Starting phenix.real_space_refine (version: dev) on Thu Dec 15 03:34:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whv_21677/12_2022/6whv_21677_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whv_21677/12_2022/6whv_21677.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whv_21677/12_2022/6whv_21677_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whv_21677/12_2022/6whv_21677_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whv_21677/12_2022/6whv_21677_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whv_21677/12_2022/6whv_21677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whv_21677/12_2022/6whv_21677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whv_21677/12_2022/6whv_21677_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whv_21677/12_2022/6whv_21677_updated.pdb" } resolution = 4.05 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= 0.008 sd= 0.860 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 172": "OE1" <-> "OE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A ARG 569": "NH1" <-> "NH2" Residue "A GLU 642": "OE1" <-> "OE2" Residue "A GLU 728": "OE1" <-> "OE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 657": "OE1" <-> "OE2" Residue "B GLU 788": "OE1" <-> "OE2" Residue "B TYR 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C GLU 549": "OE1" <-> "OE2" Residue "C PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 683": "OE1" <-> "OE2" Residue "C TYR 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 719": "OE1" <-> "OE2" Residue "C GLU 772": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 521": "OE1" <-> "OE2" Residue "D GLU 657": "OE1" <-> "OE2" Residue "D ARG 673": "NH1" <-> "NH2" Residue "D GLU 788": "OE1" <-> "OE2" Residue "D GLU 791": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 23764 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 5936 Classifications: {'peptide': 803} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 35, 'TRANS': 767} Chain breaks: 3 Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 500 Unresolved non-hydrogen dihedrals: 366 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 16, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 288 Chain: "B" Number of atoms: 5697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 5697 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'PTRANS': 27, 'TRANS': 755} Chain breaks: 2 Unresolved non-hydrogen bonds: 505 Unresolved non-hydrogen angles: 602 Unresolved non-hydrogen dihedrals: 440 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 14, 'TYR:plan': 4, 'ASN:plan1': 4, 'HIS:plan': 5, 'PHE:plan': 5, 'GLU:plan': 18, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 301 Chain: "C" Number of atoms: 6040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 6040 Classifications: {'peptide': 800} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 35, 'TRANS': 764} Chain breaks: 3 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 165 Chain: "D" Number of atoms: 5930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 5930 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 28, 'TRANS': 755} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 238 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 163 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 13.32, per 1000 atoms: 0.56 Number of scatterers: 23764 At special positions: 0 Unit cell: (137, 149.33, 189.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 6 17.00 S 145 16.00 P 2 15.00 O 4510 8.00 N 3863 7.00 C 15238 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.04 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.04 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS D 557 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.04 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.02 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS C 831 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.04 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.04 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.04 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.04 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.04 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=5, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1001 " - " ASN A 297 " " NAG B 902 " - " ASN B 542 " " NAG D 902 " - " ASN D 542 " " NAG D 903 " - " ASN D 688 " " NAG E 1 " - " ASN B 341 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.00 Conformation dependent library (CDL) restraints added in 3.6 seconds 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB QGM C1001 " Number of C-beta restraints generated: 5920 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 27 sheets defined 36.2% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 36 through 51 removed outlier: 3.554A pdb=" N ASN A 50 " --> pdb=" O ASN A 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 51 " --> pdb=" O GLN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.600A pdb=" N LEU A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 108 No H-bonds generated for 'chain 'A' and resid 105 through 108' Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 144 through 157 Processing helix chain 'A' and resid 171 through 185 removed outlier: 4.032A pdb=" N LEU A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLU A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.937A pdb=" N MET A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 removed outlier: 3.751A pdb=" N ALA A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR A 251 " --> pdb=" O ASP A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.980A pdb=" N ARG A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 318 removed outlier: 3.550A pdb=" N ASP A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU A 318 " --> pdb=" O HIS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 348 Processing helix chain 'A' and resid 480 through 491 removed outlier: 3.540A pdb=" N ARG A 489 " --> pdb=" O ILE A 485 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 527 Processing helix chain 'A' and resid 543 through 547 removed outlier: 3.752A pdb=" N TYR A 547 " --> pdb=" O ARG A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 602 removed outlier: 3.597A pdb=" N GLY A 588 " --> pdb=" O TRP A 584 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 