Starting phenix.real_space_refine on Fri Jun 13 09:25:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8swv_40822/06_2025/8swv_40822.cif Found real_map, /net/cci-nas-00/data/ceres_data/8swv_40822/06_2025/8swv_40822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8swv_40822/06_2025/8swv_40822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8swv_40822/06_2025/8swv_40822.map" model { file = "/net/cci-nas-00/data/ceres_data/8swv_40822/06_2025/8swv_40822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8swv_40822/06_2025/8swv_40822.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 102 5.16 5 C 9272 2.51 5 N 2549 2.21 5 O 2947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14870 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3371 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Chain breaks: 6 Chain: "B" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 948 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "C" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 948 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "E" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3250 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 18, 'TRANS': 391} Chain breaks: 6 Chain: "D" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 962 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "F" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3395 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 18, 'TRANS': 410} Chain breaks: 5 Chain: "H" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 610 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'TRANS': 121} Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 122 Planarities with less than four sites: {'UNK:plan-1': 122} Unresolved non-hydrogen planarities: 122 Chain: "L" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 525 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'TRANS': 104} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 105 Planarities with less than four sites: {'UNK:plan-1': 105} Unresolved non-hydrogen planarities: 105 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 9.28, per 1000 atoms: 0.62 Number of scatterers: 14870 At special positions: 0 Unit cell: (130.937, 138.154, 121.658, 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 102 16.00 O 2947 8.00 N 2549 7.00 C 9272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.10 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.11 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 149 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.01 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS E 501 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.07 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.06 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS F 501 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 73 " distance=2.02 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.05 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.02 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 149 " distance=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.02 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.02 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 ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA K 3 " - " MAN K 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 295 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 339 " " NAG A 604 " - " ASN A 363 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 88 " " NAG A 607 " - " ASN A 241 " " NAG A 608 " - " ASN A 148 " " NAG A 609 " - " ASN A 197 " " NAG A 610 " - " ASN A 234 " " NAG A 611 " - " ASN A 332 " " NAG A 612 " - " ASN A 137 " " NAG A 613 " - " ASN A 152 " " NAG A 614 " - " ASN A 289 " " NAG A 615 " - " ASN A 355 " " NAG A 616 " - " ASN A 386 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 618 " " NAG C 701 " - " ASN C 637 " " NAG C 702 " - " ASN C 618 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG D 703 " - " ASN D 618 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 197 " " NAG E 603 " - " ASN E 332 " " NAG E 604 " - " ASN E 339 " " NAG E 605 " - " ASN E 295 " " NAG E 606 " - " ASN E 241 " " NAG E 607 " - " ASN E 448 " " NAG E 608 " - " ASN E 289 " " NAG E 609 " - " ASN E 301 " " NAG E 610 " - " ASN E 152 " " NAG E 611 " - " ASN E 88 " " NAG F 601 " - " ASN F 289 " " NAG F 602 " - " ASN F 295 " " NAG F 603 " - " ASN F 386 " " NAG F 604 " - " ASN F 133 " " NAG F 605 " - " ASN F 152 " " NAG F 606 " - " ASN F 332 " " NAG F 607 " - " ASN F 392 " " NAG G 1 " - " ASN A 448 " " NAG I 1 " - " ASN A 262 " " NAG J 1 " - " ASN A 301 " " NAG K 1 " - " ASN E 262 " " NAG M 1 " - " ASN F 363 " " NAG N 1 " - " ASN F 262 " " NAG O 1 " - " ASN F 197 " Time building additional restraints: 4.41 Conformation dependent library (CDL) restraints added in 1.4 seconds 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3494 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 34 sheets defined 26.8% alpha, 39.