Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 08:00:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksr_23024/04_2023/7ksr_23024.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksr_23024/04_2023/7ksr_23024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksr_23024/04_2023/7ksr_23024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksr_23024/04_2023/7ksr_23024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksr_23024/04_2023/7ksr_23024.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksr_23024/04_2023/7ksr_23024.pdb" } resolution = 4.1 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= -0.000 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 87 5.16 5 C 7499 2.51 5 N 2106 2.21 5 O 2164 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 TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 686": "NH1" <-> "NH2" Residue "A ASP 706": "OD1" <-> "OD2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 90": "OD1" <-> "OD2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D ARG 258": "NH1" <-> "NH2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 198": "OD1" <-> "OD2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "C ASP 446": "OD1" <-> "OD2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C GLU 493": "OE1" <-> "OE2" Residue "C TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 522": "NH1" <-> "NH2" Residue "C PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 414": "NH1" <-> "NH2" Residue "B PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11863 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: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2909 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 3 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: "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: "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: "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 911 SG CYS A 299 60.232 45.699 88.425 1.00 77.53 S ATOM 939 SG CYS A 302 57.071 45.555 86.837 0.99 75.84 S ATOM 985 SG CYS A 307 59.522 45.519 84.292 0.87 75.70 S ATOM 1591 SG CYS A 531 70.136 60.350 100.152 1.00112.25 S ATOM 1734 SG CYS A 550 66.043 57.750 100.459 1.00102.41 S ATOM 1534 SG CYS A 524 70.650 56.219 95.707 1.00105.16 S ATOM 1719 SG CYS A 548 66.859 55.656 97.184 1.00 97.15 S ATOM 1973 SG CYS A 581 48.139 64.118 91.620 1.00100.74 S ATOM 2031 SG CYS A 589 45.612 62.751 95.386 1.00111.99 S ATOM 1819 SG CYS A 561 48.886 66.206 95.929 1.00 97.71 S ATOM 1973 SG CYS A 581 48.139 64.118 91.620 1.00100.74 S ATOM 1973 SG CYS A 581 48.139 64.118 91.620 1.00100.74 S ATOM 2031 SG CYS A 589 45.612 62.751 95.386 1.00111.99 S ATOM 2110 SG CYS A 602 44.703 63.403 90.988 1.00106.02 S Time building chain proxies: 6.56, per 1000 atoms: 0.55 Number of scatterers: 11863 At special positions: 0 Unit cell: (90.45, 170.1, 132.3, 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 87 16.00 O 2164 8.00 N 2106 7.00 C 7499 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: 4.77 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 307 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 302 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 299 " pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb="ZN ZN A 803 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 531 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 550 " pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb="ZN ZN A 804 " pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 524 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 548 " pdb=" ZN A 805 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 589 " pdb="ZN ZN A 805 " - pdb="ZN ZN A 807 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 581 " pdb=" ZN A 806 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 581 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 561 " pdb=" ZN A 807 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 581 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 589 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 602 " 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2924 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 22 sheets defined 20.4% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 34 through 63 removed outlier: 3.759A pdb=" N LYS A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A 63 " --> pdb=" O GLU A 59 " (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 435 through 450 Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 464 through 474 Processing helix chain 'A' and resid 535 through 541 removed outlier: 3.852A pdb=" N MET A 539 " --> pdb=" O CYS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 removed outlier: 3.850A 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 Processing helix chain 'D' and resid 12 through 28 Processing helix chain 'D' and resid 355 through 362 removed outlier: 4.058A pdb=" N ASP D 361 " --> pdb=" O GLU D 357 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.184A pdb=" N TYR D 409 " --> pdb=" O ALA D 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 107 Proline residue: C 93 - end of helix removed outlier: 3.537A pdb=" N ILE C 96 " --> pdb=" O LYS C 92 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR C 102 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 115 removed outlier: 3.506A pdb=" N LEU C 115 " --> pdb=" O HIS C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 