Starting phenix.real_space_refine on Sat Oct 11 12:24:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x85_38136/10_2025/8x85_38136.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x85_38136/10_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_38136/10_2025/8x85_38136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x85_38136/10_2025/8x85_38136.map" model { file = "/net/cci-nas-00/data/ceres_data/8x85_38136/10_2025/8x85_38136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x85_38136/10_2025/8x85_38136.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.03, per 1000 atoms: 0.21 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: 1.18 Conformation dependent library (CDL) restraints added in 641.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.58 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: 2.77 Time building geometry restraints manager: 1.54 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 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: 13.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.690 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.450 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG A 573 TYR 0.028 0.001 TYR B 795 PHE 0.016 0.001 PHE A 336 TRP 0.057 0.002 TRP A 583 HIS 0.005 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00408 (14871) covalent geometry : angle 0.77598 (20256) SS BOND : bond 0.00411 ( 26) SS BOND : angle 2.33504 ( 52) hydrogen bonds : bond 0.17163 ( 424) hydrogen bonds : angle 7.74500 ( 1209) link_BETA1-4 : bond 0.00572 ( 2) link_BETA1-4 : angle 1.17598 ( 6) link_BETA1-6 : bond 0.01944 ( 2) link_BETA1-6 : angle 2.87922 ( 6) link_NAG-ASN : bond 0.00548 ( 11) link_NAG-ASN : angle 2.49950 ( 33) *********************** 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 : 0.388 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: 0.1207 time to fit residues: 54.7883 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 : 0.408 ------------------------------------------------------------------------------- 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 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 0.0170 chunk 103 optimal weight: 0.0000 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.1478 ------------------------------------------------------------------------------- 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 B 380 GLN ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 GLN C 160 GLN D 96 GLN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.217482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.169622 restraints weight = 30557.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.174515 restraints weight = 14218.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.177598 restraints weight = 8501.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.179294 restraints weight = 6016.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.180635 restraints weight = 4851.205| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14912 Z= 0.129 Angle : 0.707 10.103 20353 Z= 0.355 Chirality : 0.047 0.335 2343 Planarity : 0.005 0.068 2507 Dihedral : 7.430 68.567 2247 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.55 % Favored : 94.17 % Rotamer: Outliers : 1.20 % Allowed : 8.97 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.21), residues: 1766 helix: 1.16 (0.37), residues: 201 sheet: -0.25 (0.22), residues: 583 loop : -1.19 (0.21), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 573 TYR 0.061 0.002 TYR D 82 PHE 0.013 0.001 PHE B 703 TRP 0.029 0.001 TRP A 583 HIS 0.010 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00276 (14871) covalent geometry : angle 0.69300 (20256) SS BOND : bond 0.00300 ( 26) SS BOND : angle 1.75924 ( 52) hydrogen bonds : bond 0.04862 ( 424) hydrogen bonds : angle 5.69201 ( 1209) link_BETA1-4 : bond 0.00544 ( 2) link_BETA1-4 : angle 2.06454 ( 6) link_BETA1-6 : bond 0.02631 ( 2) link_BETA1-6 : angle 3.30392 ( 6) link_NAG-ASN : bond 0.00546 ( 11) link_NAG-ASN : angle 2.43846 ( 33) *********************** 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 305 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 285 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 ASN cc_start: 0.7248 (p0) cc_final: 0.6869 (p0) REVERT: A 365 GLU cc_start: 0.5897 (mm-30) cc_final: 0.5637 (mm-30) REVERT: A 424 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6914 (mt-10) REVERT: A 429 ASP cc_start: 0.7132 (p0) cc_final: 0.6878 (p0) REVERT: A 497 GLU cc_start: 0.6426 (pp20) cc_final: 0.5912 (pp20) REVERT: A 499 ILE cc_start: 0.8331 (mm) cc_final: 0.8081 (mm) REVERT: A 507 SER cc_start: 0.8123 (m) cc_final: 0.7513 (p) REVERT: A 511 MET cc_start: 0.7471 (mtt) cc_final: 0.7267 (mtt) REVERT: A 573 ARG cc_start: 0.7329 (ptt180) cc_final: 0.7128 (ptt-90) REVERT: A 614 LYS cc_start: 0.7152 (tttp) cc_final: 0.6917 (tttp) REVERT: A 669 LYS cc_start: 0.8479 (mppt) cc_final: 0.7816 (mmtm) REVERT: A 728 ASN cc_start: 0.7433 (m-40) cc_final: 0.7054 (m-40) REVERT: A 774 TRP cc_start: 0.7151 (p90) cc_final: 0.6477 (p90) REVERT: B 394 PHE cc_start: 0.8175 (m-10) cc_final: 0.7786 (m-10) REVERT: B 425 LEU cc_start: 0.8620 (mt) cc_final: 0.8337 (mt) REVERT: B 427 VAL cc_start: 0.8434 (t) cc_final: 0.8104 (m) REVERT: B 429 ASP cc_start: 0.7122 (t0) cc_final: 0.6909 (t0) REVERT: B 437 GLU cc_start: 0.6627 (tm-30) cc_final: 0.6276 (tm-30) REVERT: B 507 SER cc_start: 0.8223 (m) cc_final: 0.7819 (p) REVERT: B 617 ASP cc_start: 0.7436 (m-30) cc_final: 0.7188 (m-30) REVERT: B 794 LYS cc_start: 0.7413 (tptp) cc_final: 0.6971 (tptt) REVERT: D 153 SER cc_start: 0.8119 (p) cc_final: 0.7341 (p) REVERT: D 155 GLN cc_start: 0.8183 (mp10) cc_final: 0.7783 (mp10) outliers start: 20 outliers final: 12 residues processed: 293 average time/residue: 0.1168 time to fit residues: 50.0374 Evaluate side-chains 285 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 273 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 715 LEU Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain D residue 96 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 135 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 0.3980 chunk 73 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 ASN C 84 GLN D 96 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 = 0.4854 r_free = 0.4854 target = 0.248282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.225910 restraints weight = 39491.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 91)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.222973 restraints weight = 36105.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.222576 restraints weight = 30158.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.222667 restraints weight = 24785.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.222712 restraints weight = 21134.250| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14912 Z= 0.209 Angle : 0.725 10.989 20353 Z= 0.366 Chirality : 0.048 0.312 2343 Planarity : 0.005 0.060 2507 Dihedral : 6.756 54.194 2244 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.40 % Favored : 93.32 % Rotamer: Outliers : 2.59 % Allowed : 11.61 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.20), residues: 1766 helix: 1.18 (0.36), residues: 201 sheet: -0.31 (0.21), residues: 578 loop : -1.25 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 514 TYR 0.049 0.002 TYR D 82 PHE 0.026 0.002 PHE A 701 TRP 0.031 0.002 TRP A 583 HIS 0.008 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00475 (14871) covalent geometry : angle 0.70980 (20256) SS BOND : bond 0.00301 ( 26) SS BOND : angle 1.91781 ( 52) hydrogen bonds : bond 0.05379 ( 424) hydrogen bonds : angle 5.72261 ( 1209) link_BETA1-4 : bond 0.00618 ( 2) link_BETA1-4 : angle 2.24417 ( 6) link_BETA1-6 : bond 0.02539 ( 2) link_BETA1-6 : angle 3.16651 ( 6) link_NAG-ASN : bond 0.00662 ( 11) link_NAG-ASN : angle 2.56174 ( 33) *********************** 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 325 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 282 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 ASN cc_start: 0.7510 (p0) cc_final: 0.7286 (p0) REVERT: A 365 GLU cc_start: 0.6013 (mm-30) cc_final: 0.5724 (mm-30) REVERT: A 374 GLU cc_start: 0.7293 (pm20) cc_final: 0.7036 (pm20) REVERT: A 414 ASN cc_start: 0.8423 (p0) cc_final: 0.8133 (p0) REVERT: A 424 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6982 (mt-10) REVERT: A 455 GLN cc_start: 0.7210 (mt0) cc_final: 0.6901 (mt0) REVERT: A 497 GLU cc_start: 0.6697 (pp20) cc_final: 0.6243 (pp20) REVERT: A 511 MET cc_start: 0.7807 (mtt) cc_final: 0.7580 (mtt) REVERT: A 614 LYS cc_start: 0.7285 (tttp) cc_final: 0.6898 (tttm) REVERT: A 669 LYS cc_start: 0.8690 (mppt) cc_final: 0.8359 (mmtm) REVERT: A 728 ASN cc_start: 0.7543 (m-40) cc_final: 0.6904 (m-40) REVERT: B 227 MET cc_start: -0.4372 (mmt) cc_final: -0.4934 (mmt) REVERT: B 394 PHE cc_start: 0.8195 (m-10) cc_final: 0.7029 (m-10) REVERT: B 395 ASN cc_start: 0.9047 (OUTLIER) cc_final: 0.6983 (t0) REVERT: B 404 LYS cc_start: 0.8336 (mmmt) cc_final: 0.8055 (mmmt) REVERT: B 425 LEU cc_start: 0.8496 (mt) cc_final: 0.8230 (mt) REVERT: B 427 VAL cc_start: 0.8598 (t) cc_final: 0.8257 (m) REVERT: B 429 ASP cc_start: 0.7003 (t0) cc_final: 0.6798 (t0) REVERT: B 437 GLU cc_start: 0.6791 (tm-30) cc_final: 0.6462 (tm-30) REVERT: B 617 ASP cc_start: 0.8126 (m-30) cc_final: 0.7882 (m-30) REVERT: B 794 LYS cc_start: 0.7435 (tptp) cc_final: 0.7090 (tptp) REVERT: C 84 GLN cc_start: 0.8360 (tp40) cc_final: 0.8128 (tp40) REVERT: D 151 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7503 (tt0) REVERT: D 153 SER cc_start: 0.8195 (p) cc_final: 0.7758 (p) outliers start: 43 outliers final: 24 residues processed: 299 average time/residue: 0.1178 time to fit residues: 51.3843 Evaluate side-chains 299 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 273 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 406 THR Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 635 ASP 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 395 ASN Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 641 ARG 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 58 THR 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 96 GLN Chi-restraints excluded: chain D residue 147 LEU 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 64 optimal weight: 6.9990 chunk 152 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 165 optimal weight: 0.3980 chunk 131 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 88 optimal weight: 30.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 ASN B 480 HIS ** B 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 HIS C 93 ASN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.248008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.225154 restraints weight = 39375.