636 removed outlier: 3.724A pdb=" N VAL A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 678 removed outlier: 4.220A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 693 No H-bonds generated for 'chain 'A' and resid 691 through 693' Processing helix chain 'A' and resid 709 through 715 Processing helix chain 'A' and resid 720 through 728 removed outlier: 3.990A pdb=" N ARG A 725 " --> pdb=" O THR A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 744 removed outlier: 3.615A pdb=" N GLN A 740 " --> pdb=" O ALA A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 790 through 801 Processing helix chain 'A' and resid 805 through 813 removed outlier: 3.687A pdb=" N LYS A 811 " --> pdb=" O GLU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 860 removed outlier: 3.837A pdb=" N ALA A 842 " --> pdb=" O MET A 839 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE A 852 " --> pdb=" O ILE A 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 78 through 89 Processing helix chain 'B' and resid 108 through 119 removed outlier: 3.630A pdb=" N ALA B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR B 119 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 180 through 190 Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'B' and resid 219 through 222 No H-bonds generated for 'chain 'B' and resid 219 through 222' Processing helix chain 'B' and resid 234 through 247 Processing helix chain 'B' and resid 289 through 310 Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 335 through 339 Processing helix chain 'B' and resid 461 through 472 removed outlier: 3.792A pdb=" N LYS B 466 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 502 removed outlier: 4.355A pdb=" N VAL B 501 " --> pdb=" O MET B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 522 No H-bonds generated for 'chain 'B' and resid 519 through 522' Processing helix chain 'B' and resid 556 through 577 Processing helix chain 'B' and resid 603 through 613 removed outlier: 3.832A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 651 removed outlier: 4.211A pdb=" N VAL B 634 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 672 No H-bonds generated for 'chain 'B' and resid 669 through 672' Processing helix chain 'B' and resid 690 through 695 Processing helix chain 'B' and resid 700 through 708 Processing helix chain 'B' and resid 715 through 722 Processing helix chain 'B' and resid 733 through 741 removed outlier: 4.524A pdb=" N TYR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY B 741 " --> pdb=" O ASN B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 786 removed outlier: 3.823A pdb=" N ASP B 786 " --> pdb=" O GLN B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 796 Processing helix chain 'B' and resid 818 through 844 removed outlier: 4.466A pdb=" N TYR B 843 " --> pdb=" O HIS B 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 50 removed outlier: 4.160A pdb=" N ASN C 47 " --> pdb=" O GLU C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 81 removed outlier: 5.018A pdb=" N ALA C 75 " --> pdb=" O ILE C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 107 through 114 removed outlier: 3.978A pdb=" N ALA C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 129 removed outlier: 3.505A pdb=" N SER C 129 " --> pdb=" O SER C 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 126 through 129' Processing helix chain 'C' and resid 146 through 157 removed outlier: 4.173A pdb=" N VAL C 150 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET C 154 " --> pdb=" O TRP C 151 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N MET C 155 " --> pdb=" O PHE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 184 removed outlier: 3.953A pdb=" N ALA C 175 " --> pdb=" O HIS C 171 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ALA C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 234 Processing helix chain 'C' and resid 248 through 258 removed outlier: 4.021A pdb=" N ALA C 255 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 278 through 281 No H-bonds generated for 'chain 'C' and resid 278 through 281' Processing helix chain 'C' and resid 298 through 317 removed outlier: 3.628A pdb=" N ILE C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N HIS C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 348 removed outlier: 4.561A pdb=" N SER C 348 " --> pdb=" O ARG C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 491 Processing helix chain 'C' and resid 521 through 528 Processing helix chain 'C' and resid 544 through 547 No H-bonds generated for 'chain 'C' and resid 544 through 547' Processing helix chain 'C' and resid 581 through 603 removed outlier: 4.274A pdb=" N LEU C 585 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N HIS C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG C 603 " --> pdb=" O TYR C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 636 removed outlier: 3.599A pdb=" N TRP C 632 " --> pdb=" O MET C 628 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 677 removed outlier: 3.782A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 694 No H-bonds generated for 'chain 'C' and resid 691 through 694' Processing helix chain 'C' and resid 712 through 716 Processing helix chain 'C' and resid 721 through 728 removed outlier: 4.299A pdb=" N HIS C 726 " --> pdb=" O THR C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 744 Processing helix chain 'C' and resid 754 through 760 removed outlier: 5.265A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 800 removed outlier: 3.701A pdb=" N LEU C 798 " --> pdb=" O SER C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 806 through 813 removed outlier: 4.770A pdb=" N LYS C 811 " --> pdb=" O GLU C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 861 removed outlier: 5.034A pdb=" N GLY C 836 " --> pdb=" O GLU C 832 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL C 837 " --> pdb=" O ASN C 833 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE C 838 " --> pdb=" O MET C 834 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C 840 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 841 " --> pdb=" O VAL C 837 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE C 853 " --> pdb=" O ILE C 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 57 removed outlier: 3.532A pdb=" N ASP D 52 