Starting phenix.real_space_refine on Sat Dec 9 18:54:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktp_23025/12_2023/7ktp_23025.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktp_23025/12_2023/7ktp_23025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktp_23025/12_2023/7ktp_23025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktp_23025/12_2023/7ktp_23025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktp_23025/12_2023/7ktp_23025.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktp_23025/12_2023/7ktp_23025.pdb" } resolution = 4.8 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= 0.001 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 7 6.06 5 S 88 5.16 5 C 7585 2.51 5 N 2129 2.21 5 O 2199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 686": "NH1" <-> "NH2" Residue "A PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 91": "OD1" <-> "OD2" Residue "B PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ASP 317": "OD1" <-> "OD2" Residue "B GLU 337": "OE1" <-> "OE2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 103": "NH1" <-> "NH2" Residue "C ASP 135": "OD1" <-> "OD2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 522": "NH1" <-> "NH2" Residue "C ASP 569": "OD1" <-> "OD2" Residue "C PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 9": "OD1" <-> "OD2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 232": "OD1" <-> "OD2" Residue "D ARG 258": "NH1" <-> "NH2" Residue "D ASP 270": "OD1" <-> "OD2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 395": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12008 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3098 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 19, 'TRANS': 375} Chain breaks: 4 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2917 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 352} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 2932 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 15, 'TRANS': 381} Chain breaks: 9 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 502 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 7, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 227 Chain: "D" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3054 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 22, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' ZN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 939 SG CYS A 302 30.674 93.245 115.304 0.99110.70 S ATOM 985 SG CYS A 307 27.984 95.013 113.853 0.87115.67 S ATOM 1591 SG CYS A 531 18.407 73.629 116.676 1.00169.00 S ATOM 1684 SG CYS A 544 20.797 75.718 113.378 1.00139.90 S ATOM 1734 SG CYS A 550 21.476 75.101 118.290 1.00148.49 S ATOM 1591 SG CYS A 531 18.407 73.629 116.676 1.00169.00 S ATOM 1684 SG CYS A 544 20.797 75.718 113.378 1.00139.90 S ATOM 1534 SG CYS A 524 17.395 79.645 115.870 1.00134.37 S ATOM 1719 SG CYS A 548 20.534 78.895 117.300 1.00137.34 S ATOM 1819 SG CYS A 561 38.830 72.036 108.448 1.00170.41 S ATOM 1973 SG CYS A 581 38.994 75.630 106.850 1.00146.47 S ATOM 2031 SG CYS A 589 42.140 74.320 110.087 1.00177.73 S ATOM 1819 SG CYS A 561 38.830 72.036 108.448 1.00170.41 S ATOM 1867 SG CYS A 567 40.775 73.315 104.723 1.00172.65 S ATOM 1906 SG CYS A 572 37.313 70.956 104.487 1.00183.12 S ATOM 1867 SG CYS A 567 40.775 73.315 104.723 1.00172.65 S Time building chain proxies: 6.41, per 1000 atoms: 0.53 Number of scatterers: 12008 At special positions: 0 Unit cell: (86.4, 166.05, 167.4, 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 7 29.99 S 88 16.00 O 2199 8.00 N 2129 7.00 C 7585 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: 3.99 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 302 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 307 " pdb="ZN ZN A 801 " - pdb=" ND1 HIS A 310 " pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb="ZN ZN A 804 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 544 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 531 " pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 548 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 524 " pdb=" ZN A 806 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 561 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 567 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 572 " pdb=" ZN A 807 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 567 " 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 23 sheets defined 20.8% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 34 through 62 removed outlier: 3.903A pdb=" N LYS A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 315 through 319 removed outlier: 3.970A pdb=" N VAL A 318 