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 116 removed outlier: 3.923A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 4.081A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 664 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 543 removed outlier: 3.734A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 596 Processing helix chain 'C' and resid 611 through 615 Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.837A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 664 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.510A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 3.796A pdb=" N ARG E 143 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.391A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.862A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 572 through 596 Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 662 Processing helix chain 'F' and resid 67 through 73 Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.004A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 335 through 354 removed outlier: 4.028A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 429 removed outlier: 4.431A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 480 Processing helix chain 'H' and resid 63 through 68 removed outlier: 4.692A pdb=" N UNK H 68 " --> pdb=" O UNK H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 78 No H-bonds generated for 'chain 'H' and resid 76 through 78' Processing helix chain 'H' and resid 89 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.493A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.817A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 173 through 175 Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.505A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 10.258A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 10.953A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.586A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.817A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.586A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 10.953A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.258A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.240A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 603 through 609 removed outlier: 8.180A pdb=" N CYS C 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TYR E 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N THR C 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N VAL E 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL C 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.668A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB5, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB6, first strand: chain 'E' and resid 161 through 169 Processing sheet with id=AB7, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.459A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.650A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 10.305A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.632A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.564A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.315A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.650A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 10.305A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.632A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.564A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.315A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.169A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 603 through 609 removed outlier: 7.925A pdb=" N CYS D 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N TYR F 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR D 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL F 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL D 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AC4, first strand: chain 'F' and resid 75 through 76 removed outlier: 4.195A pdb=" N VAL F 75 " --> pdb=" O CYS F 54 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AC6, first strand: chain 'F' and resid 161 through 169 Processing sheet with id=AC7, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.567A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 259 through 261 removed outlier: 10.319A pdb=" N VAL F 442 " --> pdb=" O CYS F 296 " (cutoff:3.500A) removed outlier: 11.009A pdb=" N CYS F 296 " --> pdb=" O VAL F 442 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.453A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.679A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N ASN F 448 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N GLU F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 271 through 273 removed outlier: 6.935A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N GLU F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N ASN F 448 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.679A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.453A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.009A pdb=" N CYS F 296 " --> pdb=" O VAL F 442 " (cutoff:3.500A) removed outlier: 10.319A pdb=" N VAL F 442 " --> pdb=" O CYS F 296 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N PHE F 468 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.593A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 