145 Processing helix chain 'C' and resid 459 through 470 removed outlier: 3.533A pdb=" N LEU C 463 " --> pdb=" O LYS C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 602 removed outlier: 3.931A pdb=" N ARG C 593 " --> pdb=" O PRO C 589 " (cutoff:3.500A) removed outlier: 3.642A 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: 4.139A pdb=" N MET C 637 " --> pdb=" O ASN C 633 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU C 641 " --> pdb=" O MET C 637 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN C 645 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LYS C 646 " --> pdb=" O ASN C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 666 removed outlier: 3.707A pdb=" N PHE C 666 " --> pdb=" O SER C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 686 Processing helix chain 'B' and resid 267 through 279 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.642A pdb=" N LYS B 342 " --> pdb=" O ASP B 339 " (cutoff:3.500A) removed outlier: 3.936A 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 'B' and resid 395 through 399 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: 5.865A 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: 6.617A 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: 6.785A pdb=" N PHE A 638 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA A 713 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 377 through 382 removed outlier: 3.718A pdb=" N LEU D 34 " --> pdb=" O GLN D 403 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL D 35 " --> pdb=" O LEU C 529 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C 529 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 47 through 54 removed outlier: 5.463A pdb=" N ARG D 65 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ASP D 52 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE D 63 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N THR D 54 " --> pdb=" O PHE D 61 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N PHE D 61 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ASN D 77 " --> pdb=" O ASN D 122 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASN D 122 " --> pdb=" O ASN D 77 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU D 79 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS D 120 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE D 81 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 130 through 132 Processing sheet with id=AA9, first strand: chain 'D' and resid 183 through 185 removed outlier: 3.603A pdb=" N SER D 197 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 230 through 235 removed outlier: 3.809A pdb=" N LYS D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 276 through 281 removed outlier: 3.886A pdb=" N THR D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N HIS D 311 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 320 through 322 removed outlier: 7.074A pdb=" N SER D 336 " --> pdb=" O PHE D 321 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASP D 346 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU D 366 " --> pdb=" O ASP D 346 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 160 through 161 removed outlier: 4.156A pdb=" N LEU C 355 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL C 317 " --> pdb=" O LEU C 355 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE C 357 " --> pdb=" O TYR C 315 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR C 315 " --> pdb=" O PHE C 357 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 203 through 210 removed outlier: 4.303A pdb=" N ARG C 204 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS C 190 " --> pdb=" O ARG C 204 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR C 208 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL C 186 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU C 185 " --> pdb=" O ARG C 253 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 187 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU C 250 " --> pdb=" O MET C 299 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 297 " --> pdb=" O PHE C 252 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 437 through 441 removed outlier: 4.212A pdb=" N ARG C 439 " --> pdb=" O PHE C 432 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE C 432 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLN C 441 " --> pdb=" O TYR C 430 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TYR C 430 " --> pdb=" O GLN C 441 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 83 through 89 removed outlier: 6.358A pdb=" N CYS B 84 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP B 438 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN B 86 " --> pdb=" O ARG B 436 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 98 through 101 removed outlier: 4.064A pdb=" N GLY B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN B 136 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU B 125 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU B 134 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 147 through 154 removed outlier: 4.448A pdb=" N THR B 149 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA B 166 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 167 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 184 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASN B 176 " --> pdb=" O CYS B 182 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N