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR A 319 " --> pdb=" O PRO A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 319' Processing helix chain 'A' and resid 435 through 450 Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 464 through 474 removed outlier: 3.613A pdb=" N LYS A 474 " --> pdb=" O GLN A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 removed outlier: 3.721A pdb=" N MET A 539 " --> pdb=" O CYS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 removed outlier: 4.051A pdb=" N ALA A 577 " --> pdb=" O PRO A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 683 through 688 removed outlier: 3.519A pdb=" N ALA A 688 " --> pdb=" O ILE A 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 279 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.621A pdb=" N LYS B 342 " --> pdb=" O ASP B 339 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 343 " --> pdb=" O ILE B 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 339 through 343' Processing helix chain 'C' and resid 79 through 107 removed outlier: 3.749A pdb=" N HIS C 83 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Proline residue: C 93 - end of helix removed outlier: 3.718A pdb=" N THR C 102 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 126 through 131 removed outlier: 4.005A pdb=" N LYS C 130 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR C 131 " --> pdb=" O ILE C 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 126 through 131' Processing helix chain 'C' and resid 136 through 145 removed outlier: 4.367A pdb=" N LYS C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 141 " --> pdb=" O MET C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 470 removed outlier: 3.560A pdb=" N LEU C 463 " --> pdb=" O LYS C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 602 removed outlier: 3.924A pdb=" N ARG C 593 " --> pdb=" O PRO C 589 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 600 " --> pdb=" O THR C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 624 Processing helix chain 'C' and resid 631 through 649 removed outlier: 4.162A pdb=" N MET C 637 " --> pdb=" O ASN C 633 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU C 641 " --> pdb=" O MET C 637 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLN C 645 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LYS C 646 " --> pdb=" O ASN C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 666 removed outlier: 3.645A pdb=" N PHE C 666 " --> pdb=" O SER C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 686 removed outlier: 3.516A pdb=" N ILE C 674 " --> pdb=" O SER C 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 28 Processing helix chain 'D' and resid 355 through 362 removed outlier: 3.893A pdb=" N ASP D 361 " --> pdb=" O GLU D 357 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.101A pdb=" N TYR D 409 " --> pdb=" O ALA D 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 85 Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 removed outlier: 5.856A pdb=" N SER A 115 " --> pdb=" O GLY A 682 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 122 removed outlier: 6.552A pdb=" N PHE A 121 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 615 through 619 Processing sheet with id=AA5, first strand: chain 'A' and resid 638 through 640 removed outlier: 6.985A pdb=" N PHE A 638 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA A 713 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 83 through 89 removed outlier: 6.172A pdb=" N CYS B 84 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP B 438 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN B 86 " --> pdb=" O ARG B 436 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 101 removed outlier: 4.284A pdb=" N GLY B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 116 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN B 100 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 114 " --> pdb=" O GLN B 100 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN B 136 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLU B 125 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU B 134 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 147 through 154 removed outlier: 4.537A pdb=" N THR B 149 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA B 166 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY B 167 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASN B 176 " --> pdb=" O CYS B 182 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N CYS B 182 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 193 through 198 removed outlier: 3.683A pdb=" N GLU B 195 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU B 