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 94)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.222571 restraints weight = 37189.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 88)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.221189 restraints weight = 28348.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.221651 restraints weight = 25310.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 71)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.221187 restraints weight = 20426.608| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 14912 Z= 0.206 Angle : 0.733 10.778 20353 Z= 0.371 Chirality : 0.048 0.306 2343 Planarity : 0.005 0.058 2507 Dihedral : 6.362 51.759 2244 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.63 % Favored : 93.09 % Rotamer: Outliers : 2.83 % Allowed : 13.36 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.20), residues: 1766 helix: 1.25 (0.36), residues: 201 sheet: -0.33 (0.21), residues: 588 loop : -1.28 (0.21), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 787 TYR 0.058 0.002 TYR D 82 PHE 0.016 0.002 PHE B 570 TRP 0.024 0.002 TRP A 583 HIS 0.009 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00474 (14871) covalent geometry : angle 0.71494 (20256) SS BOND : bond 0.00406 ( 26) SS BOND : angle 2.42323 ( 52) hydrogen bonds : bond 0.05213 ( 424) hydrogen bonds : angle 5.64403 ( 1209) link_BETA1-4 : bond 0.00754 ( 2) link_BETA1-4 : angle 2.18187 ( 6) link_BETA1-6 : bond 0.02508 ( 2) link_BETA1-6 : angle 3.25153 ( 6) link_NAG-ASN : bond 0.00632 ( 11) link_NAG-ASN : angle 2.42585 ( 33) *********************** 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 330 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 283 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 ASN cc_start: 0.7509 (p0) cc_final: 0.7259 (p0) REVERT: A 365 GLU cc_start: 0.6047 (mm-30) cc_final: 0.5783 (mm-30) REVERT: A 374 GLU cc_start: 0.7277 (pm20) cc_final: 0.6964 (pm20) REVERT: A 414 ASN cc_start: 0.8404 (p0) cc_final: 0.8148 (p0) REVERT: A 424 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7057 (mt-10) REVERT: A 455 GLN cc_start: 0.7253 (mt0) cc_final: 0.6965 (mt0) REVERT: A 497 GLU cc_start: 0.6806 (pp20) cc_final: 0.6481 (pp20) REVERT: A 511 MET cc_start: 0.7790 (mtt) cc_final: 0.7587 (mtt) REVERT: A 587 GLU cc_start: 0.7178 (mp0) cc_final: 0.6951 (mp0) REVERT: A 614 LYS cc_start: 0.7296 (tttp) cc_final: 0.6872 (tttm) REVERT: B 394 PHE cc_start: 0.8076 (m-10) cc_final: 0.7599 (m-10) REVERT: B 395 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.7736 (p0) REVERT: B 404 LYS cc_start: 0.8325 (mmmt) cc_final: 0.8038 (mmmt) REVERT: B 425 LEU cc_start: 0.8516 (mt) cc_final: 0.8248 (mt) REVERT: B 427 VAL cc_start: 0.8625 (t) cc_final: 0.8329 (m) REVERT: B 429 ASP cc_start: 0.7032 (t0) cc_final: 0.6831 (t0) REVERT: B 437 GLU cc_start: 0.6756 (tm-30) cc_final: 0.6441 (tm-30) REVERT: B 617 ASP cc_start: 0.7671 (m-30) cc_final: 0.7447 (m-30) REVERT: B 683 HIS cc_start: 0.5609 (OUTLIER) cc_final: 0.4746 (t-90) REVERT: B 703 PHE cc_start: 0.7384 (t80) cc_final: 0.7091 (t80) REVERT: B 787 ARG cc_start: 0.7971 (tpt-90) cc_final: 0.7527 (tpt170) REVERT: B 794 LYS cc_start: 0.7460 (tptp) cc_final: 0.7132 (tptp) REVERT: D 102 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.6135 (pm20) outliers start: 47 outliers final: 31 residues processed: 306 average time/residue: 0.1154 time to fit residues: 52.2285 Evaluate side-chains 304 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 270 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 379 SER Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 446 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 528 CYS Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 812 TYR Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 819 VAL 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 619 LEU Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 683 HIS 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 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 Chi-restraints excluded: chain D residue 147 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 0 optimal weight: 9.9990 chunk 88 optimal weight: 40.0000 chunk 153 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 103 optimal weight: 0.4980 chunk 128 optimal weight: 0.0980 chunk 26 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 A 739 ASN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.248607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.225949 restraints weight = 39678.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.224059 restraints weight = 36564.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.223247 restraints weight = 27287.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.223135 restraints weight = 23284.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.223366 restraints weight = 21257.589| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14912 Z= 0.176 Angle : 0.748 15.991 20353 Z= 0.370 Chirality : 0.049 0.340 2343 Planarity : 0.005 0.058 2507 Dihedral : 6.258 49.260 2244 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.40 % Favored : 93.32 % Rotamer: Outliers : 2.77 % Allowed : 15.70 % Favored : 81.53 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 6.