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU D 55 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP D 57 " --> pdb=" O HIS D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 89 removed outlier: 4.113A pdb=" N LEU D 88 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET D 89 " --> pdb=" O ILE D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 119 removed outlier: 3.793A pdb=" N LEU D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN D 118 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR D 119 " --> pdb=" O ILE D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 163 Processing helix chain 'D' and resid 180 through 191 Processing helix chain 'D' and resid 210 through 221 removed outlier: 4.175A pdb=" N SER D 214 " --> pdb=" O ASP D 210 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 246 removed outlier: 3.992A pdb=" N SER D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 308 removed outlier: 4.110A pdb=" N MET D 307 " --> pdb=" O ALA D 303 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 328 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 460 through 472 Processing helix chain 'D' and resid 496 through 502 removed outlier: 3.644A pdb=" N VAL D 501 " --> pdb=" O MET D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 520 No H-bonds generated for 'chain 'D' and resid 517 through 520' Processing helix chain 'D' and resid 549 through 551 No H-bonds generated for 'chain 'D' and resid 549 through 551' Processing helix chain 'D' and resid 557 through 577 Processing helix chain 'D' and resid 602 through 613 Processing helix chain 'D' and resid 627 through 651 Processing helix chain 'D' and resid 669 through 672 No H-bonds generated for 'chain 'D' and resid 669 through 672' Processing helix chain 'D' and resid 674 through 676 No H-bonds generated for 'chain 'D' and resid 674 through 676' Processing helix chain 'D' and resid 690 through 693 No H-bonds generated for 'chain 'D' and resid 690 through 693' Processing helix chain 'D' and resid 701 through 705 Processing helix chain 'D' and resid 715 through 720 Processing helix chain 'D' and resid 733 through 742 removed outlier: 4.783A pdb=" N TYR D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLY D 741 " --> pdb=" O ASN D 737 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG D 742 " --> pdb=" O TYR D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 785 Processing helix chain 'D' and resid 789 through 795 Processing helix chain 'D' and resid 815 through 843 removed outlier: 3.721A pdb=" N ALA D 819 " --> pdb=" O ILE D 815 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY D 820 " --> pdb=" O ASP D 816 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL D 821 " --> pdb=" O ASN D 817 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 30 through 32 removed outlier: 7.811A pdb=" N THR A 63 " --> pdb=" O ALA A 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.796A pdb=" N VAL A 92 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 164 through 167 removed outlier: 3.757A pdb=" N SER A 243 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL A 267 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A 242 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A 269 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 386 through 389 Processing sheet with id= E, first strand: chain 'A' and resid 418 through 422 removed outlier: 6.855A pdb=" N THR A 494 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE A 421 " --> pdb=" O THR A 494 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLU A 496 " --> pdb=" O ILE A 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 430 through 432 removed outlier: 3.539A pdb=" N TYR A 477 " --> pdb=" O TYR A 431 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 559 through 561 removed outlier: 3.850A pdb=" N TRP A 752 " --> pdb=" O THR A 560 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 534 through 538 removed outlier: 3.663A pdb=" N GLY A 782 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ALA A 536 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLY A 780 " --> pdb=" O ALA A 536 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 39 through 42 removed outlier: 8.267A pdb=" N VAL B 98 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N VAL B 42 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N ALA B 100 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 99 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP B 101 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 171 through 173 removed outlier: 5.867A pdb=" N LEU B 229 " --> pdb=" O VAL B 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 279 through 281 removed outlier: 3.613A pdb=" N SER B 279 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B 362 " --> pdb=" O TRP B 379 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP B 379 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY B 377 " --> pdb=" O ILE B 364 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 530 through 532 removed outlier: 4.007A pdb=" N ILE B 530 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR B 532 " --> pdb=" O THR B 760 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 534 through 536 Processing sheet with id= N, first strand: chain 'B' and resid 655 through 657 removed outlier: 3.795A pdb=" N GLN B 656 " --> pdb=" O VAL B 808 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 26 through 29 removed outlier: 6.220A pdb=" N GLN C 59 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE C 29 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN C 61 " --> pdb=" O ILE C 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 90 through 92 Processing sheet with id= Q, first strand: chain 'C' and resid 165 through 167 removed outlier: 6.270A pdb=" N ILE C 241 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 269 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 242 " --> pdb=" O LEU C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 372 through 377 removed outlier: 4.447A pdb=" N TYR C 372 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE C 387 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 374 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL C 385 " --> pdb=" O ILE C 374 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 419 through 422 removed outlier: 4.029A