Starting phenix.real_space_refine on Fri May 16 14:45:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x85_38136/05_2025/8x85_38136.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x85_38136/05_2025/8x85_38136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x85_38136/05_2025/8x85_38136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x85_38136/05_2025/8x85_38136.map" model { file = "/net/cci-nas-00/data/ceres_data/8x85_38136/05_2025/8x85_38136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x85_38136/05_2025/8x85_38136.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9324 2.51 5 N 2352 2.21 5 O 2714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14490 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6162 Classifications: {'peptide': 766} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 714} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 6168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6168 Classifications: {'peptide': 766} Link IDs: {'PCIS': 3, 'PTRANS': 47, 'TRANS': 715} Chain breaks: 1 Chain: "C" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1124 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain: "D" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 809 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 9.17, per 1000 atoms: 0.63 Number of scatterers: 14490 At special positions: 0 Unit cell: (124.1, 156.4, 214.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2714 8.00 N 2352 7.00 C 9324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 102 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 142 " distance=2.04 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS A 413 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 447 " distance=2.04 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 488 " - pdb=" SG CYS A 498 " distance=2.03 Simple disulfide: pdb=" SG CYS A 604 " - pdb=" SG CYS A 674 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 102 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 413 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 488 " - pdb=" SG CYS B 498 " distance=2.04 Simple disulfide: pdb=" SG CYS B 604 " - pdb=" SG CYS B 674 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 167 " distance=2.03 Simple disulfide: pdb=" SG CYS D 117 " - pdb=" SG CYS D 167 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " BETA1-6 " NAG E 1 " - " FUC E 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 2 " NAG-ASN " NAG A 901 " - " ASN A 750 " " NAG A 902 " - " ASN A 624 " " NAG A 903 " - " ASN A 397 " " NAG A 904 " - " ASN A 516 " " NAG A 905 " - " ASN A 728 " " NAG B 901 " - " ASN B 750 " " NAG B 902 " - " ASN B 624 " " NAG B 905 " - " ASN B 516 " " NAG B 906 " - " ASN B 728 " " NAG E 1 " - " ASN A 347 " " NAG F 1 " - " ASN B 347 " Time building additional restraints: 3.68 Conformation dependent library (CDL) restraints added in 1.6 seconds 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3424 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 36 sheets defined 13.9% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.873A pdb=" N PHE A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.533A pdb=" N LEU A 205 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.772A pdb=" N MET A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 235 " --> pdb=" O ILE A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 235' Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 530 through 534 Processing helix chain 'A' and resid 668 through 673 Processing helix chain 'A' and resid 734 through 738 removed outlier: 4.071A pdb=" N LYS A 737 " --> pdb=" O PRO A 734 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 738 " --> pdb=" O MET A 735 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 734 through 738' Processing helix chain 'B' and resid 116 through 123 removed outlier: 4.040A pdb=" N PHE B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 362 through 366 removed outlier: 3.944A pdb=" N ILE B 366 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 738 Processing helix chain 'C' and resid 23 through 45 removed outlier: 3.634A pdb=" N VAL C 27 " --> pdb=" O PRO C 23 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 32 " --> pdb=" O GLN C 28 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 45 " --> pdb=" O ARG C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 87 Processing helix chain 'C' and resid 91 through 115 removed outlier: 3.902A pdb=" N VAL C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 162 removed outlier: 8.295A pdb=" N TYR C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N SER C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 45 removed outlier: 3.798A pdb=" N ILE D 45 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 88 removed outlier: 3.809A pdb=" N SER D 88 " --> pdb=" O GLN D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 115 removed outlier: 4.131A pdb=" N ASN D 103 " --> pdb=" O ASN D 99 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 164 removed outlier: 3.755A pdb=" N LEU D 163 " --> pdb=" O TRP D 159 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 5.956A pdb=" N TYR A 26 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 229 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 209 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 161 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL A 159 " --> pdb=" O CYS A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 256 Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 288 Processing sheet with id=AA4, first strand: chain 'A' and resid 274 through 276 Processing sheet with id=AA5, first strand: chain 'A' and resid 333 through 334 Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 343 removed outlier: 3.505A pdb=" N THR A 342 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 374 through 375 removed outlier: 3.613A pdb=" N GLU A 374 " --> pdb=" O MET A 370 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A 370 " --> pdb=" O GLU A 374 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 381 through 383 Processing sheet with id=AA9, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AB1, first strand: chain 'A' and resid 484 through 486 removed outlier: 3.824A pdb=" N GLU A 484 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 486 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 464 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TRP A 512 " --> pdb=" O ARG A 465 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 484 through 486 removed outlier: 3.824A pdb=" N GLU A 484 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 486 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 464 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TRP