 18597 Z= 0.211 Angle : 0.648 14.435 25180 Z= 0.318 Chirality : 0.042 0.219 2772 Planarity : 0.004 0.060 3187 Dihedral : 4.932 75.258 2395 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.05 % Favored : 93.91 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.13 (0.18), residues: 2166 helix: 1.10 (0.15), residues: 1298 sheet: -1.47 (0.66), residues: 56 loop : -1.99 (0.21), residues: 812 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 172 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 38 residues processed: 213 average time/residue: 0.9313 time to fit residues: 233.0785 Evaluate side-chains 201 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 1.777 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 35 residues processed: 3 average time/residue: 0.3254 time to fit residues: 4.5406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 9.9990 chunk 125 optimal weight: 0.7980 chunk 97 optimal weight: 0.0470 chunk 143 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 198 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN C 235 GLN D 101 ASN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 18597 Z= 0.176 Angle : 0.638 14.477 25180 Z= 0.310 Chirality : 0.042 0.216 2772 Planarity : 0.004 0.062 3187 Dihedral : 4.896 75.526 2395 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.77 % Favored : 94.18 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.01 (0.18), residues: 2166 helix: 1.19 (0.15), residues: 1294 sheet: -1.37 (0.67), residues: 56 loop : -1.92 (0.21), residues: 816 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 180 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 37 residues processed: 220 average time/residue: 0.9530 time to fit residues: 246.5500 Evaluate side-chains 207 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 170 time to evaluate : 2.205 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 35 residues processed: 3 average time/residue: 0.2592 time to fit residues: 4.2376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 158 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 72 optimal weight: 0.3980 chunk 177 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN C 82 GLN C 235 GLN D 88 GLN D 101 ASN E 191 ASN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.134941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.093969 restraints weight = 28534.863| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.57 r_work: 0.3097 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 18597 Z= 0.184 Angle : 0.642 15.872 25180 Z= 0.311 Chirality : 0.042 0.244 2772 Planarity : 0.004 0.062 3187 Dihedral : 4.855 75.541 2395 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.91 % Favored : 94.04 % Rotamer Outliers : 2.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.18), residues: 2166 helix: 1.21 (0.15), residues: 1301 sheet: -1.29 (0.68), residues: 56 loop : -1.91 (0.21), residues: 809 =============================================================================== Job complete usr+sys time: 6025.79 seconds wall clock time: 108 minutes 41.31 seconds (6521.31 seconds total)