pdb=" N GLU C 496 " --> pdb=" O LEU C 419 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 430 through 434 removed outlier: 3.521A pdb=" N CYS C 476 " --> pdb=" O VAL C 455 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 508 through 511 removed outlier: 4.259A pdb=" N LYS C 516 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 749 through 753 removed outlier: 3.998A pdb=" N ILE C 561 " --> pdb=" O THR C 770 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR C 770 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C 563 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 768 " --> pdb=" O VAL C 563 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 66 through 73 removed outlier: 6.583A pdb=" N ILE D 35 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLU D 69 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE D 37 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL D 71 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL D 39 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N MET D 73 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE D 40 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 171 through 173 removed outlier: 8.167A pdb=" N VAL D 172 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU D 229 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N THR D 255 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N LEU D 230 " --> pdb=" O THR D 255 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE D 257 " --> pdb=" O LEU D 230 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'D' and resid 278 through 281 removed outlier: 3.639A pdb=" N SER D 279 " --> pdb=" O ILE D 365 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 408 through 410 removed outlier: 3.972A pdb=" N TYR D 479 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR D 410 " --> pdb=" O TYR D 479 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'D' and resid 434 through 436 removed outlier: 3.663A pdb=" N VAL D 434 " --> pdb=" O CYS D 457 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 1737 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.80 Time building geometry restraints manager: 11.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3984 1.31 - 1.44: 6492 1.44 - 1.57: 13552 1.57 - 1.70: 3 1.70 - 1.83: 253 Bond restraints: 24284 Sorted by residual: bond pdb=" C1 QGP D 901 " pdb=" P QGP D 901 " ideal model delta sigma weight residual 1.862 1.624 0.238 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C1 QGP B 901 " pdb=" P QGP B 901 " ideal model delta sigma weight residual 1.862 1.645 0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C4 QGP B 901 " pdb=" O6 QGP B 901 " ideal model delta sigma weight residual 1.400 1.225 0.175 2.00e-02 2.50e+03 7.63e+01 bond pdb=" C4 QGP D 901 " pdb=" O6 QGP D 901 " ideal model delta sigma weight residual 1.400 1.226 0.174 2.00e-02 2.50e+03 7.59e+01 bond pdb=" C12 QGP B 901 " pdb=" C7 QGP B 901 " ideal model delta sigma weight residual 1.528 1.381 0.147 2.00e-02 2.50e+03 5.41e+01 ... (remaining 24279 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.19: 613 106.19 - 113.17: 13555 113.17 - 120.15: 8656 120.15 - 127.13: 10054 127.13 - 134.11: 273 Bond angle restraints: 33151 Sorted by residual: angle pdb=" N GLY B 129 " pdb=" CA GLY B 129 " pdb=" C GLY B 129 " ideal model delta sigma weight residual 114.66 105.10 9.56 1.24e+00 6.50e-01 5.95e+01 angle pdb=" C THR C 812 " pdb=" N TRP C 813 " pdb=" CA TRP C 813 " ideal model delta sigma weight residual 121.52 113.26 8.26 1.74e+00 3.30e-01 2.25e+01 angle pdb=" N SER B 170 " pdb=" CA SER B 170 " pdb=" C SER B 170 " ideal model delta sigma weight residual 110.24 115.64 -5.40 1.30e+00 5.92e-01 1.73e+01 angle pdb=" C TRP C 813 " pdb=" N VAL C 814 " pdb=" CA VAL C 814 " ideal model delta sigma weight residual 122.77 118.88 3.89 1.05e+00 9.07e-01 1.37e+01 angle pdb=" C THR A 830 " pdb=" N CYS A 831 " pdb=" CA CYS A 831 " ideal model delta sigma weight residual 121.54 128.51 -6.97 1.91e+00 2.74e-01 1.33e+01 ... (remaining 33146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12736 17.94 - 35.88: 1254 35.88 - 53.82: 189 53.82 - 71.76: 42 71.76 - 89.70: 25 Dihedral angle restraints: 14246 sinusoidal: 5064 harmonic: 9182 Sorted by residual: dihedral pdb=" CB CYS B 86 " pdb=" SG CYS B 86 " pdb=" SG CYS B 321 " pdb=" CB CYS B 321 " ideal model delta sinusoidal sigma weight residual -86.00 -2.18 -83.82 1 1.00e+01 1.00e-02 8.57e+01 dihedral pdb=" CB CYS D 86 " pdb=" SG CYS D 86 " pdb=" SG CYS D 321 " pdb=" CB CYS D 321 " ideal model delta sinusoidal sigma weight residual -86.00 -5.64 -80.36 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" CB CYS B 429 " pdb=" SG CYS B 429 " pdb=" SG CYS B 456 " pdb=" CB CYS B 456 " ideal model delta sinusoidal sigma weight residual 93.00 171.23 -78.23 1 1.00e+01 1.00e-02 7.64e+01 ... (remaining 14243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.882: 3893 0.882 - 1.764: 0 1.764 - 2.645: 0 2.645 - 3.527: 0 3.527 - 4.409: 1 Chirality restraints: 3894 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 2.01 -4.41 2.00e-02 2.50e+03 4.86e+04 chirality pdb=" CG QGM C1001 " pdb=" CB QGM C1001 " pdb=" CD1 QGM C1001 " pdb=" ND2 QGM C1001 " both_signs ideal model delta sigma weight residual False -2.43 -2.67 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA THR C 103 " pdb=" N THR C 103 " pdb=" C THR C 103 " pdb=" CB THR C 103 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.98e-01 ... (remaining 3891 not shown) Planarity restraints: 4226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 825 " 0.056 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO A 826 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 826 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 826 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 679 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.65e+00 pdb=" N PRO D 680 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO D 680 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 680 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 414 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO D 415 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 415 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 415 " -0.032 5.00e-02 4.00e+02 ... (remaining 4223 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 