A 512 " --> pdb=" O ARG A 465 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 541 through 547 removed outlier: 6.162A pdb=" N SER A 542 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU A 559 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 584 through 588 Processing sheet with id=AB5, first strand: chain 'A' and resid 645 through 649 Processing sheet with id=AB6, first strand: chain 'A' and resid 692 through 696 removed outlier: 3.684A pdb=" N GLU A 693 " --> pdb=" O ILE A 681 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 681 " --> pdb=" O GLU A 693 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 695 " --> pdb=" O TYR A 679 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR A 679 " --> pdb=" O VAL A 695 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 741 through 750 removed outlier: 6.349A pdb=" N CYS A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 784 through 789 removed outlier: 3.849A pdb=" N LEU A 786 " --> pdb=" O ILE A 772 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE A 772 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A 788 " --> pdb=" O PHE A 770 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR A 769 " --> pdb=" O ILE A 814 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 775 " --> pdb=" O GLN A 808 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 818 " --> pdb=" O PHE A 815 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 784 through 789 removed outlier: 3.849A pdb=" N LEU A 786 " --> pdb=" O ILE A 772 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE A 772 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A 788 " --> pdb=" O PHE A 770 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR A 769 " --> pdb=" O ILE A 814 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 775 " --> pdb=" O GLN A 808 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 26 through 27 removed outlier: 5.665A pdb=" N TYR B 26 " --> pdb=" O SER B 228 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 85 through 92 current: chain 'B' and resid 182 through 185 Processing sheet with id=AC2, first strand: chain 'B' and resid 97 through 98 removed outlier: 4.297A pdb=" N ASN B 98 " --> pdb=" O PHE B 91 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE B 91 " --> pdb=" O ASN B 98 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 209 through 217 current: chain 'B' and resid 126 through 131 removed outlier: 3.655A pdb=" N VAL B 198 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 267 through 268 Processing sheet with id=AC4, first strand: chain 'B' and resid 271 through 272 Processing sheet with id=AC5, first strand: chain 'B' and resid 304 through 306 removed outlier: 3.852A pdb=" N VAL B 306 " --> pdb=" O ARG B 326 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG B 326 " --> pdb=" O VAL B 306 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 333 through 335 Processing sheet with id=AC7, first strand: chain 'B' and resid 341 through 343 Processing sheet with id=AC8, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AC9, first strand: chain 'B' and resid 381 through 383 Processing sheet with id=AD1, first strand: chain 'B' and resid 435 through 438 Processing sheet with id=AD2, first strand: chain 'B' and resid 484 through 486 removed outlier: 3.845A pdb=" N LEU B 464 " --> pdb=" O LYS B 486 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 484 through 486 removed outlier: 3.845A pdb=" N LEU B 464 " --> pdb=" O LYS B 486 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET B 511 " --> pdb=" O THR B 527 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B 527 " --> pdb=" O MET B 511 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 541 through 547 removed outlier: 5.609A pdb=" N SER B 542 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU B 559 " --> pdb=" O SER B 542 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 584 through 588 Processing sheet with id=AD6, first strand: chain 'B' and resid 646 through 647 Processing sheet with id=AD7, first strand: chain 'B' and resid 678 through 685 removed outlier: 3.859A pdb=" N ARG B 678 " --> pdb=" O ILE B 717 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 744 through 747 Processing sheet with id=AD9, first strand: chain 'B' and resid 784 through 786 removed outlier: 3.983A pdb=" N LYS B 784 " --> pdb=" O TRP B 774 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP B 774 " --> pdb=" O LYS B 784 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR B 769 " --> pdb=" O ILE B 814 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 811 " --> pdb=" O LYS B 823 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.50 Time building geometry restraints manager: 4.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4153 1.33 - 1.46: 3762 1.46 - 1.59: 6815 1.59 - 1.71: 1 1.71 - 1.84: 140 Bond restraints: 14871 Sorted by residual: bond pdb=" C1 FUC F 2 " pdb=" O5 FUC F 2 " ideal model delta sigma weight residual 1.400 1.481 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" N LEU B 471 " pdb=" CA LEU B 471 " ideal model delta sigma weight residual 1.457 1.481 -0.024 6.40e-03 2.44e+04 1.41e+01 bond pdb=" C1 FUC F 2 " pdb=" C2 FUC F 2 " ideal model delta sigma weight residual 1.528 1.600 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" N TYR B 472 " pdb=" CA TYR B 472 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.31e-02 5.83e+03 7.49e+00 bond pdb=" CA SER B 470 " pdb=" CB SER B 470 " ideal model delta sigma weight residual 1.530 1.485 0.046 1.69e-02 3.50e+03 7.30e+00 ... (remaining 14866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 19994 2.76 - 5.53: 224 5.53 - 8.29: 34 8.29 - 11.06: 3 11.06 - 13.82: 1 Bond angle restraints: 20256 Sorted by residual: angle pdb=" C SER B 470 " pdb=" N LEU B 471 " pdb=" CA LEU B 471 " ideal model delta sigma weight residual 123.04 115.92 7.12 1.08e+00 8.57e-01 4.35e+01 angle pdb=" CA CYS A 436 " pdb=" CB CYS A 436 " pdb=" SG CYS A 436 " ideal model delta sigma weight residual 114.40 128.22 -13.82 2.30e+00 1.89e-01 3.61e+01 angle pdb=" N CYS A 447 " pdb=" CA CYS A 447 " pdb=" C CYS A 447 " ideal model delta sigma weight residual 108.38 115.05 -6.67 1.35e+00 5.49e-01 2.44e+01 angle pdb=" N SER A 452 " pdb=" CA SER A 452 " pdb=" C SER A 452 " ideal model delta sigma weight residual 113.88 107.97 5.91 1.23e+00 6.61e-01 2.31e+01 angle pdb=" C ALA B 458 " pdb=" N GLU B 459 " pdb=" CA GLU B 459 " ideal model delta sigma weight residual 125.02 132.94 -7.92 1.76e+00 3.23e-01 2.03e+01 ... (remaining 20251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 8581 21.81 - 43.62: 550 43.62 - 65.43: 50 65.43 - 87.24: 21 87.24 - 109.05: 5 Dihedral angle restraints: 9207 