215 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ILE B 228 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 217 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N GLN B 292 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL B 226 " --> pdb=" O GLN B 292 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 239 through 244 Processing sheet with id=AB2, first strand: chain 'B' and resid 312 through 315 removed outlier: 7.314A pdb=" N LYS B 332 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE B 352 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 368 through 369 Processing sheet with id=AB4, first strand: chain 'C' and resid 230 through 234 Processing sheet with id=AB5, first strand: chain 'C' and resid 203 through 211 removed outlier: 7.020A pdb=" N VAL C 186 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS C 210 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU C 184 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 440 through 441 removed outlier: 4.531A pdb=" N GLN C 440 " --> pdb=" O PHE C 432 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 432 " --> pdb=" O GLN C 440 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE C 429 " --> pdb=" O ILE C 487 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL C 489 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN C 431 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE C 491 " --> pdb=" O GLN C 431 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 486 " --> pdb=" O VAL C 479 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL C 479 " --> pdb=" O ARG C 486 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 525 through 527 removed outlier: 3.689A pdb=" N LEU D 34 " --> pdb=" O GLN D 403 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 565 through 566 removed outlier: 4.796A pdb=" N TYR C 565 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 47 through 49 removed outlier: 7.274A pdb=" N ASN D 77 " --> pdb=" O ASN D 122 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASN D 122 " --> pdb=" O ASN D 77 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU D 79 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYS D 120 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE D 81 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 130 through 132 Processing sheet with id=AC2, first strand: chain 'D' and resid 183 through 185 removed outlier: 3.590A pdb=" N SER D 197 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 230 through 235 removed outlier: 3.785A pdb=" N LYS D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 276 through 281 removed outlier: 3.956A pdb=" N THR D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS D 311 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 320 through 322 removed outlier: 7.042A pdb=" N SER D 336 " --> pdb=" O PHE D 321 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASP D 346 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU D 366 " --> pdb=" O ASP D 346 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 4.43 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: 3943 1.34 - 1.46: 2770 1.46 - 1.58: 5448 1.58 - 1.70: 0 1.70 - 1.82: 121 Bond restraints: 12282 Sorted by residual: bond pdb=" C THR D 28 " pdb=" N PRO D 29 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.25e+00 bond pdb=" C ASN D 282 " pdb=" N PRO D 283 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.36e+00 bond pdb=" CA ILE B 290 " pdb=" CB ILE B 290 " ideal model delta sigma weight residual 1.527 1.546 -0.019 1.31e-02 5.83e+03 2.07e+00 bond pdb=" CA ARG C 196 " pdb=" C ARG C 196 " ideal model delta sigma weight residual 1.522 1.542 -0.019 1.36e-02 5.41e+03 2.04e+00 bond pdb=" CB PHE D 223 " pdb=" CG PHE D 223 " ideal model delta sigma weight residual 1.502 1.534 -0.032 2.30e-02 1.89e+03 1.95e+00 ... (remaining 12277 not shown) Histogram of bond angle deviations from ideal: 100.24 - 107.00: 407 107.00 - 113.76: 6688 113.76 - 120.53: 4629 120.53 - 127.29: 4738 127.29 - 134.06: 190 Bond angle restraints: 16652 Sorted by residual: angle pdb=" N ILE C 627 " pdb=" CA ILE C 627 " pdb=" C ILE C 627 " ideal model delta sigma weight residual 112.96 109.09 3.87 1.00e+00 1.00e+00 1.50e+01 angle pdb=" N THR D 28 " pdb=" CA THR D 28 " pdb=" C THR D 28 " ideal model delta sigma weight residual 109.81 116.73 -6.92 2.21e+00 2.05e-01 9.81e+00 angle pdb=" CA THR D 28 " pdb=" C THR D 28 " pdb=" N PRO D 29 " ideal model delta sigma weight residual 118.44 123.03 -4.59 1.59e+00 3.96e-01 8.33e+00 angle pdb=" N ARG C 196 " pdb=" CA ARG C 196 " pdb=" C ARG C 196 " ideal model delta sigma weight residual 111.71 115.02 -3.31 1.15e+00 7.56e-01 8.31e+00 angle pdb=" CA