599 2.64 - 3.21: 25351 3.21 - 3.77: 35301 3.77 - 4.34: 45833 4.34 - 4.90: 68962 Nonbonded interactions: 176046 Sorted by model distance: nonbonded pdb=" O VAL D 243 " pdb=" OG SER D 246 " model vdw 2.076 2.440 nonbonded pdb=" O ASP B 113 " pdb=" OG SER B 116 " model vdw 2.079 2.440 nonbonded pdb=" OG SER D 34 " pdb=" O VAL D 65 " model vdw 2.115 2.440 nonbonded pdb=" OH TYR D 507 " pdb=" OG SER D 770 " model vdw 2.137 2.440 nonbonded pdb=" OG SER D 352 " pdb=" OD1 ASP D 354 " model vdw 2.141 2.440 ... (remaining 176041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 98 or (resid 99 through 102 and (name N or name \ CA or name C or name O or name CB )) or resid 103 through 114 or (resid 115 and \ (name N or name CA or name C or name O or name CB )) or resid 116 through 169 o \ r (resid 170 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 71 or (resid 172 and (name N or name CA or name C or name O or name CB )) or res \ id 173 through 190 or resid 207 through 210 or (resid 211 through 212 and (name \ N or name CA or name C or name O or name CB )) or resid 213 through 222 or (resi \ d 223 and (name N or name CA or name C or name O or name CB )) or resid 224 thro \ ugh 271 or (resid 272 and (name N or name CA or name C or name O or name CB )) o \ r resid 273 or (resid 274 and (name N or name CA or name C or name O or name CB \ )) or resid 275 through 280 or (resid 281 and (name N or name CA or name C or na \ me O or name CB )) or resid 282 through 295 or (resid 296 and (name N or name CA \ or name C or name O or name CB )) or resid 297 through 320 or (resid 321 and (n \ ame N or name CA or name C or name O or name CB )) or resid 322 through 435 or ( \ resid 436 and (name N or name CA or name C or name O or name CB )) or resid 437 \ through 441 or (resid 442 and (name N or name CA or name C or name O or name CB \ )) or resid 443 through 512 or (resid 513 and (name N or name CA or name C or na \ me O or name CB )) or resid 514 through 515 or (resid 516 through 517 and (name \ N or name CA or name C or name O or name CB )) or resid 518 through 568 or (resi \ d 569 and (name N or name CA or name C or name O or name CB )) or resid 570 thro \ ugh 839 or (resid 840 and (name N or name CA or name C or name O or name CB )) o \ r resid 841 through 850 or (resid 851 and (name N or name CA or name C or name O \ or name CB )) or resid 852 through 862)) selection = (chain 'C' and (resid 25 through 38 or (resid 39 through 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 through 47 or (resid 48 through \ 49 and (name N or name CA or name C or name O or name CB )) or resid 50 or (res \ id 51 through 52 and (name N or name CA or name C or name O or name CB )) or res \ id 58 or (resid 59 and (name N or name CA or name C or name O or name CB )) or r \ esid 60 or (resid 61 through 62 and (name N or name CA or name C or name O or na \ me CB )) or resid 63 through 152 or (resid 153 and (name N or name CA or name C \ or name O or name CB )) or resid 154 through 155 or (resid 156 and (name N or na \ me CA or name C or name O or name CB )) or resid 157 through 185 or (resid 186 t \ hrough 188 and (name N or name CA or name C or name O or name CB )) or resid 189 \ through 213 or (resid 214 and (name N or name CA or name C or name O or name CB \ )) or resid 215 through 232 or (resid 233 and (name N or name CA or name C or n \ ame O or name CB )) or resid 234 through 235 or (resid 236 through 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 through 297 or (res \ id 298 and (name N or name CA or name C or name O or name CB )) or resid 299 thr \ ough 310 or (resid 311 through 312 and (name N or name CA or name C or name O or \ name CB )) or resid 313 through 314 or (resid 315 and (name N or name CA or nam \ e C or name O or name CB )) or resid 316 through 317 or (resid 318 through 321 a \ nd (name N or name CA or name C or name O or name CB )) or resid 322 through 346 \ or (resid 347 and (name N or name CA or name C or name O or name CB )) or resid \ 348 through 349 or (resid 350 and (name N or name CA or name C or name O or nam \ e CB )) or resid 351 through 357 or (resid 358 and (name N or name CA or name C \ or name O or name CB )) or resid 359 through 361 or (resid 362 through 364 and ( \ name N or name CA or name C or name O or name CB )) or resid 365 through 366 or \ (resid 367 through 368 and (name N or name CA or name C or name O or name CB )) \ or resid 369 through 387 or (resid 388 and (name N or name CA or name C or name \ O or name CB )) or resid 389 through 395 or (resid 396 through 399 and (name N o \ r name CA or name C or name O or name CB )) or resid 400 through 405 or (resid 4 \ 06 and (name N or name CA or name C or name O or name CB )) or resid 407 through \ 461 or (resid 462 and (name N or name CA or name C or name O or name CB )) or r \ esid 463 through 495 or (resid 496 and (name N or name CA or name C or name O or \ name CB )) or resid 497 through 516 or (resid 517 and (name N or name CA or nam \ e C or name O or name CB )) or resid 518 through 524 or (resid 525 and (name N o \ r name CA or name C or name O or name CB )) or resid 526 through 563 or (resid 5 \ 64 through 565 and (name N or name CA or name C or name O or name CB )) or resid \ 566 through 691 or (resid 692 and (name N or name CA or name C or name O or nam \ e CB )) or resid 693 through 706 or (resid 707 and (name N or name CA or name C \ or name O or name CB )) or resid 708 through 762 or (resid 763 through 764 and ( \ name N or name CA or name C or name O or name CB )) or resid 765 through 774 or \ (resid 775 and (name N or name CA or name C or name O or name CB )) or resid 776 \ through 814 or (resid 815 and (name N or name CA or name C or name O or name CB \ )) or resid 816 through 862)) } ncs_group { reference = (chain 'B' and (resid 35 through 206 or (resid 207 and (name N or name CA or nam \ e C or name O or name CB )) or resid 208 through 210 or (resid 211 and (name N o \ r name CA or name C or name O or name CB )) or resid 212 or (resid 213 and (name \ N or name CA or name C or name O or name CB )) or resid 214 through 285 or (res \ id 286 and (name N or name CA or name C or name O or name CB )) or resid 287 thr \ ough 293 or (resid 294 and (name N or name CA or name C or name O or name CB )) \ or resid 295 through 309 or (resid 310 and (name N or name CA or name C or name \ O or name CB )) or resid 311 through 393 or (resid 394 and (name N or name CA or \ name C or name O or name CB )) or resid 404 through 438 or (resid 439 and (name \ N or name CA or name C or name O or name CB )) or resid 440 through 444 or resi \ d 447 through 504 or (resid 505 through 506 and (name N or name CA or name C or \ name O or name CB )) or resid 507 through 576 or (resid 577 and (name N or name \ CA or name C or name O or name CB )) or resid 578 through 603 or (resid 604 thro \ ugh 605 and (name N or name CA or name C or name O or name CB )) or resid 606 th \ rough 841 or (resid 842 and (name N or name CA or name C or name O or name CB )) \ or resid 843 through 845 or resid 901 through 902)) selection = (chain 'D' and (resid 35 through 57 or (resid 58 through 62 and (name N or name \ CA or name C or name O or name CB )) or resid 63 through 74 or (resid 75 and (na \ me N or name CA or name C or name O or name CB )) or resid 76 through 78 or (res \ id 79 and (name N or name CA or name C or name O or name CB )) or resid 80 throu \ gh 84 or (resid 85 and (name N or name CA or name C or name O or name CB )) or r \ esid 86 or (resid 87 through 89 and (name N or name CA or name C or name O or na \ me CB )) or resid 90 or (resid 91 through 94 and (name N or name CA or name C or \ name O or name CB )) or resid 95 through 100 or (resid 101 and (name N or name \ CA or name C or name O or name CB )) or resid 102 through 131 or (resid 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 through 135 or \ (resid 136 through 139 and (name N or name CA or name C or name O or name CB )) \ or resid 140 or (resid 141 and (name N or name CA or name C or name O or name C \ B )) or resid 142 through 169 or (resid 170 and (name N or name CA or name C or \ name O or name CB )) or resid 171 through 200 or (resid 201 and (name N or name \ CA or name C or name O or name CB )) or resid 202 through 216 or (resid 217 and \ (name N or name CA or name C or name O or name CB )) or resid 218 through 222 or \ (resid 223 through 224 and (name N or name CA or name C or name O or name CB )) \ or resid 225 through 233 or (resid 234 and (name N or name CA or name C or name \ O or name CB )) or resid 235 through 251 or (resid 252 and (name N or name CA o \ r name C or name O or name CB )) or resid 253 through 312 or (resid 313 and (nam \ e N or name CA or name C or name O or name CB )) or resid 314 through 321 or (re \ sid 322 and (name N or name CA or name C or name O or name CB )) or resid 323 th \ rough 324 or (resid 325 through 328 and (name N or name CA or name C or name O o \ r name CB )) or resid 329 or (resid 330 through 331 and (name N or name CA or na \ me C or name O or name CB )) or resid 332 or (resid 333 and (name N or name CA o \ r name C or name O or name CB )) or resid 334 through 336 or (resid 337 and (nam \ e N or name CA or name C or name O or name CB )) or resid 338 through 342 or (re \ sid 343 through 345 and (name N or name CA or name C or name O or name CB )) or \ resid 346 or (resid 347 and (name N or name CA or name C or name O or name CB )) \ or resid 348 through 356 or (resid 357 and (name N or name CA or name C or name \ O or name CB )) or resid 358 through 368 or (resid 369 through 370 and (name N \ or name CA or name C or name O or name CB )) or resid 371 through 379 or (resid \ 380 and (name N or name CA or name C or name O or name CB )) or resid 381 throug \ h 388 or (resid 389 and (name N or name CA or name C or name O or name CB )) or \ resid 390 through 403 or resid 405 through 430 or (resid 431 and (name N or name \ CA or name C or name O or name CB )) or resid 432 through 440 or (resid 441 and \ (name N or name CA or name C or name O or name CB )) or resid 442 through 453 o \ r (resid 454 through 455 and (name N or name CA or name C or name O or name CB ) \ ) or resid 456 through 457 or (resid 458 and (name N or name CA or name C or nam \ e O or name CB )) or resid 459 through 484 or (resid 485 and (name N or name CA \ or name C or name O or name CB )) or resid 486 through 488 or (resid 489 and (na \ me N or name CA or name C or name O or name CB )) or resid 490 or (resid 491 and \ (name N or name CA or name C or name O or name CB )) or resid 492 through 503 o \ r (resid 504 through 506 and (name N or name CA or name C or name O or name CB ) \ ) or resid 507 through 530 or (resid 531 and (name N or name CA or name C or nam \ e O or name CB )) or resid 532 through 551 or (resid 552 and (name N or name CA \ or name C or name O or name CB )) or resid 553 through 579 or (resid 599 through \ 601 and (name N or name CA or name C or name O or name CB )) or resid 602 throu \ gh 669 or (resid 670 and (name N or name CA or name C or name O or name CB )) or \ resid 671 through 672 or (resid 673 and (name N or name CA or name C or name O \ or name CB )) or resid 674 through 676 or (resid 677 and (name N or name CA or n \ ame C or name O or name CB )) or resid 678 through 700 or (resid 701 through 704 \ and (name N or name CA or name C or name O or name CB )) or resid 705 through 7 \ 11 or (resid 712 and (name N or name CA or name C or name O or name CB )) or res \ id 713 through 721 or (resid 722 and (name N or name CA or name C or name O or n \ ame CB )) or resid 723 through 724 or (resid 725 and (name N or name CA or name \ C or name O or name CB )) or resid 726 through 741 or (resid 742 through 744 and \ (name N or name CA or name C or name O or name CB )) or resid 745 through 785 o \ r (resid 786 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 87 through 804 or (resid 805 and (name N or name CA or name C or name O or name \ CB )) or resid 806 through 808 or (resid 809 and (name N or name CA or name C or \ name O or name CB )) or resid 810 through 811 or (resid 812 through 814 and (na \ me N or name CA or name C or name O or name CB )) or resid 815 or (resid 816 thr \ ough 817 and (name N or name CA or name C or name O or name CB )) or resid 818 t \ hrough 838 or (resid 839 and (name N or name CA or name C or name O or name CB ) \ ) or resid 840 through 845 or resid 901 through 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 145 5.16 5 Cl 6 4.86 5 C 15238 2.51 5 N 3863 2.21 5 O 4510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 5.720 Check model and