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.20), residues: 1766 helix: 1.35 (0.37), residues: 200 sheet: -0.35 (0.21), residues: 590 loop : -1.29 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 647 TYR 0.055 0.002 TYR D 82 PHE 0.031 0.002 PHE A 703 TRP 0.030 0.001 TRP B 368 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00398 (14871) covalent geometry : angle 0.72319 (20256) SS BOND : bond 0.00271 ( 26) SS BOND : angle 2.27902 ( 52) hydrogen bonds : bond 0.04996 ( 424) hydrogen bonds : angle 5.50590 ( 1209) link_BETA1-4 : bond 0.00664 ( 2) link_BETA1-4 : angle 2.04449 ( 6) link_BETA1-6 : bond 0.02565 ( 2) link_BETA1-6 : angle 3.25501 ( 6) link_NAG-ASN : bond 0.00600 ( 11) link_NAG-ASN : angle 3.68273 ( 33) *********************** 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 331 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 285 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 ASN cc_start: 0.7418 (p0) cc_final: 0.7194 (p0) REVERT: A 365 GLU cc_start: 0.6105 (mm-30) cc_final: 0.5822 (mm-30) REVERT: A 374 GLU cc_start: 0.7301 (pm20) cc_final: 0.6943 (pm20) REVERT: A 414 ASN cc_start: 0.8376 (p0) cc_final: 0.8113 (p0) REVERT: A 424 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7022 (mt-10) REVERT: A 428 ILE cc_start: 0.7506 (mm) cc_final: 0.7271 (mm) REVERT: A 455 GLN cc_start: 0.7281 (mt0) cc_final: 0.7022 (mt0) REVERT: A 497 GLU cc_start: 0.6809 (pp20) cc_final: 0.6277 (pp20) REVERT: A 587 GLU cc_start: 0.7159 (mp0) cc_final: 0.6944 (mp0) REVERT: A 614 LYS cc_start: 0.7259 (tttp) cc_final: 0.6763 (tttm) REVERT: A 787 ARG cc_start: 0.8225 (ttt90) cc_final: 0.8005 (ttt90) REVERT: B 394 PHE cc_start: 0.7995 (m-10) cc_final: 0.7782 (m-10) REVERT: B 404 LYS cc_start: 0.8320 (mmmt) cc_final: 0.8063 (mmmt) REVERT: B 425 LEU cc_start: 0.8504 (mt) cc_final: 0.8250 (mt) REVERT: B 427 VAL cc_start: 0.8631 (t) cc_final: 0.8303 (m) REVERT: B 437 GLU cc_start: 0.6876 (tm-30) cc_final: 0.6619 (tm-30) REVERT: B 617 ASP cc_start: 0.7812 (m-30) cc_final: 0.7555 (m-30) REVERT: B 645 PHE cc_start: 0.7948 (p90) cc_final: 0.7557 (p90) REVERT: B 683 HIS cc_start: 0.5625 (OUTLIER) cc_final: 0.4683 (t-90) REVERT: B 703 PHE cc_start: 0.7331 (t80) cc_final: 0.6866 (t80) REVERT: B 794 LYS cc_start: 0.7459 (tptp) cc_final: 0.7150 (tptp) REVERT: D 102 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.6083 (pm20) REVERT: D 157 MET cc_start: 0.7417 (mmt) cc_final: 0.7211 (mmt) outliers start: 46 outliers final: 33 residues processed: 303 average time/residue: 0.1203 time to fit residues: 53.1982 Evaluate side-chains 311 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 276 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 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 693 GLU Chi-restraints excluded: chain A residue 703 PHE 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 510 THR Chi-restraints excluded: chain B residue 553 LEU 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 668 MET Chi-restraints excluded: chain B residue 683 HIS 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 Chi-restraints excluded: chain D residue 147 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 92 optimal weight: 50.0000 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 87 optimal weight: 30.0000 chunk 74 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.218474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.167493 restraints weight = 29473.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.172213 restraints weight = 13811.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.175056 restraints weight = 8374.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.176776 restraints weight = 6002.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.177819 restraints weight = 4865.940| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14912 Z= 0.258 Angle : 0.783 12.573 20353 Z= 0.396 Chirality : 0.050 0.315 2343 Planarity : 0.005 0.063 2507 Dihedral : 6.288 45.360 2244 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.53 % Favored : 92.19 % Rotamer: Outliers : 3.01 % Allowed : 16.06 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.20), residues: 1766 helix: 0.92 (0.36), residues: 200 sheet: -0.40 (0.22), residues: 585 loop : -1.34 (0.21), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 514 TYR 0.057 0.002 TYR D 82 PHE 0.023 0.002 PHE A 703 TRP 0.025 0.002 TRP A 583 HIS 0.008 0.001 HIS B 467 Details of bonding type rmsd covalent geometry : bond 0.00588 (14871) covalent geometry : angle 0.76468 (20256) SS BOND : bond 0.00316 ( 26) SS BOND : angle 2.30973 ( 52) hydrogen bonds : bond 0.05802 ( 424) hydrogen bonds : angle 5.74676 ( 1209) link_BETA1-4 : bond 0.00745 ( 2) link_BETA1-4 : angle 1.85190 ( 6) link_BETA1-6 : bond 0.02466 ( 2) link_BETA1-6 : angle 3.35892 ( 6) link_NAG-ASN : bond 0.00756 ( 11) link_NAG-ASN : angle 2.78555 ( 33) *********************** 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 334 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 284 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 ASN cc_start: 0.7448 (p0) cc_final: 0.6992 (p0) REVERT: A 355 LYS cc_start: 0.8211 (tttt) cc_final: 0.7706 (tttm) REVERT: A 365 GLU cc_start: 0.6080 (mm-30) cc_final: 0.5791 (mm-30) REVERT: A 374 GLU