GLU C 493 " pdb=" CB GLU C 493 " pdb=" CG GLU C 493 " ideal model delta sigma weight residual 114.10 119.61 -5.51 2.00e+00 2.50e-01 7.59e+00 ... (remaining 16647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 6839 17.15 - 34.30: 417 34.30 - 51.45: 58 51.45 - 68.60: 15 68.60 - 85.75: 11 Dihedral angle restraints: 7340 sinusoidal: 2812 harmonic: 4528 Sorted by residual: dihedral pdb=" CA THR D 297 " pdb=" C THR D 297 " pdb=" N VAL D 298 " pdb=" CA VAL D 298 " ideal model delta harmonic sigma weight residual 180.00 160.16 19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ASP C 588 " pdb=" C ASP C 588 " pdb=" N PRO C 589 " pdb=" CA PRO C 589 " ideal model delta harmonic sigma weight residual -180.00 -160.77 -19.23 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA TYR B 244 " pdb=" C TYR B 244 " pdb=" N ASP B 245 " pdb=" CA ASP B 245 " ideal model delta harmonic sigma weight residual 180.00 161.39 18.61 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 7337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1163 0.036 - 0.072: 460 0.072 - 0.108: 122 0.108 - 0.144: 75 0.144 - 0.180: 13 Chirality restraints: 1833 Sorted by residual: chirality pdb=" CA VAL D 298 " pdb=" N VAL D 298 " pdb=" C VAL D 298 " pdb=" CB VAL D 298 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.12e-01 chirality pdb=" CA THR D 28 " pdb=" N THR D 28 " pdb=" C THR D 28 " pdb=" CB THR D 28 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CA ILE B 228 " pdb=" N ILE B 228 " pdb=" C ILE B 228 " pdb=" CB ILE B 228 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.15e-01 ... (remaining 1830 not shown) Planarity restraints: 2152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 28 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO D 29 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 29 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 29 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 195 " 0.009 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C LYS C 195 " -0.029 2.00e-02 2.50e+03 pdb=" O LYS C 195 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG C 196 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 86 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO D 87 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 87 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 87 " 0.023 5.00e-02 4.00e+02 ... (remaining 2149 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1275 2.76 - 3.29: 11705 3.29 - 3.83: 18342 3.83 - 4.36: 21638 4.36 - 4.90: 38319 Nonbonded interactions: 91279 Sorted by model distance: nonbonded pdb=" OD1 ASP B 431 " pdb=" OG SER B 433 " model vdw 2.221 2.440 nonbonded pdb=" OG SER D 147 " pdb=" O HIS D 176 " model vdw 2.281 2.440 nonbonded pdb=" O LEU C 100 " pdb=" ND2 ASN C 104 " model vdw 2.291 2.520 nonbonded pdb=" O ARG C 427 " pdb=" N ALA C 485 " model vdw 2.309 2.520 nonbonded pdb=" O ALA A 591 " pdb=" NH2 ARG A 609 " model vdw 2.320 2.520 ... (remaining 91274 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=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.680 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: 6.390 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 35.780 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 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 0.054 12282 Z= 0.304 Angle : 0.725 8.935 16652 Z= 0.382 Chirality : 0.047 0.180 1833 Planarity : 0.004 0.047 2152 Dihedral : 11.993 85.753 4380 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: -4.13 (0.17), residues: 1508 helix: -1.87 (0.23), residues: 267 sheet: -3.01 (0.23), residues: 324 loop : -3.04 (0.16), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 345 HIS 0.004 0.001 HIS B 213 PHE 0.022 0.001 PHE C 86 TYR 0.015 0.001 TYR B 244 ARG 0.003 0.000 ARG A 715 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.2875 time to fit residues: 156.6342 Evaluate side-chains 200 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 138 optimal weight: 20.