map are aligned: 0.370 Convert atoms to be neutral: 0.210 Process input model: 60.550 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 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 : 0.007 0.238 24284 Z= 0.499 Angle : 0.851 10.202 33151 Z= 0.478 Chirality : 0.085 4.409 3894 Planarity : 0.005 0.086 4221 Dihedral : 14.938 89.700 8287 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 17.32 % Favored : 82.58 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.16 % 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: -5.39 (0.11), residues: 3140 helix: -2.86 (0.12), residues: 1081 sheet: -3.66 (0.23), residues: 319 loop : -4.22 (0.12), residues: 1740 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 301 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 309 average time/residue: 0.3046 time to fit residues: 154.2027 Evaluate side-chains 235 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 228 time to evaluate : 2.915 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2048 time to fit residues: 6.5050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 20.0000 chunk 239 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 161 optimal weight: 30.0000 chunk 127 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 150 optimal weight: 0.6980 chunk 184 optimal weight: 20.0000 chunk 286 optimal weight: 0.6980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 HIS A 177 GLN A 291 GLN A 294 ASN A 498 HIS A 513 ASN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 HIS A 817 GLN A 824 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 ASN B 782 GLN B 803 ASN B 840 HIS C 59 GLN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS C 217 GLN C 425 HIS ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 HIS C 508 GLN C 542 ASN C 546 GLN C 580 GLN C 730 HIS C 731 ASN D 118 GLN D 153 GLN D 184 ASN ** D 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN D 662 GLN D 672 GLN D 698 ASN D 775 GLN D 802 HIS D 817 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 24284 Z= 0.243 Angle : 0.703 11.608 33151 Z= 0.368 Chirality : 0.046 0.211 3894 Planarity : 0.005 0.082 4221 Dihedral : 6.898 83.808 3382 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.20 % 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: -4.14 (0.13), residues: 3140 helix: -1.62 (0.14), residues: 1089 sheet: -3.23 (0.27), residues: 289 loop : -3.57 (0.13), residues: 1762 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 307 time to evaluate : 3.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 312 average time/residue: 0.3082 time to fit residues: 159.3039 Evaluate side-chains 233 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 231 time to evaluate : 2.945 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2269 time to fit residues: 4.6061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 159 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 238 optimal weight: 0.7980 chunk 195 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 287 optimal weight: 9.9990 chunk 310 optimal weight: 5.9990 chunk 256 optimal weight: 6.9990 chunk 285 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 230 optimal weight: 1.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 GLN A 425 HIS ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 730 HIS ** C 801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 24284 Z= 0.228 Angle : 0.669 11.918 33151 Z= 0.348 Chirality : 0.045 0.201 3894 Planarity : 0.005 0.083 4221 Dihedral : 6.570 82.069 3382 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.16 % 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: -3.64 (0.14), residues: 3140 helix: -1.13 (0.15), residues: 1111 sheet: -3.00 (0.26), residues: 319 loop : -3.32 (0.13), residues: 1710 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 3.031 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: 304 average time/residue: 0.2936 time to fit residues: 149.1029 Evaluate side-chains 228 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.790 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 284 optimal weight: 10.0000 chunk 216 optimal weight: 0.5980 chunk 149 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 chunk 193 optimal weight: 4.9990 chunk 288 optimal weight: 0.0010 chunk 305 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 273 optimal weight: 0.3980 chunk 82 optimal weight: 50.0000 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 GLN ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 HIS D 323 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 24284 Z= 0.168 Angle : 0.627 11.294 33151 Z= 0.326 Chirality : 0.044 0.194 3894 Planarity : 0.005 0.080 4221 Dihedral : 6.239 81.221 3382 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.16 % 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: -3.20 (0.14), residues: 3140 helix: -0.77 (0.15), residues: 1107 sheet: -2.73 (0.27), residues: 303 loop : -3.06 (0.14), residues: 1730 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 3.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.3079 time to fit residues: 168.2250 Evaluate side-chains 237 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 3.659 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 254 optimal weight: 0.0030 chunk 173 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 227 optimal weight: 0.0980 chunk 126 optimal weight: 9.9990 chunk 260 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 155 optimal weight: 4.9990 chunk 274 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 overall best weight: 2.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 153 GLN ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 24284 Z= 0.213 Angle : 0.644 11.909 33151 Z= 0.332 Chirality : 0.044 0.206 3894 Planarity : 0.005 0.079 4221 Dihedral : 6.145 80.266 3382 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.06 (0.14), residues: 3140 helix: -0.66 (0.15), residues: 1106 sheet: -2.66 (0.26), residues: 321 loop : -2.96 (0.14), residues: 1713 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2942 time to fit residues: 150.1945 Evaluate side-chains 230 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 3.246 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 102 optimal weight: 0.7980 chunk 275 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 179 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 305 optimal weight: 6.9990 chunk 253 optimal weight: 0.8980 chunk 141 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 HIS B 153 GLN ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 HIS ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN C 637 ASN D 817 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 24284 Z= 0.205 Angle : 0.643 12.360 33151 Z= 0.331 Chirality : 0.044 0.223 3894 Planarity : 0.005 0.077 4221 Dihedral : 6.069 79.654 3382 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.88 (0.14), residues: 3140 helix: -0.59 (0.15), residues: 1095 sheet: -2.53 (0.26), residues: 323 loop : -2.79 (0.14), residues: 1722 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 3.