cc_start: 0.7199 (pm20) cc_final: 0.6827 (pm20) REVERT: A 428 ILE cc_start: 0.7640 (mm) cc_final: 0.7291 (mt) REVERT: A 556 ILE cc_start: 0.5784 (mm) cc_final: 0.3844 (tp) REVERT: A 727 PHE cc_start: 0.6942 (m-10) cc_final: 0.6673 (m-10) REVERT: A 787 ARG cc_start: 0.8256 (ttt90) cc_final: 0.7915 (ttt90) REVERT: B 394 PHE cc_start: 0.8390 (m-10) cc_final: 0.8151 (m-10) REVERT: B 404 LYS cc_start: 0.8357 (mmmt) cc_final: 0.8112 (mmmt) REVERT: B 425 LEU cc_start: 0.8580 (mt) cc_final: 0.8266 (mt) REVERT: B 427 VAL cc_start: 0.8736 (t) cc_final: 0.8536 (m) REVERT: B 437 GLU cc_start: 0.6837 (tm-30) cc_final: 0.6588 (tm-30) REVERT: B 507 SER cc_start: 0.8369 (m) cc_final: 0.8060 (p) REVERT: B 617 ASP cc_start: 0.7558 (m-30) cc_final: 0.7279 (m-30) REVERT: B 645 PHE cc_start: 0.8157 (p90) cc_final: 0.7153 (p90) REVERT: B 787 ARG cc_start: 0.8187 (tpt-90) cc_final: 0.7945 (tpt-90) REVERT: B 794 LYS cc_start: 0.7534 (tptp) cc_final: 0.7208 (tptp) REVERT: C 42 ILE cc_start: 0.8494 (mm) cc_final: 0.8261 (mt) REVERT: C 119 LEU cc_start: 0.8280 (mt) cc_final: 0.8070 (mp) REVERT: D 102 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.6128 (pm20) REVERT: D 153 SER cc_start: 0.8193 (p) cc_final: 0.7654 (p) REVERT: D 157 MET cc_start: 0.7416 (mmt) cc_final: 0.7127 (mmt) outliers start: 50 outliers final: 31 residues processed: 308 average time/residue: 0.1182 time to fit residues: 53.0830 Evaluate side-chains 308 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 276 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 446 THR 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 693 GLU 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 527 THR Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 735 MET 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 136 GLU Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 147 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 60 optimal weight: 0.7980 chunk 154 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 chunk 160 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 41 optimal weight: 0.0770 chunk 43 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.248072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.225271 restraints weight = 39361.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 85)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.223007 restraints weight = 36010.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.221610 restraints weight = 31134.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.222218 restraints weight = 26623.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.222449 restraints weight = 19961.982| |-----------------------------------------------------------------------------| r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.2350 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= 0.173 Angle : 0.755 10.214 20353 Z= 0.382 Chirality : 0.049 0.310 2343 Planarity : 0.005 0.058 2507 Dihedral : 5.973 39.286 2244 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.00 % Favored : 93.71 % Rotamer: Outliers : 2.83 % Allowed : 17.93 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.20), residues: 1766 helix: 1.17 (0.37), residues: 200 sheet: -0.36 (0.22), residues: 589 loop : -1.34 (0.21), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 647 TYR 0.052 0.002 TYR D 82 PHE 0.034 0.002 PHE A 701 TRP 0.046 0.002 TRP B 368 HIS 0.005 0.001 HIS B 710 Details of bonding type rmsd covalent geometry : bond 0.00397 (14871) covalent geometry : angle 0.73913 (20256) SS BOND : bond 0.00570 ( 26) SS BOND : angle 2.20479 ( 52) hydrogen bonds : bond 0.04942 ( 424) hydrogen bonds : angle 5.48821 ( 1209) link_BETA1-4 : bond 0.00660 ( 2) link_BETA1-4 : angle 1.48720 ( 6) link_BETA1-6 : bond 0.02424 ( 2) link_BETA1-6 : angle 3.29565 ( 6) link_NAG-ASN : bond 0.00592 ( 11) link_NAG-ASN : angle 2.55446 ( 33) *********************** 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 326 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 279 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 ASN cc_start: 0.7136 (p0) cc_final: 0.6883 (p0) REVERT: A 355 LYS cc_start: 0.8195 (tttt) cc_final: 0.7733 (tttp) REVERT: A 365 GLU cc_start: 0.6070 (mm-30) cc_final: 0.5746 (mm-30) REVERT: A 374 GLU cc_start: 0.7270 (pm20) cc_final: 0.6793 (pm20) REVERT: A 428 ILE cc_start: 0.7520 (mm) cc_final: 0.7147 (mt) REVERT: A 437 GLU cc_start: 0.6056 (OUTLIER) cc_final: 0.5839 (mm-30) REVERT: A 614 LYS cc_start: 0.7195 (tttp) cc_final: 0.6811 (tttm) REVERT: A 727 PHE cc_start: 0.6965 (m-10) cc_final: 0.6668 (m-10) REVERT: B 425 LEU cc_start: 0.8508 (mt) cc_final: 0.8203 (mt) REVERT: B 427 VAL cc_start: 0.8661 (t) cc_final: 0.8427 (m) REVERT: B 437 GLU cc_start: 0.6807 (tm-30) cc_final: 0.6560 (tm-30) REVERT: B 572 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7729 (pt) REVERT: B 617 ASP cc_start: 0.7737 (m-30) cc_final: 0.7481 (m-30) REVERT: B 683 HIS cc_start: 0.5641 (OUTLIER) cc_final: 0.4774 (t-90) REVERT: B 794 LYS cc_start: 0.7416 (tptp) cc_final: 0.7106 (tptp) REVERT: C 42 ILE cc_start: 0.8279 (mm) cc_final: 0.8048 (mt) REVERT: D 102 GLU cc_start: 0.6296 (OUTLIER) cc_final: 0.5987 (pm20) REVERT: D 153 SER cc_start: 0.8245 (p) cc_final: 0.7633 (p) REVERT: D 157 MET cc_start: 0.7325 (mmt) cc_final: 0.7032 (mmt) outliers start: 47 outliers final: 34 residues