CYS B 182 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 193 through 198 removed outlier: 3.670A pdb=" N GLU B 195 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU B 215 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ILE B 228 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU B 217 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 10.746A pdb=" N GLN B 292 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N VAL B 226 " --> pdb=" O GLN B 292 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 239 through 244 Processing sheet with id=AC3, first strand: chain 'B' and resid 312 through 315 removed outlier: 7.226A pdb=" N LYS B 332 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE B 352 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 368 through 369 385 hydrogen bonds defined for protein. 1077 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: 4.02 Time building geometry restraints manager: 5.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3911 1.35 - 1.46: 2795 1.46 - 1.58: 5305 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 12131 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 5.26e+00 bond pdb=" CB ILE A 456 " pdb=" CG2 ILE A 456 " ideal model delta sigma weight residual 1.521 1.565 -0.044 3.30e-02 9.18e+02 1.80e+00 bond pdb=" C ASN D 186 " pdb=" N PRO D 187 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.74e+00 bond pdb=" C ASN D 282 " pdb=" N PRO D 283 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.69e+00 bond pdb=" C SER D 326 " pdb=" N PRO D 327 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.62e+00 ... (remaining 12126 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.98: 397 106.98 - 113.73: 6600 113.73 - 120.48: 4495 120.48 - 127.24: 4764 127.24 - 133.99: 187 Bond angle restraints: 16443 Sorted by residual: angle pdb=" N THR D 28 " pdb=" CA THR D 28 " pdb=" C THR D 28 " ideal model delta sigma weight residual 109.81 116.61 -6.80 2.21e+00 2.05e-01 9.48e+00 angle pdb=" CA THR D 28 " pdb=" C THR D 28 " pdb=" N PRO D 29 " ideal model delta sigma weight residual 118.44 122.81 -4.37 1.59e+00 3.96e-01 7.55e+00 angle pdb=" C LYS C 587 " pdb=" N ASP C 588 " pdb=" CA ASP C 588 " ideal model delta sigma weight residual 121.80 128.43 -6.63 2.44e+00 1.68e-01 7.39e+00 angle pdb=" CA LYS C 92 " pdb=" C LYS C 92 " pdb=" N PRO C 93 " ideal model delta sigma weight residual 118.44 122.75 -4.31 1.59e+00 3.96e-01 7.36e+00 angle pdb=" N SER D 184 " pdb=" CA SER D 184 " pdb=" C SER D 184 " ideal model delta sigma weight residual 108.32 112.42 -4.10 1.64e+00 3.72e-01 6.25e+00 ... (remaining 16438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 6781 17.54 - 35.08: 390 35.08 - 52.61: 51 52.61 - 70.15: 13 70.15 - 87.69: 8 Dihedral angle restraints: 7243 sinusoidal: 2773 harmonic: 4470 Sorted by residual: 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 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA LYS D 251 " pdb=" C LYS D 251 " pdb=" N LEU D 252 " pdb=" CA LEU D 252 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 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 180.00 160.26 19.74 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 7240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1146 0.035 - 0.071: 459 0.071 - 0.106: 117 0.106 - 0.142: 77 0.142 - 0.177: 16 Chirality restraints: 1815 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 7.83e-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 0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA ILE D 81 " pdb=" N ILE D 81 " pdb=" C ILE D 81 " pdb=" CB ILE D 81 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 1812 not shown) Planarity restraints: 2118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 201 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.54e+00 pdb=" N PRO C 202 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 202 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 202 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 28 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO D 29 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 29 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 29 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 86 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO D 87 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 87 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 87 " -0.024 5.00e-02 4.00e+02 ... (remaining 2115 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 756 2.74 - 3.28: 11601 3.28 - 3.82: 17769 3.82 - 4.36: 21450 4.36 - 4.90: 37885 Nonbonded interactions: 89461 Sorted by model distance: nonbonded pdb=" OG SER D 147 " pdb=" O HIS D 176 " model vdw 2.200 2.440 nonbonded pdb=" O ASP C 136 " pdb=" OG SER C 139 " model vdw 2.216 2.440 nonbonded pdb=" OG SER D 285 " pdb=" OD1 ASP C 135 " model vdw 2.218 2.440 nonbonded pdb=" OD1 ASP B 431 " pdb=" OG SER B 433 " model vdw 2.237 2.440 nonbonded pdb=" OG1 THR A 315 " pdb=" OD1 ASN A 317 " model vdw 2.308 2.440 ... (remaining 89456 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: 1.120 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: 0.010 Extract box with map and model: 6.810 Check model and map are aligned: 0.190 Set scattering table: 0.100 Process input model: 35.990 Find NCS groups from input model: 0.530 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 12131 Z= 0.289 Angle : 0.697 