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 636 ASN A 690 HIS ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN ** B 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN C 88 GLN C 95 GLN C 659 HIS D 27 ASN D 267 HIS ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12282 Z= 0.275 Angle : 0.652 6.367 16652 Z= 0.344 Chirality : 0.045 0.224 1833 Planarity : 0.005 0.073 2152 Dihedral : 4.597 20.152 1639 Min Nonbonded Distance : 1.585 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.16 % Allowed : 4.38 % Favored : 95.46 % 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: -2.82 (0.19), residues: 1508 helix: -0.25 (0.29), residues: 282 sheet: -2.10 (0.24), residues: 367 loop : -2.40 (0.18), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 218 HIS 0.008 0.002 HIS A 313 PHE 0.023 0.002 PHE A 294 TYR 0.021 0.002 TYR A 659 ARG 0.008 0.001 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 228 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 229 average time/residue: 0.2359 time to fit residues: 79.6684 Evaluate side-chains 156 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.601 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1376 time to fit residues: 2.5889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 0.5980 chunk 42 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 470 GLN A 542 ASN ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 ASN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN C 88 GLN C 112 HIS D 192 HIS D 329 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.6161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12282 Z= 0.274 Angle : 0.659 9.105 16652 Z= 0.346 Chirality : 0.045 0.173 1833 Planarity : 0.004 0.061 2152 Dihedral : 4.889 21.400 1639 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.08 % Allowed : 3.90 % Favored : 96.02 % 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: -2.21 (0.20), residues: 1508 helix: 0.20 (0.30), residues: 289 sheet: -1.50 (0.25), residues: 379 loop : -2.11 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 218 HIS 0.007 0.002 HIS B 92 PHE 0.022 0.002 PHE A 687 TYR 0.025 0.002 TYR A 642 ARG 0.007 0.001 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.2114 time to fit residues: 59.4048 Evaluate side-chains 140 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.442 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 5.9990 chunk 103 optimal weight: 0.0270 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 138 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 overall best weight: 1.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 HIS C 88 GLN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.7010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12282 Z= 0.257 Angle : 0.625 8.771 16652 Z= 0.330 Chirality : 0.045 0.194 1833 Planarity : 0.004 0.045 2152 Dihedral : 4.923 21.160 1639 Min Nonbonded Distance : 0.990 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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: -1.92 (0.21), residues: 1508 helix: 0.23 (0.30), residues: 286 sheet: -1.26 (0.25), residues: 386 loop : -1.85 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 218 HIS 0.018 0.002 HIS B 92 PHE 0.013 0.002 PHE A 687 TYR 0.024 0.002 TYR A 659 ARG 0.007 0.001 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2241 time to fit residues: 61.9957 Evaluate side-chains 123 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.500 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 109 optimal weight: 0.0570 chunk 60 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 ASN ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.7279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12282 Z= 0.181 Angle : 0.557 6.483 16652 Z= 0.293 Chirality : 0.044 0.191 1833 Planarity : 0.003 0.041 2152 Dihedral : 4.575 21.035 1639 Min Nonbonded Distance : 1.174 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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: -1.66 (0.21), residues: 1508 helix: 0.29 (0.30), residues: 286 sheet: -1.05 (0.25), residues: 397 loop : -1.65 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 218 HIS 0.017 0.001 HIS B 92 PHE 0.019 0.001 PHE B 296 TYR 0.020 0.002 TYR A 659 ARG 0.006 0.000 ARG A 443 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2192 time to fit residues: 56.8942 Evaluate side-chains 129 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.430 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.7411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12282 Z= 0.152 Angle : 0.539 6.577 16652 Z= 0.282 Chirality : 0.043 0.205 1833 Planarity : 0.003 0.037 2152 Dihedral : 4.335 19.396 1639 Min Nonbonded Distance : 1.196 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: -1.34 (0.21), residues: 1508 helix: 0.60 (0.31), residues: 280 sheet: -0.91 (0.26), residues: 402 loop : -1.40 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 218 HIS 0.011 0.001 HIS B 92 PHE 0.015 0.001 PHE C 86 TYR 0.017 0.001 TYR A 659 ARG 0.004 0.000 ARG B 367 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2213 time to fit residues: 60.5430 Evaluate side-chains 131 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.447 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 4.9990 chunk 16 optimal weight: 0.0980 chunk 83 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 89 optimal weight: 0.3980 