sinusoidal: 3936 harmonic: 5271 Sorted by residual: dihedral pdb=" CB CYS A 436 " pdb=" SG CYS A 436 " pdb=" SG CYS A 447 " pdb=" CB CYS A 447 " ideal model delta sinusoidal sigma weight residual -86.00 -6.95 -79.05 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CB CYS A 102 " pdb=" SG CYS A 102 " pdb=" SG CYS A 212 " pdb=" CB CYS A 212 " ideal model delta sinusoidal sigma weight residual -86.00 -164.13 78.13 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CA CYS A 447 " pdb=" C CYS A 447 " pdb=" N ARG A 448 " pdb=" CA ARG A 448 " ideal model delta harmonic sigma weight residual -180.00 -137.98 -42.02 0 5.00e+00 4.00e-02 7.06e+01 ... (remaining 9204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1933 0.062 - 0.124: 373 0.124 - 0.186: 28 0.186 - 0.248: 5 0.248 - 0.310: 4 Chirality restraints: 2343 Sorted by residual: chirality pdb=" CB ILE B 681 " pdb=" CA ILE B 681 " pdb=" CG1 ILE B 681 " pdb=" CG2 ILE B 681 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA CYS A 447 " pdb=" N CYS A 447 " pdb=" C CYS A 447 " pdb=" CB CYS A 447 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2340 not shown) Planarity restraints: 2518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 821 " 0.067 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO B 822 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO B 822 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 822 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 583 " -0.020 2.00e-02 2.50e+03 2.17e-02 1.18e+01 pdb=" CG TRP A 583 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A 583 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 583 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 583 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 583 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 583 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 583 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 583 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 583 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 450 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.52e+00 pdb=" C SER A 450 " 0.051 2.00e-02 2.50e+03 pdb=" O SER A 450 " -0.019 2.00e-02 2.50e+03 pdb=" N THR A 451 " -0.017 2.00e-02 2.50e+03 ... (remaining 2515 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 255 2.67 - 3.23: 13643 3.23 - 3.78: 21430 3.78 - 4.34: 28116 4.34 - 4.90: 45424 Nonbonded interactions: 108868 Sorted by model distance: nonbonded pdb=" OG1 THR A 248 " pdb=" OD1 ASN A 252 " model vdw 2.110 3.040 nonbonded pdb=" OD1 ASP B 635 " pdb=" OG SER B 675 " model vdw 2.113 3.040 nonbonded pdb=" O TRP B 733 " pdb=" OG SER B 736 " model vdw 2.126 3.040 nonbonded pdb=" OG SER A 274 " pdb=" OD1 ASN A 276 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR B 713 " pdb=" OD1 ASN B 728 " model vdw 2.224 3.040 ... (remaining 108863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 23 through 467 or (resid 468 and (name N or name CA or nam \ e C or name O or name CB )) or resid 469 through 829 or resid 901 through 905)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 26.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 35.350 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 14912 Z= 0.208 Angle : 0.791 13.823 20353 Z= 0.428 Chirality : 0.049 0.310 2343 Planarity : 0.006 0.101 2507 Dihedral : 13.698 109.050 5705 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.57 % Favored : 93.09 % Rotamer: Outliers : 0.18 % Allowed : 0.42 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.20), residues: 1766 helix: 0.13 (0.37), residues: 199 sheet: -0.28 (0.21), residues: 595 loop : -1.25 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 583 HIS 0.005 0.001 HIS A 387 PHE 0.016 0.001 PHE A 336 TYR 0.028 0.001 TYR B 795 ARG 0.006 0.001 ARG A 573 Details of bonding type rmsd link_NAG-ASN : bond 0.00548 ( 11) link_NAG-ASN : angle 2.49950 ( 33) link_BETA1-4 : bond 0.00572 ( 2) link_BETA1-4 : angle 1.17598 ( 6) hydrogen bonds : bond 0.17163 ( 424) hydrogen bonds : angle 7.74500 ( 1209) link_BETA1-6 : bond 0.01944 ( 2) link_BETA1-6 : angle 2.87922 ( 6) SS BOND : bond 0.00411 ( 26) SS BOND : angle 2.33504 ( 52) covalent geometry : bond 0.00408 (14871) covalent geometry : angle 0.77598 (20256) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 311 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 MET cc_start: 0.6603 (mpp) cc_final: 0.5998 (mpp) REVERT: A 252 ASN cc_start: 0.7242 (p0) cc_final: 0.6659 (p0) REVERT: A 365 GLU cc_start: 0.5730 (mm-30) cc_final: 0.5509 (mm-30) REVERT: A 414 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.8106 (p0) REVERT: A 424 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6895 (mt-10) REVERT: A 497 GLU cc_start: 0.6652 (pp20) cc_final: 0.6043 (pp20) REVERT: A 507 SER cc_start: 0.8165 (m) cc_final: 0.7563 (p) REVERT: A 573 ARG cc_start: 0.7624 (ptt180) cc_final: 0.6995 (ptt90) REVERT: A 614 LYS cc_start: 0.7292 (tttp) cc_final: 0.6959 (tttm) REVERT: B 227 MET cc_start: -0.4087 (mmt) cc_final: -0.5045 (mmt) REVERT: B 425 LEU cc_start: 0.8680 (mt) cc_final: 0.8335 (mt) REVERT: B 429 ASP cc_start: 0.7172 (t0) cc_final: 0.6887 (t0) REVERT: B 437 GLU cc_start: 0.6652 (tm-30) cc_final: 0.6251 (tm-30) REVERT: B 617 ASP cc_start: 0.7471 (m-30) cc_final: 0.7199 (m-30) REVERT: B 663 LEU cc_start: 0.7778 (mt) cc_final: 0.7568 (mt) REVERT: B 682 ASN cc_start: 0.7958 (t0) cc_final: 0.7734 (t0) REVERT: B 794 LYS cc_start: 0.7598 (tptp) cc_final: 0.7039 (tptp) REVERT: B 821 LYS cc_start: 0.7998 (mtmm) cc_final: 0.7730 (mtmm) REVERT: C 84 GLN cc_start: 0.8325 (tp40) cc_final: 0.7952 (tp40) REVERT: D 153 SER cc_start: 0.8356 (p) cc_final: 0.8089 (p) outliers start: 3 outliers final: 1 residues processed: 313 average time/residue: 0.2770 time to fit residues: 125.5605 Evaluate side-chains 277 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 275 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 452 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.9990 chunk 133 optimal weight: 0.0170 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 0.0770 chunk 89 optimal weight: 20.0000 chunk 71 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 83 optimal weight: 40.0000 chunk 102 optimal weight: 6.9990 chunk 159 optimal weight: 0.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN A 387 HIS A 414 ASN A 739 ASN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN B 742 GLN C 160 GLN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.249846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.226745 restraints weight = 39498.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 91)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.224359 restraints weight = 35289.