8.135 16443 Z= 0.366 Chirality : 0.047 0.177 1815 Planarity : 0.004 0.047 2118 Dihedral : 11.737 87.689 4319 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 0.00 % 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: -4.46 (0.16), residues: 1484 helix: -2.26 (0.21), residues: 274 sheet: -3.18 (0.23), residues: 303 loop : -3.26 (0.16), residues: 907 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 497 time to evaluate : 1.403 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 497 average time/residue: 0.2851 time to fit residues: 193.4268 Evaluate side-chains 226 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.425 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 ASN A 556 ASN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN D 188 ASN D 267 HIS C 104 ASN C 440 GLN C 624 HIS C 634 HIS C 664 HIS B 104 HIS B 194 ASN B 204 ASN B 235 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 12131 Z= 0.240 Angle : 0.599 7.652 16443 Z= 0.317 Chirality : 0.045 0.227 1815 Planarity : 0.004 0.052 2118 Dihedral : 4.508 20.254 1617 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 0.24 % 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: -3.15 (0.19), residues: 1484 helix: -0.58 (0.28), residues: 284 sheet: -2.25 (0.25), residues: 326 loop : -2.65 (0.18), residues: 874 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 251 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 253 average time/residue: 0.2457 time to fit residues: 93.2166 Evaluate side-chains 171 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.492 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 0.0870 chunk 113 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 37 optimal weight: 0.0980 chunk 136 optimal weight: 0.0570 chunk 147 optimal weight: 10.0000 chunk 121 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 HIS D 272 HIS ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 HIS ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 HIS B 415 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 12131 Z= 0.146 Angle : 0.523 6.989 16443 Z= 0.275 Chirality : 0.044 0.187 1815 Planarity : 0.003 0.041 2118 Dihedral : 4.179 19.191 1617 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.00 % 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: -2.47 (0.20), residues: 1484 helix: 0.21 (0.30), residues: 291 sheet: -1.78 (0.25), residues: 329 loop : -2.33 (0.18), residues: 864 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.687 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: 239 average time/residue: 0.2224 time to fit residues: 79.8279 Evaluate side-chains 168 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.412 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 129 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 ASN D 267 HIS D 272 HIS ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS B 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 12131 Z= 0.166 Angle : 0.528 7.136 16443 Z= 0.279 Chirality : 0.043 0.176 1815 Planarity : 0.003 0.038 2118 Dihedral : 4.182 20.353 1617 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.20), residues: 1484 helix: 0.60 (0.32), residues: 285 sheet: -1.22 (0.27), residues: 352 loop : -2.10 (0.19), residues: 847 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 230 time to evaluate : 1.464 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 outliers start: 1 outliers final: 1 residues processed: 231 average time/residue: 0.2106 time to fit residues: 73.9844 Evaluate side-chains 163 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 1.468 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1158 time to fit residues: 2.2301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 3.9990 chunk 82 optimal weight: 30.0000 chunk 2 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 100 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 HIS D 272 HIS ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 HIS ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN B 397 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 12131 Z= 0.190 Angle : 0.547 8.668 16443 Z= 0.288 Chirality : 0.044 0.235 1815 Planarity : 0.003 0.037 2118 Dihedral : 4.216 21.810 1617 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 0.00 % 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: -1.78 (0.21), residues: 1484 helix: 0.53 (0.32), residues: 287 sheet: -1.13 (0.27), residues: 363 loop : -1.87 (0.19), residues: 834 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2031 time to fit residues: 64.4855 Evaluate side-chains 151 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.499 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 35 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 HIS ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS D 277 ASN D 354 GLN ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 12131 Z= 0.171 Angle : 0.523 7.131 16443 Z= 0.276 Chirality : 0.044 0.205 1815 Planarity : 0.003 0.036 2118 Dihedral : 4.201 21.391 1617 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 0.00 % 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: -1.48 (0.21), residues: 1484 helix: 0.75 (0.32), residues: 282 sheet: -0.66 (0.28), residues: 352 loop : -1.79 (0.20), residues: 850 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1931 time to fit residues: 59.0737 Evaluate side-chains 145 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.464 