chunk 67 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.7827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12282 Z= 0.191 Angle : 0.563 6.692 16652 Z= 0.298 Chirality : 0.043 0.186 1833 Planarity : 0.003 0.038 2152 Dihedral : 4.524 20.467 1639 Min Nonbonded Distance : 1.167 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: -1.16 (0.21), residues: 1508 helix: 0.68 (0.31), residues: 279 sheet: -0.65 (0.26), residues: 386 loop : -1.33 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 218 HIS 0.019 0.001 HIS B 92 PHE 0.018 0.001 PHE C 90 TYR 0.017 0.001 TYR A 642 ARG 0.004 0.000 ARG B 367 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2217 time to fit residues: 56.7034 Evaluate side-chains 127 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.451 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 72 optimal weight: 0.0050 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 133 optimal weight: 0.4980 chunk 140 optimal weight: 8.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.7943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12282 Z= 0.161 Angle : 0.550 6.931 16652 Z= 0.285 Chirality : 0.043 0.155 1833 Planarity : 0.003 0.039 2152 Dihedral : 4.336 19.431 1639 Min Nonbonded Distance : 1.200 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: -1.02 (0.21), residues: 1508 helix: 0.78 (0.31), residues: 278 sheet: -0.61 (0.26), residues: 395 loop : -1.21 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 218 HIS 0.018 0.001 HIS B 92 PHE 0.014 0.001 PHE C 90 TYR 0.015 0.001 TYR A 659 ARG 0.004 0.000 ARG B 367 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2188 time to fit residues: 58.0550 Evaluate side-chains 126 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.464 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 123 optimal weight: 0.3980 chunk 129 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.8333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12282 Z= 0.202 Angle : 0.590 7.276 16652 Z= 0.307 Chirality : 0.044 0.179 1833 Planarity : 0.003 0.050 2152 Dihedral : 4.536 19.933 1639 Min Nonbonded Distance : 1.166 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: -1.01 (0.21), residues: 1508 helix: 0.57 (0.30), residues: 285 sheet: -0.49 (0.26), residues: 391 loop : -1.21 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 218 HIS 0.019 0.001 HIS B 92 PHE 0.016 0.001 PHE C 90 TYR 0.015 0.001 TYR A 659 ARG 0.006 0.000 ARG B 367 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2297 time to fit residues: 57.4710 Evaluate side-chains 128 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.486 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 chunk 100 optimal weight: 0.0770 chunk 151 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 HIS ** C 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.8381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12282 Z= 0.152 Angle : 0.563 8.078 16652 Z= 0.290 Chirality : 0.044 0.172 1833 Planarity : 0.003 0.039 2152 Dihedral : 4.400 19.584 1639 Min Nonbonded Distance : 1.210 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -0.85 (0.21), residues: 1508 helix: 0.78 (0.31), residues: 281 sheet: -0.34 (0.27), residues: 383 loop : -1.14 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 345 HIS 0.018 0.001 HIS B 92 PHE 0.012 0.001 PHE C 90 TYR 0.016 0.001 TYR B 308 ARG 0.006 0.000 ARG B 367 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2258 time to fit residues: 58.6489 Evaluate side-chains 125 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.390 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.9990 chunk 111 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.080095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.060080 restraints weight = 61752.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.061744 restraints weight = 40528.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.062979 restraints weight = 29758.627| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.8483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12282 Z= 0.151 Angle : 0.553 7.612 16652 Z= 0.286 Chirality : 0.044 0.168 1833 Planarity : 0.003 0.039 2152 Dihedral : 4.302 19.969 1639 Min Nonbonded Distance : 1.209 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: -0.82 (0.21), residues: 1508 helix: 0.80 (0.31), residues: 281 sheet: -0.38 (0.26), residues: 391 loop : -1.08 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 345 HIS 0.018 0.001 HIS B 92 PHE 0.012 0.001 PHE C 90 TYR 0.015 0.001 TYR A 659 ARG 0.006 0.000 ARG B 367 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2602.19 seconds wall clock time: 48 minutes 46.13 seconds (2926.13 seconds total)