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.224119 restraints weight = 30125.391| |-----------------------------------------------------------------------------| r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14912 Z= 0.170 Angle : 0.721 10.321 20353 Z= 0.365 Chirality : 0.048 0.339 2343 Planarity : 0.005 0.068 2507 Dihedral : 7.760 72.569 2247 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.34 % Favored : 93.37 % Rotamer: Outliers : 0.96 % Allowed : 8.97 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.20), residues: 1766 helix: 1.02 (0.37), residues: 201 sheet: -0.32 (0.21), residues: 595 loop : -1.24 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 583 HIS 0.012 0.001 HIS A 387 PHE 0.014 0.001 PHE B 570 TYR 0.057 0.002 TYR D 82 ARG 0.005 0.000 ARG B 641 Details of bonding type rmsd link_NAG-ASN : bond 0.00618 ( 11) link_NAG-ASN : angle 2.53688 ( 33) link_BETA1-4 : bond 0.00728 ( 2) link_BETA1-4 : angle 1.96097 ( 6) hydrogen bonds : bond 0.05624 ( 424) hydrogen bonds : angle 5.94370 ( 1209) link_BETA1-6 : bond 0.02234 ( 2) link_BETA1-6 : angle 3.29525 ( 6) SS BOND : bond 0.00363 ( 26) SS BOND : angle 1.87368 ( 52) covalent geometry : bond 0.00381 (14871) covalent geometry : angle 0.70614 (20256) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 288 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 GLU cc_start: 0.5996 (mm-30) cc_final: 0.5700 (mm-30) REVERT: A 374 GLU cc_start: 0.7319 (pm20) cc_final: 0.7055 (pm20) REVERT: A 424 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7035 (mt-10) REVERT: A 497 GLU cc_start: 0.6678 (pp20) cc_final: 0.6146 (pp20) REVERT: A 499 ILE cc_start: 0.8334 (mm) cc_final: 0.8015 (mm) REVERT: A 511 MET cc_start: 0.7661 (mtt) cc_final: 0.7425 (mtt) REVERT: A 583 TRP cc_start: 0.6775 (m-10) cc_final: 0.6500 (m-10) REVERT: A 614 LYS cc_start: 0.7151 (tttp) cc_final: 0.6845 (tttp) REVERT: A 669 LYS cc_start: 0.8541 (mppt) cc_final: 0.7910 (mmtm) REVERT: A 812 TYR cc_start: 0.7375 (m-10) cc_final: 0.7127 (m-10) REVERT: A 815 PHE cc_start: 0.6862 (m-80) cc_final: 0.6651 (m-80) REVERT: B 394 PHE cc_start: 0.8125 (m-10) cc_final: 0.7748 (m-10) REVERT: B 425 LEU cc_start: 0.8481 (mt) cc_final: 0.8227 (mt) REVERT: B 427 VAL cc_start: 0.8468 (t) cc_final: 0.8123 (m) REVERT: B 429 ASP cc_start: 0.7057 (t0) cc_final: 0.6828 (t0) REVERT: B 432 ILE cc_start: 0.8881 (mp) cc_final: 0.8619 (mm) REVERT: B 437 GLU cc_start: 0.6709 (tm-30) cc_final: 0.6335 (tm-30) REVERT: B 617 ASP cc_start: 0.8149 (m-30) cc_final: 0.7924 (m-30) REVERT: B 823 LYS cc_start: 0.7022 (tptm) cc_final: 0.6819 (tptm) REVERT: C 84 GLN cc_start: 0.8383 (tp40) cc_final: 0.7976 (tp40) REVERT: D 82 TYR cc_start: 0.8299 (m-80) cc_final: 0.8063 (m-80) REVERT: D 153 SER cc_start: 0.8220 (p) cc_final: 0.7304 (p) REVERT: D 157 MET cc_start: 0.7271 (mmt) cc_final: 0.7060 (mmt) outliers start: 16 outliers final: 11 residues processed: 294 average time/residue: 0.2782 time to fit residues: 118.3857 Evaluate side-chains 284 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 273 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 668 MET Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 136 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 175 optimal weight: 0.9990 chunk 149 optimal weight: 0.4980 chunk 4 optimal weight: 0.0270 chunk 105 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 88 optimal weight: 20.0000 chunk 11 optimal weight: 0.3980 chunk 94 optimal weight: 0.0670 chunk 15 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.216731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.168127 restraints weight = 30491.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.173071 restraints weight = 14163.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.176118 restraints weight = 8483.225| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14912 Z= 0.135 Angle : 0.686 10.197 20353 Z= 0.345 Chirality : 0.046 0.309 2343 Planarity : 0.004 0.065 2507 Dihedral : 6.711 54.755 2244 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.27 % Favored : 94.45 % Rotamer: Outliers : 2.17 % Allowed : 11.43 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.20), residues: 1766 helix: 1.28 (0.37), residues: 201 sheet: -0.34 (0.21), residues: 604 loop : -1.16 (0.21), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 583 HIS 0.006 0.001 HIS B 480 PHE 0.023 0.001 PHE A 701 TYR 0.043 0.002 TYR D 82 ARG 0.004 0.000 ARG B 312 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 11) link_NAG-ASN : angle 2.42470 ( 33) link_BETA1-4 : bond 0.00682 ( 2) link_BETA1-4 : angle 2.17282 ( 6) hydrogen bonds : bond 0.04694 ( 424) hydrogen bonds : angle 5.53482 ( 1209) link_BETA1-6 : bond 0.02703 ( 2) link_BETA1-6 : angle 3.29263 ( 6) SS BOND : bond 0.00401 ( 26) SS BOND : angle 1.79545 ( 52) covalent geometry : bond 0.00300 (14871) covalent geometry : angle 0.67088 (20256) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 282 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 GLU cc_start: 0.6000 (mm-30) cc_final: 0.5742 (mm-30) REVERT: A 374 GLU cc_start: 0.7239 (pm20) cc_final: 0.7039 (pm20) REVERT: A 414 ASN cc_start: 0.8339 (p0) cc_final: 0.8042 (p0) REVERT: A 424 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7097 (mt-10) REVERT: A 455 GLN cc_start: 0.7215 (mt0) cc_final: 0.6909 (mt0) REVERT: A 497 GLU cc_start: 0.6642 (pp20) cc_final: 0.6159 (pp20) REVERT: A 570 PHE cc_start: 0.8150 (m-10) cc_final: 0.7258 (m-80) REVERT: A 573 ARG cc_start: 0.7525 (ptt180) cc_final: 0.7283 (ptt-90) REVERT: A 669 LYS cc_start: 0.8668 (mppt) cc_final: 0.8300 (mmtm) REVERT: A 728 ASN cc_start: 0.7468 (m-40) cc_final: 0.6728 (m-40) REVERT: B 227 MET cc_start: -0.4279 (mmt) cc_final: -0.4701 (mmt) REVERT: B 394 PHE cc_start: 0.8267 (m-10) cc_final: 0.7932 (m-10) REVERT: B 404 LYS cc_start: 0.8411 (mmmt) cc_final: 0.8107 (mmmt) REVERT: B 425 LEU cc_start: 0.8616 (mt) cc_final: 0.8314 (mt) REVERT: B 427 VAL cc_start: 0.8548 (t) cc_final: 0.8215 (m) REVERT: B 429 ASP cc_start: 0.7161 (t0) cc_final: 0.6951 (t0) REVERT: B 437 GLU cc_start: 0.6694 (tm-30) cc_final: 0.6376 (tm-30) REVERT: B 498 CYS cc_start: 0.6351 (OUTLIER) cc_final: 0.6127 (t) REVERT: B 617 ASP cc_start: 0.7491 (m-30) cc_final: 0.7238 (m-30) REVERT: C 107 LEU cc_start: 0.8165 (tt) cc_final: 0.7964 (tt) REVERT: D 82 TYR cc_start: 0.8320 (m-80) cc_final: 0.7992 (m-80) REVERT: D 151 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: D 153 SER cc_start: 0.8202 (p) cc_final: 0.7393 (p) REVERT: D 155 GLN cc_start: 0.8387 (mp10) cc_final: 0.7910 (mp10) outliers start: 36 outliers final: 17 residues processed: 297 average time/residue: 0.2766 time to fit residues: 119.4097 Evaluate side-chains 291 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 272 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 498 CYS Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 668 MET Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 151 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 77 optimal weight: 20.0000 chunk 39 optimal weight: 0.0170 chunk 169 optimal weight: 0.9980 chunk 5 optimal weight: 30.0000 chunk 60 optimal weight: 0.3980 chunk 105 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 25 optimal weight: 0.0030 chunk 37 optimal weight: 0.8980 chunk 88 optimal weight: 40.0000 chunk 41 optimal weight: 0.0570 overall best weight: 0.2746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 HIS ** B 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.217226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.168857 restraints weight = 30425.