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.3198 time to fit residues: 163.4594 Evaluate side-chains 226 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 2.932 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 294 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 174 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 257 optimal weight: 0.2980 chunk 170 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 190 optimal weight: 0.3980 chunk 185 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 697 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 GLN C 542 ASN ** C 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 24284 Z= 0.175 Angle : 0.624 12.088 33151 Z= 0.320 Chirality : 0.044 0.232 3894 Planarity : 0.005 0.076 4221 Dihedral : 5.907 79.130 3382 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.15), residues: 3140 helix: -0.49 (0.16), residues: 1099 sheet: -2.28 (0.27), residues: 313 loop : -2.72 (0.14), residues: 1728 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 3.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.3246 time to fit residues: 169.3619 Evaluate side-chains 237 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 3.215 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 188 optimal weight: 0.0050 chunk 121 optimal weight: 0.8980 chunk 181 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 193 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 chunk 277 optimal weight: 10.0000 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 697 ASN B 806 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN C 730 HIS ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 24284 Z= 0.170 Angle : 0.619 11.771 33151 Z= 0.316 Chirality : 0.044 0.240 3894 Planarity : 0.005 0.076 4221 Dihedral : 5.760 79.082 3382 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.15), residues: 3140 helix: -0.37 (0.16), residues: 1098 sheet: -2.07 (0.28), residues: 311 loop : -2.63 (0.15), residues: 1731 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 315 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 316 average time/residue: 0.3086 time to fit residues: 165.2174 Evaluate side-chains 236 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 2.831 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 291 optimal weight: 9.9990 chunk 266 optimal weight: 30.0000 chunk 283 optimal weight: 6.9990 chunk 170 optimal weight: 0.7980 chunk 123 optimal weight: 7.9990 chunk 222 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 256 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 186 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 HIS ** C 801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 672 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 24284 Z= 0.221 Angle : 0.650 12.576 33151 Z= 0.329 Chirality : 0.044 0.259 3894 Planarity : 0.005 0.075 4221 Dihedral : 5.836 78.228 3382 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.15), residues: 3140 helix: -0.37 (0.16), residues: 1101 sheet: -2.03 (0.28), residues: 312 loop : -2.62 (0.15), residues: 1727 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.2980 time to fit residues: 153.3823 Evaluate side-chains 237 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 3.217 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 300 optimal weight: 9.9990 chunk 183 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 208 optimal weight: 0.8980 chunk 314 optimal weight: 0.9980 chunk 289 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 199 optimal weight: 20.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 24284 Z= 0.155 Angle : 0.618 11.815 33151 Z= 0.313 Chirality : 0.043 0.241 3894 Planarity : 0.005 0.076 4221 Dihedral : 5.610 77.952 3382 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.37 (0.15), residues: 3140 helix: -0.25 (0.16), residues: 1104 sheet: -1.80 (0.29), residues: 320 loop : -2.52 (0.15), residues: 1716 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 310 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 310 average time/residue: 0.3100 time to fit residues: 163.1698 Evaluate side-chains 237 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 2.953 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 267 optimal weight: 0.0170 chunk 76 optimal weight: 30.0000 chunk 231 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 251 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 257 optimal weight: 6.9990 chunk 31 optimal weight: 0.0030 chunk 46 optimal weight: 9.9990 chunk 220 optimal weight: 0.6980 overall best weight: 0.5230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 HIS ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 HIS ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.095668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.080471 restraints weight = 95254.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.082377 restraints weight = 60452.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.082878 restraints weight = 41115.602| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 24284 Z= 0.153 Angle : 0.629 14.668 33151 Z= 0.314 Chirality : 0.043 0.239 3894 Planarity : 0.005 0.076 4221 Dihedral : 5.449 77.208 3382 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.30 (0.15), residues: 3140 helix: -0.26 (0.16), residues: 1109 sheet: -1.59 (0.30), residues: 295 loop : -2.47 (0.15), residues: 1736 =============================================================================== Job complete usr+sys time: 4067.39 seconds wall clock time: 75 minutes 15.38 seconds (4515.38 seconds total)