processed: 299 average time/residue: 0.1171 time to fit residues: 51.2595 Evaluate side-chains 309 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 271 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 379 SER 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 437 GLU Chi-restraints excluded: chain A residue 446 THR 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 693 GLU 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 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 683 HIS Chi-restraints excluded: chain B residue 735 MET 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 B residue 821 LYS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 151 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 55 optimal weight: 0.0970 chunk 158 optimal weight: 0.2980 chunk 110 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 166 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 134 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 610 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.248079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.225307 restraints weight = 39099.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 84)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.222825 restraints weight = 35749.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.222349 restraints weight = 34665.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.222344 restraints weight = 24513.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.222649 restraints weight = 21046.787| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14912 Z= 0.174 Angle : 0.760 11.137 20353 Z= 0.381 Chirality : 0.049 0.314 2343 Planarity : 0.005 0.058 2507 Dihedral : 5.837 38.991 2244 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.23 % Favored : 93.49 % Rotamer: Outliers : 2.83 % Allowed : 18.23 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.20), residues: 1766 helix: 1.14 (0.37), residues: 200 sheet: -0.37 (0.22), residues: 590 loop : -1.30 (0.21), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 787 TYR 0.050 0.002 TYR D 82 PHE 0.044 0.002 PHE B 394 TRP 0.035 0.002 TRP B 368 HIS 0.006 0.001 HIS B 683 Details of bonding type rmsd covalent geometry : bond 0.00403 (14871) covalent geometry : angle 0.74560 (20256) SS BOND : bond 0.00349 ( 26) SS BOND : angle 2.07216 ( 52) hydrogen bonds : bond 0.04864 ( 424) hydrogen bonds : angle 5.44311 ( 1209) link_BETA1-4 : bond 0.00599 ( 2) link_BETA1-4 : angle 1.43235 ( 6) link_BETA1-6 : bond 0.02366 ( 2) link_BETA1-6 : angle 3.28774 ( 6) link_NAG-ASN : bond 0.00587 ( 11) link_NAG-ASN : angle 2.44035 ( 33) *********************** 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 335 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 288 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 LYS cc_start: 0.8190 (tttt) cc_final: 0.7717 (tttp) REVERT: A 365 GLU cc_start: 0.6063 (mm-30) cc_final: 0.5749 (mm-30) REVERT: A 374 GLU cc_start: 0.7269 (pm20) cc_final: 0.6801 (pm20) REVERT: A 428 ILE cc_start: 0.7531 (mm) cc_final: 0.7170 (mt) REVERT: A 437 GLU cc_start: 0.6106 (OUTLIER) cc_final: 0.5906 (mm-30) REVERT: A 587 GLU cc_start: 0.7172 (mp0) cc_final: 0.6929 (mp0) REVERT: A 614 LYS cc_start: 0.7331 (tttp) cc_final: 0.7119 (tttt) REVERT: A 727 PHE cc_start: 0.6946 (m-10) cc_final: 0.6711 (m-10) REVERT: B 404 LYS cc_start: 0.8535 (tppt) cc_final: 0.8064 (mmmt) REVERT: B 425 LEU cc_start: 0.8508 (mt) cc_final: 0.8204 (mt) REVERT: B 427 VAL cc_start: 0.8664 (t) cc_final: 0.8427 (m) REVERT: B 437 GLU cc_start: 0.6903 (tm-30) cc_final: 0.6634 (tm-30) REVERT: B 572 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.7791 (pt) REVERT: B 617 ASP cc_start: 0.7714 (m-30) cc_final: 0.7470 (m-30) REVERT: B 683 HIS cc_start: 0.5551 (OUTLIER) cc_final: 0.4498 (t-90) REVERT: B 773 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7366 (tm-30) REVERT: B 794 LYS cc_start: 0.7446 (tptp) cc_final: 0.7120 (tptp) REVERT: C 42 ILE cc_start: 0.8305 (mm) cc_final: 0.8076 (mt) REVERT: D 102 GLU cc_start: 0.6314 (OUTLIER) cc_final: 0.6020 (pm20) REVERT: D 153 SER cc_start: 0.8270 (p) cc_final: 0.7626 (p) REVERT: D 157 MET cc_start: 0.7291 (mmt) cc_final: 0.7019 (mmt) outliers start: 47 outliers final: 36 residues processed: 311 average time/residue: 0.1158 time to fit residues: 53.2813 Evaluate side-chains 316 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 276 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 379 SER 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 437 GLU Chi-restraints excluded: chain A residue 446 THR 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 633 VAL Chi-restraints excluded: chain A residue 693 GLU 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 680 VAL Chi-restraints excluded: chain B residue 683 HIS 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 809 PHE Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 821 LYS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 151 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 20 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 HIS ** 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 = 0.4585 r_free = 0.4585 target = 0.214535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.164758 restraints weight = 30059.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.169551 restraints weight = 13974.