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.173781 restraints weight = 14095.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.176808 restraints weight = 8429.792| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14912 Z= 0.129 Angle : 0.669 10.166 20353 Z= 0.335 Chirality : 0.047 0.304 2343 Planarity : 0.004 0.056 2507 Dihedral : 6.065 51.154 2244 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.38 % Favored : 94.34 % Rotamer: Outliers : 2.29 % Allowed : 13.00 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.20), residues: 1766 helix: 1.45 (0.37), residues: 200 sheet: -0.21 (0.21), residues: 594 loop : -1.19 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 583 HIS 0.006 0.001 HIS B 480 PHE 0.036 0.001 PHE A 703 TYR 0.032 0.001 TYR D 82 ARG 0.003 0.000 ARG B 312 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 11) link_NAG-ASN : angle 2.35359 ( 33) link_BETA1-4 : bond 0.00618 ( 2) link_BETA1-4 : angle 2.06810 ( 6) hydrogen bonds : bond 0.04337 ( 424) hydrogen bonds : angle 5.32427 ( 1209) link_BETA1-6 : bond 0.02420 ( 2) link_BETA1-6 : angle 3.26917 ( 6) SS BOND : bond 0.00215 ( 26) SS BOND : angle 1.74282 ( 52) covalent geometry : bond 0.00288 (14871) covalent geometry : angle 0.65439 (20256) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 277 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 ASN cc_start: 0.7451 (p0) cc_final: 0.7157 (p0) REVERT: A 365 GLU cc_start: 0.6048 (mm-30) cc_final: 0.5796 (mm-30) REVERT: A 414 ASN cc_start: 0.8291 (p0) cc_final: 0.8027 (p0) REVERT: A 424 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7070 (mt-10) REVERT: A 429 ASP cc_start: 0.7017 (p0) cc_final: 0.6759 (p0) REVERT: A 455 GLN cc_start: 0.7222 (mt0) cc_final: 0.7010 (mt0) REVERT: A 497 GLU cc_start: 0.6694 (pp20) cc_final: 0.6228 (pp20) REVERT: A 614 LYS cc_start: 0.7339 (tttp) cc_final: 0.7034 (tttp) REVERT: A 663 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7980 (pp) REVERT: A 728 ASN cc_start: 0.7500 (m-40) cc_final: 0.6808 (m-40) REVERT: B 394 PHE cc_start: 0.8284 (m-10) cc_final: 0.7948 (m-10) REVERT: B 404 LYS cc_start: 0.8349 (mmmt) cc_final: 0.8027 (mmmt) REVERT: B 425 LEU cc_start: 0.8588 (mt) cc_final: 0.8313 (mt) REVERT: B 427 VAL cc_start: 0.8551 (t) cc_final: 0.8258 (m) REVERT: B 437 GLU cc_start: 0.6713 (tm-30) cc_final: 0.6395 (tm-30) REVERT: B 498 CYS cc_start: 0.6376 (OUTLIER) cc_final: 0.6136 (t) REVERT: B 617 ASP cc_start: 0.7484 (m-30) cc_final: 0.7226 (m-30) REVERT: C 42 ILE cc_start: 0.8438 (mm) cc_final: 0.8223 (mt) REVERT: C 107 LEU cc_start: 0.8193 (tt) cc_final: 0.7962 (tt) REVERT: D 82 TYR cc_start: 0.8374 (m-80) cc_final: 0.8126 (m-80) REVERT: D 102 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.6088 (pm20) REVERT: D 153 SER cc_start: 0.8181 (p) cc_final: 0.7679 (p) outliers start: 38 outliers final: 23 residues processed: 293 average time/residue: 0.2624 time to fit residues: 112.2766 Evaluate side-chains 298 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 272 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 812 TYR Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 498 CYS Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 157 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 50 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 174 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 129 optimal weight: 0.0170 chunk 30 optimal weight: 0.9990 chunk 164 optimal weight: 0.5980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS A 517 HIS ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.248826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.226389 restraints weight = 39639.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.224735 restraints weight = 37116.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 112)---------------| | r_work = 0.4637 r_free = 0.4637 target = 0.223145 restraints weight = 29390.368| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14912 Z= 0.173 Angle : 0.682 9.299 20353 Z= 0.344 Chirality : 0.047 0.309 2343 Planarity : 0.005 0.052 2507 Dihedral : 5.848 47.035 2244 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.95 % Favored : 93.77 % Rotamer: Outliers : 2.47 % Allowed : 14.74 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.20), residues: 1766 helix: 1.46 (0.37), residues: 200 sheet: -0.22 (0.21), residues: 593 loop : -1.24 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 583 HIS 0.005 0.001 HIS A 160 PHE 0.025 0.002 PHE A 703 TYR 0.025 0.002 TYR D 82 ARG 0.004 0.000 ARG A 326 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 11) link_NAG-ASN : angle 2.48265 ( 33) link_BETA1-4 : bond 0.00669 ( 2) link_BETA1-4 : angle 1.97650 ( 6) hydrogen bonds : bond 0.04714 ( 424) hydrogen bonds : angle 5.34114 ( 1209) link_BETA1-6 : bond 0.02420 ( 2) link_BETA1-6 : angle 3.21330 ( 6) SS BOND : bond 0.00228 ( 26) SS BOND : angle 1.80193 ( 52) covalent geometry : bond 0.00396 (14871) covalent geometry : angle 0.66665 (20256) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 285 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 ASN cc_start: 0.7444 (p0) cc_final: 0.7142 (p0) REVERT: A 355 LYS cc_start: 0.8221 (tttt) cc_final: 0.7677 (tttp) REVERT: A 365 GLU cc_start: 0.6080 (mm-30) cc_final: 0.5801 (mm-30) REVERT: A 374 GLU cc_start: 0.7177 (pm20) cc_final: 0.6973 (pm20) REVERT: A 424 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7026 (mt-10) REVERT: A 428 ILE cc_start: 0.7458 (mm) cc_final: 0.7232 (mm) REVERT: A 455 GLN cc_start: 0.7328 (mt0) cc_final: 0.7070 (mt0) REVERT: A 497 GLU cc_start: 0.6777 (pp20) cc_final: 0.6258 (pp20) REVERT: A 728 ASN cc_start: 0.7492 (m-40) cc_final: 0.6808 (m-40) REVERT: B 394 PHE cc_start: 0.8228 (m-10) cc_final: 0.7907 (m-10) REVERT: B 404 LYS cc_start: 0.8307 (mmmt) cc_final: 0.8035 (mmmt) REVERT: B 425 LEU cc_start: 0.8436 (mt) cc_final: 0.8175 (mt) REVERT: B 427 VAL cc_start: 0.8607 (t) cc_final: 0.8296 (m) REVERT: B 437 GLU cc_start: 0.6783 (tm-30) cc_final: 0.6451 (tm-30) REVERT: B 617 ASP cc_start: 0.7757 (m-30) cc_final: 0.7483 (m-30) REVERT: D 102 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.6070 (pm20) REVERT: D 153 SER cc_start: 0.8184 (p) cc_final: 0.7903 (p) outliers start: 41 outliers final: 32 residues processed: 302 average time/residue: 0.2753 time to fit residues: 121.1393 Evaluate side-chains 312 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 279 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 583 TRP Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 812 TYR Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 140 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 46 optimal weight: 0.2980 chunk 94 optimal weight: 0.0670 chunk 143 optimal weight: 0.0470 chunk 170 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS B 395 ASN ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.249793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.226492 restraints weight = 39772.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 79)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.223957 restraints weight = 37487.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 92)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.223013 restraints weight = 28395.802| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14912 Z= 0.157 Angle : 0.702 10.248 20353 Z= 0.353 Chirality : 0.047 0.310 2343 Planarity : 0.004 0.052 2507 Dihedral : 5.751 41.116 2244 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.06 % Favored : 93.71 % Rotamer: Outliers : 2.77 % Allowed : 15.58 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.20), residues: 1766 helix: 1.29 (0.37), residues: 200 sheet: -0.20 (0.21), residues: 593 loop : -1.24 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 583 HIS 0.011 0.001 HIS B 683 PHE 0.019 0.001 PHE A 703 TYR 0.052 0.002 TYR D 82 ARG 0.004 0.000 ARG B 647 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 11) link_NAG-ASN : angle 2.35546 ( 33) link_BETA1-4 : bond 0.00580 ( 2) link_BETA1-4 : angle 1.65886 ( 6) hydrogen bonds : bond 0.04589 ( 424) hydrogen bonds : angle 5.29846 ( 1209) link_BETA1-6 : bond 0.02497 ( 2) link_BETA1-6 : angle 3.28545 ( 6) SS BOND : bond 0.00195 ( 26) SS BOND : angle 1.99334 ( 52) covalent geometry : bond 0.00353 (14871) covalent geometry : angle 0.68663 (20256) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 287 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 ASN cc_start: 0.7386 (p0) cc_final: 0.7060 (p0) REVERT: A 355 LYS cc_start: 0.8252 (tttt) cc_final: 0.7719 (tttp) REVERT: A 365 GLU cc_start: 0.6094 (mm-30) cc_final: 0.5807 (mm-30) REVERT: A 374 GLU cc_start: 0.7196 (pm20) cc_final: 0.6987 (pm20) REVERT: A 414 ASN cc_start: 0.8273 (p0) cc_final: 0.7969 (p0) REVERT: A 424 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7014 (mt-10) REVERT: A 428 ILE cc_start: 0.7451 (mm) cc_final: 0.7247 (mm) REVERT: A 437 GLU cc_start: 0.6044 (OUTLIER) cc_final: 0.5834 (mm-30) REVERT: A 614 LYS cc_start: 0.7386 (tttp) cc_final: 0.6926 (tttm) REVERT: A 728 ASN cc_start: 0.7548 (m-40) cc_final: 0.6835 (m-40) REVERT: A 787 ARG cc_start: 0.8210 (ttt90) cc_final: 0.7925 (ttt-90) REVERT: B 394 PHE cc_start: 0.8227 (m-10) cc_final: 0.7208 (m-10) REVERT: B 395 ASN cc_start: 0.9064 (OUTLIER) cc_final: 0.6904 (t0) REVERT: B 404 LYS cc_start: 0.8285 (mmmt) cc_final: 0.8045 (mmmt) REVERT: B 425 LEU cc_start: 0.8457 (mt) cc_final: 0.8189 (mt) REVERT: B 427 VAL cc_start: 0.8563 (t) cc_final: 0.8335 (m) REVERT: B 437 GLU cc_start: 0.6747 (tm-30) cc_final: 0.6444 (tm-30) REVERT: B 572 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.7480 (mt) REVERT: B 617 ASP cc_start: 0.7614 (m-30) cc_final: 0.7361 (m-30) REVERT: D 102 GLU cc_start: 0.6296 (OUTLIER) cc_final: 0.6034 (pm20) outliers start: 46 outliers final: 33 residues processed: 306 average time/residue: 0.2691 time to fit residues: 120.2453 Evaluate side-chains 314 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 277 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 812 TYR Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 735 MET Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 104 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 40.0000 chunk 144 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 123 optimal weight: 0.5980 chunk 106 optimal weight: 0.0030 chunk 155 optimal weight: 0.1980 chunk 174 optimal weight: 1.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS B 395 ASN ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.249548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.226510 restraints weight = 39682.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 130)---------------| | r_work = 0.4647 r_free = 0.4647 target = 0.222859 restraints weight = 36603.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.221783 restraints weight = 30120.272| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14912 Z= 0.163 Angle : 0.753 19.979 20353 Z= 0.375 Chirality : 0.049 0.529 2343 Planarity : 0.005 0.052 2507 Dihedral : 5.719 46.642 2244 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.17 % Favored : 93.60 % Rotamer: Outliers : 3.01 % Allowed : 16.73 % Favored : 80.26 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 6.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.20), residues: 1766 helix: 1.15 (0.37), residues: 200 sheet: -0.24 (0.21), residues: 593 loop : -1.23 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 583 HIS 0.012 0.001 HIS B 683 PHE 0.020 0.001 PHE C 113 TYR 0.061 0.002 TYR D 82 ARG 0.006 0.000 ARG B 647 Details of bonding type rmsd link_NAG-ASN : bond 0.00587 ( 11) link_NAG-ASN : angle 2.40206 ( 33) link_BETA1-4 : bond 0.00692 ( 2) link_BETA1-4 : angle 1.52214 ( 6) hydrogen bonds : bond 0.04647 ( 424) hydrogen bonds : angle 5.34195 ( 1209) link_BETA1-6 : bond 0.02416 ( 2) link_BETA1-6 : angle 3.24905 ( 6) SS BOND : bond 0.00381 ( 26) SS BOND : angle 3.46963 ( 52) covalent geometry : bond 0.00376 (14871) covalent geometry : angle 0.72538 (20256) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 282 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 ASN cc_start: 0.7366 (p0) cc_final: 0.7044 (p0) REVERT: A 355 LYS cc_start: 0.8243 (tttt) cc_final: 0.7731 (tttp) REVERT: A 365 GLU cc_start: 0.6115 (mm-30) cc_final: 0.5835 (mm-30) REVERT: A 374 GLU cc_start: 0.7214 (pm20) cc_final: 0.6977 (pm20) REVERT: A 414 ASN cc_start: 0.8295 (p0) cc_final: 0.8021 (p0) REVERT: A 424 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7036 (mt-10) REVERT: A 428 ILE cc_start: 0.7462 (mm) cc_final: 0.7124 (mt) REVERT: A 614 LYS cc_start: 0.7350 (tttp) cc_final: 0.7106 (tttp) REVERT: A 