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.8980 chunk 82 optimal weight: 30.0000 chunk 105 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 81 optimal weight: 0.4980 chunk 144 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 GLN D 272 HIS ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 HIS ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.6684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 12131 Z= 0.269 Angle : 0.609 6.898 16443 Z= 0.323 Chirality : 0.046 0.193 1815 Planarity : 0.004 0.037 2118 Dihedral : 4.645 26.412 1617 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.21), residues: 1484 helix: 0.62 (0.32), residues: 284 sheet: -0.71 (0.27), residues: 381 loop : -1.78 (0.20), residues: 819 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 185 average time/residue: 0.2139 time to fit residues: 60.8820 Evaluate side-chains 133 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 1.438 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1448 time to fit residues: 2.2470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.0770 chunk 43 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 0.3980 chunk 13 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 126 optimal weight: 0.0470 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 272 HIS ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS B 219 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.6659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 12131 Z= 0.137 Angle : 0.519 6.960 16443 Z= 0.273 Chirality : 0.043 0.173 1815 Planarity : 0.003 0.036 2118 Dihedral : 4.211 22.027 1617 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 0.00 % 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: -1.23 (0.21), residues: 1484 helix: 0.78 (0.31), residues: 282 sheet: -0.42 (0.28), residues: 359 loop : -1.60 (0.20), residues: 843 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.378 Fit side-chains 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: 186 average time/residue: 0.1884 time to fit residues: 56.2732 Evaluate side-chains 133 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.493 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.2980 chunk 138 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 86 optimal weight: 0.0010 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 HIS D 272 HIS ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN B 219 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.6796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 12131 Z= 0.155 Angle : 0.537 8.312 16443 Z= 0.280 Chirality : 0.044 0.185 1815 Planarity : 0.003 0.036 2118 Dihedral : 4.176 23.657 1617 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 0.00 % 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: -1.15 (0.22), residues: 1484 helix: 0.79 (0.31), residues: 283 sheet: -0.47 (0.27), residues: 385 loop : -1.50 (0.21), residues: 816 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.450 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: 0.1982 time to fit residues: 55.9470 Evaluate side-chains 137 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.500 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 91 optimal weight: 0.0370 chunk 72 optimal weight: 6.9990 chunk 94 optimal weight: 0.4980 chunk 126 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 272 HIS ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.6912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 12131 Z= 0.159 Angle : 0.540 9.479 16443 Z= 0.280 Chirality : 0.044 0.185 1815 Planarity : 0.003 0.036 2118 Dihedral : 4.118 24.244 1617 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 0.00 % 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: -1.09 (0.21), residues: 1484 helix: 0.78 (0.31), residues: 283 sheet: -0.40 (0.28), residues: 364 loop : -1.44 (0.21), residues: 837 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.478 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: 171 average time/residue: 0.1855 time to fit residues: 51.1736 Evaluate side-chains 133 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.528 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 119 optimal weight: 0.0040 chunk 49 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 104 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 86 optimal weight: 0.3980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 HIS ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.129773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.100956 restraints weight = 29888.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.100590 restraints weight = 19411.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.101981 restraints weight = 14790.772| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.6970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 12131 Z= 0.143 Angle : 0.531 7.610 16443 Z= 0.277 Chirality : 0.044 0.201 1815 Planarity : 0.003 0.036 2118 Dihedral : 4.083 26.149 1617 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 0.00 % 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: -1.06 (0.22), residues: 1484 helix: 0.72 (0.31), residues: 282 sheet: -0.35 (0.27), residues: 380 loop : -1.41 (0.21), residues: 822 =============================================================================== Job complete usr+sys time: 2584.44 seconds wall clock time: 47 minutes 57.42 seconds (2877.42 seconds total)