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.172521 restraints weight = 8389.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.174281 restraints weight = 5967.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.175216 restraints weight = 4780.247| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 14912 Z= 0.227 Angle : 0.804 11.775 20353 Z= 0.405 Chirality : 0.050 0.317 2343 Planarity : 0.005 0.059 2507 Dihedral : 5.977 40.010 2244 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.30 % Favored : 92.41 % Rotamer: Outliers : 2.65 % Allowed : 19.31 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.20), residues: 1766 helix: 0.97 (0.36), residues: 200 sheet: -0.26 (0.22), residues: 574 loop : -1.34 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 787 TYR 0.051 0.002 TYR D 82 PHE 0.040 0.002 PHE A 336 TRP 0.070 0.002 TRP B 368 HIS 0.007 0.001 HIS B 467 Details of bonding type rmsd covalent geometry : bond 0.00520 (14871) covalent geometry : angle 0.78880 (20256) SS BOND : bond 0.00419 ( 26) SS BOND : angle 2.23098 ( 52) hydrogen bonds : bond 0.05424 ( 424) hydrogen bonds : angle 5.55507 ( 1209) link_BETA1-4 : bond 0.00750 ( 2) link_BETA1-4 : angle 1.43414 ( 6) link_BETA1-6 : bond 0.02457 ( 2) link_BETA1-6 : angle 3.32866 ( 6) link_NAG-ASN : bond 0.00683 ( 11) link_NAG-ASN : angle 2.48585 ( 33) *********************** 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 328 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 284 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 LYS cc_start: 0.8189 (tttt) cc_final: 0.7639 (tttm) REVERT: A 365 GLU cc_start: 0.6062 (mm-30) cc_final: 0.5709 (mm-30) REVERT: A 374 GLU cc_start: 0.7217 (pm20) cc_final: 0.6745 (pm20) REVERT: A 428 ILE cc_start: 0.7621 (mm) cc_final: 0.7259 (mt) REVERT: A 437 GLU cc_start: 0.6123 (OUTLIER) cc_final: 0.5912 (mm-30) REVERT: A 556 ILE cc_start: 0.5758 (mm) cc_final: 0.3847 (tp) REVERT: A 614 LYS cc_start: 0.7471 (tttp) cc_final: 0.7266 (tttt) REVERT: A 727 PHE cc_start: 0.7113 (m-10) cc_final: 0.6849 (m-10) REVERT: B 404 LYS cc_start: 0.8572 (tppt) cc_final: 0.8079 (mmmt) REVERT: B 425 LEU cc_start: 0.8632 (mt) cc_final: 0.8288 (mt) REVERT: B 427 VAL cc_start: 0.8760 (t) cc_final: 0.8527 (m) REVERT: B 437 GLU cc_start: 0.6898 (tm-30) cc_final: 0.6648 (tm-30) REVERT: B 546 GLU cc_start: 0.6846 (pp20) cc_final: 0.6035 (pp20) REVERT: B 572 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.7790 (pt) REVERT: B 617 ASP cc_start: 0.7537 (m-30) cc_final: 0.7245 (m-30) REVERT: B 683 HIS cc_start: 0.5449 (OUTLIER) cc_final: 0.4027 (t-90) REVERT: B 703 PHE cc_start: 0.7262 (t80) cc_final: 0.6381 (t80) REVERT: B 773 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7396 (tm-30) REVERT: B 794 LYS cc_start: 0.7581 (tptp) cc_final: 0.7230 (tptp) REVERT: C 42 ILE cc_start: 0.8465 (mm) cc_final: 0.8231 (mt) REVERT: D 102 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.6148 (pm20) REVERT: D 153 SER cc_start: 0.8277 (p) cc_final: 0.7587 (p) REVERT: D 157 MET cc_start: 0.7282 (mmt) cc_final: 0.7001 (mmt) outliers start: 44 outliers final: 35 residues processed: 304 average time/residue: 0.1184 time to fit residues: 52.8684 Evaluate side-chains 315 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 276 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 379 SER 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 437 GLU Chi-restraints excluded: chain A residue 446 THR 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 633 VAL Chi-restraints excluded: chain A residue 693 GLU 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 527 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 668 MET Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 683 HIS 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 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 136 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 112 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 79 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 128 optimal weight: 0.4980 chunk 143 optimal weight: 0.1980 chunk 94 optimal weight: 0.0030 chunk 165 optimal weight: 0.0060 chunk 137 optimal weight: 1.9990 overall best weight: 0.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 ASN ** A 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 HIS ** 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 = 0.4606 r_free = 0.4606 target = 0.216717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.167977 restraints weight = 30445.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.172884 restraints weight = 14050.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.175907 restraints weight = 8390.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.177774 restraints weight = 5928.