728 ASN cc_start: 0.7531 (m-40) cc_final: 0.6786 (m-40) REVERT: A 787 ARG cc_start: 0.8170 (ttt90) cc_final: 0.7946 (ttt-90) REVERT: B 394 PHE cc_start: 0.8252 (m-10) cc_final: 0.8011 (m-10) REVERT: B 404 LYS cc_start: 0.8288 (mmmt) cc_final: 0.8059 (mmmt) REVERT: B 425 LEU cc_start: 0.8464 (mt) cc_final: 0.8201 (mt) REVERT: B 427 VAL cc_start: 0.8618 (t) cc_final: 0.8367 (m) REVERT: B 437 GLU cc_start: 0.6729 (tm-30) cc_final: 0.6468 (tm-30) REVERT: B 572 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.7826 (pt) REVERT: B 617 ASP cc_start: 0.8176 (m-30) cc_final: 0.7956 (m-30) REVERT: B 793 LYS cc_start: 0.7967 (tppt) cc_final: 0.7181 (tppt) REVERT: D 102 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.6041 (pm20) REVERT: D 155 GLN cc_start: 0.8434 (mp10) cc_final: 0.8185 (mp10) outliers start: 50 outliers final: 35 residues processed: 304 average time/residue: 0.2666 time to fit residues: 119.0909 Evaluate side-chains 307 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 270 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 812 TYR Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 647 ARG Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 735 MET Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.0770 chunk 69 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 8 optimal weight: 0.0170 chunk 91 optimal weight: 9.9990 chunk 86 optimal weight: 30.0000 chunk 107 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 113 optimal weight: 0.4980 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 ASN ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.248472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.225982 restraints weight = 39354.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 156)---------------| | r_work = 0.4639 r_free = 0.4639 target = 0.222265 restraints weight = 36337.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.221459 restraints weight = 32591.142| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14912 Z= 0.173 Angle : 0.748 12.141 20353 Z= 0.375 Chirality : 0.049 0.373 2343 Planarity : 0.005 0.053 2507 Dihedral : 5.710 49.370 2244 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.29 % Favored : 93.43 % Rotamer: Outliers : 2.59 % Allowed : 17.81 % Favored : 79.60 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 6.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.20), residues: 1766 helix: 1.02 (0.37), residues: 200 sheet: -0.16 (0.22), residues: 576 loop : -1.25 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 583 HIS 0.013 0.001 HIS B 683 PHE 0.021 0.002 PHE C 113 TYR 0.058 0.002 TYR D 82 ARG 0.007 0.000 ARG B 468 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 11) link_NAG-ASN : angle 2.37117 ( 33) link_BETA1-4 : bond 0.00679 ( 2) link_BETA1-4 : angle 1.42396 ( 6) hydrogen bonds : bond 0.04777 ( 424) hydrogen bonds : angle 5.33296 ( 1209) link_BETA1-6 : bond 0.02403 ( 2) link_BETA1-6 : angle 3.19727 ( 6) SS BOND : bond 0.00298 ( 26) SS BOND : angle 2.81817 ( 52) covalent geometry : bond 0.00396 (14871) covalent geometry : angle 0.72698 (20256) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 278 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 ASN cc_start: 0.7343 (p0) cc_final: 0.7028 (p0) REVERT: A 355 LYS cc_start: 0.8228 (tttt) cc_final: 0.7732 (tttp) REVERT: A 365 GLU cc_start: 0.6111 (mm-30) cc_final: 0.5826 (mm-30) REVERT: A 374 GLU cc_start: 0.7219 (pm20) cc_final: 0.6921 (pm20) REVERT: A 414 ASN cc_start: 0.8343 (p0) cc_final: 0.8046 (p0) REVERT: A 424 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7017 (mt-10) REVERT: A 428 ILE cc_start: 0.7518 (mm) cc_final: 0.7184 (mt) REVERT: A 614 LYS cc_start: 0.7351 (tttp) cc_final: 0.7092 (tttp) REVERT: A 787 ARG cc_start: 0.8203 (ttt90) cc_final: 0.7890 (ttt-90) REVERT: B 425 LEU cc_start: 0.8433 (mt) cc_final: 0.8163 (mt) REVERT: B 427 VAL cc_start: 0.8652 (t) cc_final: 0.8397 (m) REVERT: B 437 GLU cc_start: 0.6746 (tm-30) cc_final: 0.6449 (tm-30) REVERT: B 572 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.7762 (pt) REVERT: D 102 GLU cc_start: 0.6239 (OUTLIER) cc_final: 0.6007 (pm20) REVERT: D 155 GLN cc_start: 0.8467 (mp10) cc_final: 0.8213 (mp10) outliers start: 43 outliers final: 36 residues processed: 293 average time/residue: 0.2776 time to fit residues: 119.7056 Evaluate side-chains 312 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 274 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 812 TYR Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 647 ARG Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 735 MET Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 794 LYS Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 35 optimal weight: 0.0870 chunk 158 optimal weight: 0.3980 chunk 162 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 76 optimal weight: 40.0000 chunk 70 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 80 optimal weight: 30.0000 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.249242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.226224 restraints weight = 39630.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 88)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.224164 restraints weight = 34379.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.223378 restraints weight = 31084.093| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14912 Z= 0.157 Angle : 0.738 9.788 20353 Z= 0.370 Chirality : 0.048 0.313 2343 Planarity : 0.004 0.053 2507 Dihedral : 5.614 52.733 2244 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.12 % Favored : 93.66 % Rotamer: Outliers : 2.47 % Allowed : 18.77 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.20), residues: 1766 helix: 0.99 (0.36), residues: 200 sheet: -0.15 (0.22), residues: 573 loop : -1.23 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 583 HIS 0.013 0.001 HIS B 683 PHE 0.021 0.001 PHE C 113 TYR 0.053 0.002 TYR D 82 ARG 0.007 0.000 ARG B 468 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 11) link_NAG-ASN : angle 2.29062 ( 33) link_BETA1-4 : bond 0.00671 ( 2) link_BETA1-4 : angle 1.32542 ( 6) hydrogen bonds : bond 0.04596 ( 424) hydrogen bonds : angle 5.26153 ( 1209) link_BETA1-6 : bond 0.02478 ( 2) link_BETA1-6 : angle 3.25197 ( 6) SS BOND : bond 0.00415 ( 26) SS BOND : angle 1.85931 ( 52) covalent geometry : bond 0.00359 (14871) covalent geometry : angle 0.72583 (20256) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 268 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 LYS cc_start: 0.8208 (tttt) cc_final: 0.7724 (tttp) REVERT: A 365 GLU cc_start: 0.6103 (mm-30) cc_final: 0.5820 (mm-30) REVERT: A 374 GLU cc_start: 0.7237 (pm20) cc_final: 0.6921 (pm20) REVERT: A 414 ASN cc_start: 0.8281 (p0) cc_final: 