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.178922 restraints weight = 4713.072| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14912 Z= 0.133 Angle : 0.767 11.901 20353 Z= 0.383 Chirality : 0.048 0.308 2343 Planarity : 0.005 0.056 2507 Dihedral : 5.535 38.415 2244 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.04 % Favored : 94.68 % Rotamer: Outliers : 1.99 % Allowed : 20.22 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.21), residues: 1766 helix: 1.17 (0.37), residues: 200 sheet: -0.26 (0.22), residues: 579 loop : -1.24 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 787 TYR 0.055 0.001 TYR D 82 PHE 0.036 0.002 PHE A 336 TRP 0.041 0.001 TRP B 368 HIS 0.005 0.001 HIS B 683 Details of bonding type rmsd covalent geometry : bond 0.00300 (14871) covalent geometry : angle 0.75545 (20256) SS BOND : bond 0.00373 ( 26) SS BOND : angle 1.90353 ( 52) hydrogen bonds : bond 0.04244 ( 424) hydrogen bonds : angle 5.16239 ( 1209) link_BETA1-4 : bond 0.00647 ( 2) link_BETA1-4 : angle 1.17572 ( 6) link_BETA1-6 : bond 0.02551 ( 2) link_BETA1-6 : angle 3.30414 ( 6) link_NAG-ASN : bond 0.00494 ( 11) link_NAG-ASN : angle 2.23878 ( 33) ********************** 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 321 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 288 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 GLU cc_start: 0.6088 (mm-30) cc_final: 0.5768 (mm-30) REVERT: A 374 GLU cc_start: 0.7229 (pm20) cc_final: 0.6783 (pm20) REVERT: A 428 ILE cc_start: 0.7463 (mm) cc_final: 0.7112 (mt) REVERT: A 437 GLU cc_start: 0.5982 (OUTLIER) cc_final: 0.5781 (mm-30) REVERT: A 614 LYS cc_start: 0.7195 (tttp) cc_final: 0.6933 (tttm) REVERT: A 727 PHE cc_start: 0.7108 (m-10) cc_final: 0.6901 (m-10) REVERT: A 774 TRP cc_start: 0.7276 (p90) cc_final: 0.6708 (p90) REVERT: A 808 GLN cc_start: 0.7422 (pp30) cc_final: 0.6725 (pp30) REVERT: B 404 LYS cc_start: 0.8558 (tppt) cc_final: 0.8064 (mmmt) REVERT: B 425 LEU cc_start: 0.8673 (mt) cc_final: 0.8356 (mt) REVERT: B 427 VAL cc_start: 0.8664 (t) cc_final: 0.8442 (m) REVERT: B 437 GLU cc_start: 0.6786 (tm-30) cc_final: 0.6583 (tm-30) REVERT: B 546 GLU cc_start: 0.6791 (pp20) cc_final: 0.5961 (pp20) REVERT: B 572 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.7829 (pt) REVERT: B 617 ASP cc_start: 0.7467 (m-30) cc_final: 0.7206 (m-30) REVERT: B 647 ARG cc_start: 0.7636 (tpt90) cc_final: 0.7384 (tpt90) REVERT: B 683 HIS cc_start: 0.5235 (OUTLIER) cc_final: 0.4278 (t-90) REVERT: B 773 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7447 (tm-30) REVERT: C 157 MET cc_start: 0.7893 (ttm) cc_final: 0.7574 (ttm) REVERT: D 102 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.5958 (pm20) REVERT: D 153 SER cc_start: 0.8237 (p) cc_final: 0.7510 (p) REVERT: D 157 MET cc_start: 0.7141 (mmt) cc_final: 0.6836 (mmt) outliers start: 33 outliers final: 27 residues processed: 302 average time/residue: 0.1172 time to fit residues: 51.6411 Evaluate side-chains 309 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 278 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 446 THR 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 588 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 812 TYR Chi-restraints excluded: chain B residue 448 ARG 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 680 VAL Chi-restraints excluded: chain B residue 683 HIS Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 735 MET 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 136 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 174 optimal weight: 0.5980 chunk 133 optimal weight: 0.3980 chunk 125 optimal weight: 0.4980 chunk 90 optimal weight: 8.9990 chunk 155 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 13 optimal weight: 7.9990 chunk 164 optimal weight: 0.0980 chunk 45 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 HIS ** B 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** 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 = 0.4857 r_free = 0.4857 target = 0.248797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.226405 restraints weight = 39328.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 169)---------------| | r_work = 0.4648 r_free = 0.4648 target = 0.222619 restraints weight = 35102.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 101)---------------| | r_work = 0.4604 r_free = 0.4604 target = 0.221063 restraints weight = 32800.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 80)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.221688 restraints weight = 28400.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 86)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.221110 restraints weight = 23016.835| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14912 Z= 0.155 Angle : 0.769 11.452 20353 Z= 0.385 Chirality : 0.049 0.316 2343 Planarity : 0.005 0.057 2507 Dihedral : 5.508 39.263 2244 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.32 % Favored : 94.39 % Rotamer: Outliers : 2.17 % Allowed : 20.82 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.20), residues: 1766 helix: 1.26 (0.37), residues: 194 sheet: -0.11 (0.22), residues: 560 loop : -1.21 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 787 TYR 0.056 0.002 TYR D 82 PHE 0.020 0.001 PHE C 113 TRP 0.041 0.002 TRP B 368 HIS 0.006 0.001 HIS B 683 Details of bonding type rmsd covalent geometry : bond 0.00359 (14871) covalent geometry : angle 0.75627 (20256) SS BOND : bond 0.00352 ( 26) SS BOND : angle 1.94243 ( 52) hydrogen bonds : bond 0.04481 ( 424) hydrogen bonds : angle 5.18927 ( 1209) link_BETA1-4 : bond 0.00611 ( 2) link_BETA1-4 : angle 1.25097 ( 6) link_BETA1-6 : bond 0.02462 ( 2) link_BETA1-6 : angle 3.23028 ( 6) link_NAG-ASN : bond 0.00536 ( 11) link_NAG-ASN : angle 2.37814 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3705.37 seconds wall clock time: 64 minutes 25.59 seconds (3865.59 seconds total)