0.8005 (p0) REVERT: A 424 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6996 (mt-10) REVERT: A 428 ILE cc_start: 0.7483 (mm) cc_final: 0.7165 (mt) REVERT: A 614 LYS cc_start: 0.7348 (tttp) cc_final: 0.7088 (tttt) REVERT: A 635 ASP cc_start: 0.6033 (t70) cc_final: 0.5405 (t70) REVERT: A 767 LEU cc_start: 0.6728 (tp) cc_final: 0.6473 (tp) REVERT: A 787 ARG cc_start: 0.8196 (ttt90) cc_final: 0.7674 (ttm-80) REVERT: B 425 LEU cc_start: 0.8452 (mt) cc_final: 0.8174 (mt) REVERT: B 427 VAL cc_start: 0.8645 (t) cc_final: 0.8397 (m) REVERT: B 437 GLU cc_start: 0.6736 (tm-30) cc_final: 0.6451 (tm-30) REVERT: B 507 SER cc_start: 0.8266 (m) cc_final: 0.7985 (p) REVERT: B 572 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.7779 (pt) REVERT: D 102 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.5993 (pm20) REVERT: D 155 GLN cc_start: 0.8411 (mp10) cc_final: 0.8116 (mp10) outliers start: 41 outliers final: 35 residues processed: 284 average time/residue: 0.2582 time to fit residues: 107.8012 Evaluate side-chains 302 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 265 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 812 TYR Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 735 MET Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 794 LYS Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 141 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 124 optimal weight: 0.0870 chunk 50 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 173 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.249398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.226463 restraints weight = 39626.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 131)---------------| | r_work = 0.4645 r_free = 0.4645 target = 0.222965 restraints weight = 35732.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.223152 restraints weight = 31550.166| |-----------------------------------------------------------------------------| r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14912 Z= 0.150 Angle : 0.736 10.092 20353 Z= 0.368 Chirality : 0.048 0.313 2343 Planarity : 0.004 0.053 2507 Dihedral : 5.527 51.856 2244 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.12 % Favored : 93.66 % Rotamer: Outliers : 2.47 % Allowed : 19.13 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.20), residues: 1766 helix: 0.98 (0.37), residues: 200 sheet: -0.15 (0.22), residues: 573 loop : -1.22 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 583 HIS 0.012 0.001 HIS B 683 PHE 0.034 0.002 PHE A 701 TYR 0.055 0.002 TYR D 82 ARG 0.008 0.000 ARG B 647 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 11) link_NAG-ASN : angle 2.26426 ( 33) link_BETA1-4 : bond 0.00643 ( 2) link_BETA1-4 : angle 1.27114 ( 6) hydrogen bonds : bond 0.04488 ( 424) hydrogen bonds : angle 5.19660 ( 1209) link_BETA1-6 : bond 0.02434 ( 2) link_BETA1-6 : angle 3.20647 ( 6) SS BOND : bond 0.00390 ( 26) SS BOND : angle 1.78032 ( 52) covalent geometry : bond 0.00340 (14871) covalent geometry : angle 0.72422 (20256) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 270 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 LYS cc_start: 0.8214 (tttt) cc_final: 0.7725 (tttp) REVERT: A 365 GLU cc_start: 0.6087 (mm-30) cc_final: 0.5805 (mm-30) REVERT: A 374 GLU cc_start: 0.7226 (pm20) cc_final: 0.6912 (pm20) REVERT: A 414 ASN cc_start: 0.8262 (p0) cc_final: 0.7994 (p0) REVERT: A 424 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7011 (mt-10) REVERT: A 428 ILE cc_start: 0.7484 (mm) cc_final: 0.7167 (mt) REVERT: A 614 LYS cc_start: 0.7322 (tttp) cc_final: 0.6870 (tttm) REVERT: A 767 LEU cc_start: 0.6601 (tp) cc_final: 0.6382 (tp) REVERT: A 787 ARG cc_start: 0.8203 (ttt90) cc_final: 0.7641 (ttm-80) REVERT: B 394 PHE cc_start: 0.8339 (m-10) cc_final: 0.7271 (m-80) REVERT: B 395 ASN cc_start: 0.9049 (OUTLIER) cc_final: 0.6752 (t0) REVERT: B 425 LEU cc_start: 0.8471 (mt) cc_final: 0.8180 (mt) REVERT: B 427 VAL cc_start: 0.8675 (t) cc_final: 0.8411 (m) REVERT: B 437 GLU cc_start: 0.6787 (tm-30) cc_final: 0.6519 (tm-30) REVERT: B 507 SER cc_start: 0.8259 (m) cc_final: 0.7966 (p) REVERT: B 647 ARG cc_start: 0.7628 (tpt90) cc_final: 0.7397 (tpt90) REVERT: B 794 LYS cc_start: 0.7653 (mppt) cc_final: 0.6915 (tppt) REVERT: D 102 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.6006 (pm20) REVERT: D 155 GLN cc_start: 0.8438 (mp10) cc_final: 0.8161 (mp10) outliers start: 41 outliers final: 35 residues processed: 285 average time/residue: 0.2551 time to fit residues: 107.4584 Evaluate side-chains 301 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 264 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 812 TYR Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 735 MET Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 136 optimal weight: 0.9980 chunk 125 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 139 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 146 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 141 optimal weight: 0.0970 chunk 12 optimal weight: 3.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.248976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.225833 restraints weight = 39716.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 112)---------------| | r_work = 0.4644 r_free = 0.4644 target = 0.222678 restraints weight = 36219.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.222397 restraints weight = 34334.761| |-----------------------------------------------------------------------------| r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14912 Z= 0.160 Angle : 0.734 9.755 20353 Z= 0.367 Chirality : 0.048 0.314 2343 Planarity : 0.005 0.053 2507 Dihedral : 5.521 50.789 2244 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.34 % Favored : 93.43 % Rotamer: Outliers : 2.59 % Allowed : 18.95 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.20), residues: 1766 helix: 1.04 (0.37), residues: 194 sheet: -0.15 (0.22), residues: 573 loop : -1.20 (0.21), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 583 HIS 0.012 0.001 HIS B 683 PHE 0.032 0.002 PHE B 394 TYR 0.054 0.002 TYR D 82 ARG 0.008 0.001 ARG B 647 Details of bonding type rmsd link_NAG-ASN : bond 0.00563 ( 11) link_NAG-ASN : angle 2.23789 ( 33) link_BETA1-4 : bond 0.00603 ( 2) link_BETA1-4 : angle 1.26342 ( 6) hydrogen bonds : bond 0.04583 ( 424) hydrogen bonds : angle 5.20317 ( 1209) link_BETA1-6 : bond 0.02373 ( 2) link_BETA1-6 : angle 3.17705 ( 6) SS BOND : bond 0.00315 ( 26) SS BOND : angle 1.78486 ( 52) covalent geometry : bond 0.00365 (14871) covalent geometry : angle 0.72255 (20256) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6510.08 seconds wall clock time: 114 minutes 48.03 seconds (6888.03 seconds total)