13 through 14 removed outlier: 5.862A pdb=" N UNK H 13 " --> pdb=" O UNK H 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'H' and resid 60 through 62 removed outlier: 5.672A pdb=" N UNK H 49 " --> pdb=" O UNK H 40 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N UNK H 40 " --> pdb=" O UNK H 49 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N UNK H 96 " --> pdb=" O UNK H 116 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N UNK H 116 " --> pdb=" O UNK H 96 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N UNK H 98 " --> pdb=" O UNK H 114 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AD6, first strand: chain 'L' and resid 43 through 46 removed outlier: 6.547A pdb=" N UNK L 33 " --> pdb=" O UNK L 45 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 43 through 46 removed outlier: 6.547A pdb=" N UNK L 33 " --> pdb=" O UNK L 45 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1617 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.95 Time building geometry restraints manager: 5.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2906 1.32 - 1.45: 4525 1.45 - 1.59: 7459 1.59 - 1.72: 92 1.72 - 1.86: 130 Bond restraints: 15112 Sorted by residual: bond pdb=" NE ARG E 469 " pdb=" CZ ARG E 469 " ideal model delta sigma weight residual 1.326 1.402 -0.076 1.10e-02 8.26e+03 4.80e+01 bond pdb=" NE ARG E 504 " pdb=" CZ ARG E 504 " ideal model delta sigma weight residual 1.326 1.397 -0.071 1.10e-02 8.26e+03 4.22e+01 bond pdb=" NE1 TRP F 427 " pdb=" CE2 TRP F 427 " ideal model delta sigma weight residual 1.370 1.300 0.070 1.10e-02 8.26e+03 3.99e+01 bond pdb=" CD2 TRP D 571 " pdb=" CE3 TRP D 571 " ideal model delta sigma weight residual 1.398 1.497 -0.099 1.60e-02 3.91e+03 3.84e+01 bond pdb=" NE ARG F 504 " pdb=" CZ ARG F 504 " ideal model delta sigma weight residual 1.326 1.394 -0.068 1.10e-02 8.26e+03 3.84e+01 ... (remaining 15107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 17847 2.38 - 4.76: 2361 4.76 - 7.14: 286 7.14 - 9.52: 36 9.52 - 11.90: 2 Bond angle restraints: 20532 Sorted by residual: angle pdb=" N GLU F 370 " pdb=" CA GLU F 370 " pdb=" C GLU F 370 " ideal model delta sigma weight residual 114.62 103.65 10.97 1.14e+00 7.69e-01 9.26e+01 angle pdb=" C GLU E 492 " pdb=" N PRO E 493 " pdb=" CA PRO E 493 " ideal model delta sigma weight residual 119.56 128.24 -8.68 1.02e+00 9.61e-01 7.24e+01 angle pdb=" C ARG F 298 " pdb=" N PRO F 299 " pdb=" CA PRO F 299 " ideal model delta sigma weight residual 119.56 127.71 -8.15 1.01e+00 9.80e-01 6.52e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.56 127.53 -7.97 1.01e+00 9.80e-01 6.23e+01 angle pdb=" N GLU A 87 " pdb=" CA GLU A 87 " pdb=" C GLU A 87 " ideal model delta sigma weight residual 111.28 119.81 -8.53 1.09e+00 8.42e-01 6.13e+01 ... (remaining 20527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.18: 9648 21.18 - 42.37: 167 42.37 - 63.55: 59 63.55 - 84.74: 33 84.74 - 105.92: 14 Dihedral angle restraints: 9921 sinusoidal: 4560 harmonic: 5361 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -131.42 45.42 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -127.65 41.65 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -127.02 41.02 1 1.00e+01 1.00e-02 2.36e+01 ... (remaining 9918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1770 0.103 - 0.205: 495 0.205 - 0.308: 165 0.308 - 0.411: 90 0.411 - 0.513: 39 Chirality restraints: 2559 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.10e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.49e+01 ... (remaining 2556 not shown) Planarity restraints: 2591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 339 " 0.111 2.00e-02 2.50e+03 1.18e-01 1.73e+02 pdb=" CG ASN E 339 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN E 339 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN E 339 " -0.184 2.00e-02 2.50e+03 pdb=" C1 NAG E 604 " 0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 133 " 0.090 2.00e-02 2.50e+03 9.24e-02 1.07e+02 pdb=" CG ASN F 133 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN F 133 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN F 133 " -0.142 2.00e-02 2.50e+03 pdb=" C1 NAG F 604 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 133 " 0.078 2.00e-02 2.50e+03 8.21e-02 8.43e+01 pdb=" CG ASN E 133 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN E 133 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN E 133 " -0.129 2.00e-02 2.50e+03 pdb=" C1 NAG E 601 " 0.098 2.00e-02 2.50e+03 ... (remaining 2588 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2033 2.74 - 3.28: 13222 3.28 - 3.82: 22720 3.82 - 4.36: 28825 4.36 - 4.90: 47467 Nonbonded interactions: 114267 Sorted by model distance: nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.201 3.040 nonbonded pdb=" OG1 THR E 37 " pdb=" OG1 THR E 499 " model vdw 2.274 3.040 nonbonded pdb=" OG1 THR F 37 " pdb=" OG1 THR F 499 " model vdw 2.304 3.040 nonbonded pdb=" OD2 ASP C 632 " pdb=" NZ LYS E 46 " model vdw 2.385 3.120 nonbonded pdb=" N ILE E 213 " pdb=" O ILE E 213 " model vdw 2.398 2.496 ... (remaining 114262 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' and (resid 34 through 56 or resid 66 through 353 or resid 363 through \ 456 or resid 470 through 504 or resid 601 through 607)) selection = (chain 'E' and (resid 34 through 155 or resid 160 through 176 or resid 189 throu \ gh 504 or resid 601 through 607)) selection = (chain 'F' and (resid 34 through 56 or resid 66 through 155 or resid 160 through \ 176 or resid 189 through 353 or resid 363 through 456 or resid 470 through 504 \ or resid 601 through 607)) } ncs_group { reference = (chain 'B' and (resid 521 through 664 or resid 701 through 702)) selection = chain 'C' selection = (chain 'D' and (resid 521 through 547 or resid 572 through 664 or resid 701 thro \ ugh 702)) } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'O' } ncs_group { reference = (chain 'H' and resid 19 through 123) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'K' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 26.070 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 36.080 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.022 0.139 15208 Z= 1.166 Angle : 1.675 11.902 20787 Z= 1.065 Chirality : 0.134 0.513 2559 Planarity : 0.009 0.049 2542 Dihedral : 11.213 105.922 6328 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.03 % Favored : 97.90 % Rotamer: Outliers : 0.21 % Allowed : 0.35 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.20), residues: 1574 helix: -0.01 (0.25), residues: 417 sheet: 1.10 (0.23), residues: 461 loop : 0.56 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.009 TRP A 35 HIS 0.016 0.002 HIS F 374 PHE 0.036 0.007 PHE A 383 TYR 0.064 0.007 TYR A 191 ARG 0.007 0.001 ARG F 503 Details of bonding type rmsd link_NAG-ASN : bond 0.07702 ( 49) link_NAG-ASN : angle 2.87819 ( 147) link_ALPHA1-6 : bond 0.06315 ( 2) link_ALPHA1-6 : angle 3.75455 ( 6) link_BETA1-4 : bond 0.07053 ( 10) link_BETA1-4 : angle 4.69142 ( 30) link_ALPHA1-3 : bond 0.08991 ( 2) link_ALPHA1-3 : angle 4.52923 ( 6) hydrogen bonds : bond 0.15783 ( 578) hydrogen bonds : angle 7.00547 ( 1617) SS BOND : bond 0.02205 ( 33) SS BOND : angle 2.72285 ( 66) covalent geometry : bond 0.02198 (15112) covalent geometry : angle 1.64743 (20532) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 374 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.6851 (m-30) cc_final: 0.6636 (m-30) REVERT: A 211 GLU cc_start: 0.7976 (tt0) cc_final: 0.7745 (tt0) REVERT: E 113 ASP cc_start: 0.7277 (m-30) cc_final: 0.7037 (m-30) REVERT: E 248 THR cc_start: 0.8098 (p) cc_final: 0.7765 (p) REVERT: E 315 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7552 (mt0) REVERT: E 482 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7168 (mm-30) REVERT: F 35 TRP cc_start: 0.8913 (m100) cc_final: 0.8661 (m-90) REVERT: F 142 MET cc_start: 0.8786 (mmm) cc_final: 0.8474 (mmt) REVERT: F 419 ARG cc_start: 0.8278 (mmm-85) cc_final: 0.8033 (mmm160) REVERT: F 478 ASN cc_start: 0.8204 (m-40) cc_final: 0.7890 (m-40) outliers start: 3 outliers final: 2 residues processed: 376 average time/residue: 0.3626 time to fit residues: 194.5893 Evaluate side-chains 245 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 243 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain D residue 618 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN C 590 GLN E 137 ASN E 203 GLN D 630 GLN F 85 HIS F 203 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.154798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.132427 restraints weight = 18820.290| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.35 r_work: 0.3295 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15208 Z= 0.173 Angle : 0.725 10.788 20787 Z= 0.355 Chirality : 0.048 0.400 2559 Planarity : 0.004 0.044 2542 Dihedral : 8.014 80.061 3255 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.65 % Favored : 98.28 % Rotamer: Outliers : 1.66 % Allowed : 6.09 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.21), residues: 1574 helix: 1.02 (0.27), residues: 417 sheet: 0.81 (0.23), residues: 454 loop : 0.12 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 479 HIS 0.008 0.001 HIS E 352 PHE 0.035 0.003 PHE B 522 TYR 0.012 0.001 TYR C 643 ARG 0.004 0.001 ARG E 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 49) link_NAG-ASN : angle 3.43767 ( 147) link_ALPHA1-6 : bond 0.01081 ( 2) link_ALPHA1-6 : angle 1.42972 ( 6) link_BETA1-4 : bond 0.00802 ( 10) link_BETA1-4 : angle 3.04806 ( 30) link_ALPHA1-3 : bond 0.01412 ( 2) link_ALPHA1-3 : angle 2.19183 ( 6) hydrogen bonds : bond 0.05768 ( 578) hydrogen bonds : angle 5.40566 ( 1617) SS BOND : bond 0.00488 ( 33) SS BOND : angle 1.08187 ( 66) covalent geometry : bond 0.00386 (15112) covalent geometry : angle 0.65473 (20532) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 260 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ILE cc_start: 0.7150 (tt) cc_final: 0.6839 (pt) REVERT: A 211 GLU cc_start: 0.8827 (tt0) cc_final: 0.8567 (tt0) REVERT: B 542 ARG cc_start: 0.8958 (ttp-170) cc_final: 0.8721 (ttp-170) REVERT: C 633 LYS cc_start: 0.8620 (mmtp) cc_final: 0.8332 (mttp) REVERT: E 248 THR cc_start: 0.8554 (p) cc_final: 0.8280 (p) REVERT: E 315 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7289 (mt0) REVERT: F 35 TRP cc_start: 0.9002 (m100) cc_final: 0.8683 (m-90) REVERT: F 142 MET cc_start: 0.8916 (mmm) cc_final: 0.8669 (tpt) REVERT: F 475 MET cc_start: 0.8702 (mmt) cc_final: 0.8260 (mmt) REVERT: F 504 ARG cc_start: 0.7574 (tpm170) cc_final: 0.6896 (tpp80) outliers start: 24 outliers final: 17 residues processed: 272 average time/residue: 0.3225 time to fit residues: 123.4713 Evaluate side-chains 238 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 467 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 180 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 150 optimal weight: 0.2980 chunk 139 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 181 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN A 258 GLN A 280 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 GLN E 352 HIS ** F 72 HIS ** 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 = 0.3661 r_free = 0.3661 target = 0.152543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.130455 restraints weight = 18709.435| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.30 r_work: 0.3248 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15208 Z= 0.144 Angle : 0.616 8.145 20787 Z= 0.302 Chirality : 0.045 0.270 2559 Planarity : 0.003 0.039 2542 Dihedral : 6.913 69.790 3255 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.94 % Allowed : 7.82 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1574 helix: 1.27 (0.28), residues: 415 sheet: 0.66 (0.23), residues: 460 loop : -0.08 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 479 HIS 0.005 0.001 HIS E 352 PHE 0.023 0.002 PHE E 391 TYR 0.011 0.001 TYR D 638 ARG 0.005 0.000 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 49) link_NAG-ASN : angle 2.69568 ( 147) link_ALPHA1-6 : bond 0.00994 ( 2) link_ALPHA1-6 : angle 1.53356 ( 6) link_BETA1-4 : bond 0.00755 ( 10) link_BETA1-4 : angle 1.98782 ( 30) link_ALPHA1-3 : bond 0.01206 ( 2) link_ALPHA1-3 : angle 1.51120 ( 6) hydrogen bonds : bond 0.04662 ( 578) hydrogen bonds : angle 4.96729 ( 1617) SS BOND : bond 0.00252 ( 33) SS BOND : angle 0.90627 ( 66) covalent geometry : bond 0.00326 (15112) covalent geometry : angle 0.56782 (20532) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 245 time to evaluate : 3.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7130 (tm130) REVERT: A 170 ARG cc_start: 0.8498 (tpt-90) cc_final: 0.8107 (ttp-170) REVERT: A 176 ILE cc_start: 0.7307 (tt) cc_final: 0.7048 (pt) REVERT: A 211 GLU cc_start: 0.8798 (tt0) cc_final: 0.8539 (tt0) REVERT: E 315 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7355 (mt0) REVERT: E 370 GLU cc_start: 0.7956 (mp0) cc_final: 0.7743 (mp0) REVERT: D 595 ILE cc_start: 0.8773 (tt) cc_final: 0.8553 (tt) REVERT: D 601 LYS cc_start: 0.9334 (mttm) cc_final: 0.9099 (mttm) REVERT: D 634 GLU cc_start: 0.7493 (tp30) cc_final: 0.6829 (mm-30) REVERT: F 35 TRP cc_start: 0.8997 (m100) cc_final: 0.8784 (m-90) REVERT: F 87 GLU cc_start: 0.8571 (tp30) cc_final: 0.7829 (mm-30) REVERT: F 142 MET cc_start: 0.8906 (mmm) cc_final: 0.8017 (mmt) REVERT: F 255 VAL cc_start: 0.9240 (t) cc_final: 0.8833 (m) outliers start: 28 outliers final: 19 residues processed: 261 average time/residue: 0.4605 time to fit residues: 173.9715 Evaluate side-chains 245 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 225 time to evaluate : 4.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 346 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 144 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 158 optimal weight: 0.0070 chunk 16 optimal weight: 0.1980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN C 590 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.153465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.131431 restraints weight = 18739.933| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.31 r_work: 0.3258 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 15208 Z= 0.114 Angle : 0.584 11.978 20787 Z= 0.284 Chirality : 0.044 0.261 2559 Planarity : 0.003 0.041 2542 Dihedral : 6.330 64.044 3255 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.31 % Allowed : 9.48 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.21), residues: 1574 helix: 1.39 (0.28), residues: 415 sheet: 0.60 (0.23), residues: 470 loop : -0.11 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 69 HIS 0.003 0.001 HIS F 72 PHE 0.026 0.002 PHE F 53 TYR 0.012 0.001 TYR F 486 ARG 0.006 0.000 ARG F 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 49) link_NAG-ASN : angle 2.60800 ( 147) link_ALPHA1-6 : bond 0.00968 ( 2) link_ALPHA1-6 : angle 1.68584 ( 6) link_BETA1-4 : bond 0.00539 ( 10) link_BETA1-4 : angle 1.76325 ( 30) link_ALPHA1-3 : bond 0.01047 ( 2) link_ALPHA1-3 : angle 1.98643 ( 6) hydrogen bonds : bond 0.04186 ( 578) hydrogen bonds : angle 4.80867 ( 1617) SS BOND : bond 0.00200 ( 33) SS BOND : angle 0.89797 ( 66) covalent geometry : bond 0.00246 (15112) covalent geometry : angle 0.53593 (20532) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 247 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.8412 (tpt-90) cc_final: 0.7985 (ttp80) REVERT: A 176 ILE cc_start: 0.7262 (tt) cc_final: 0.7047 (pt) REVERT: A 211 GLU cc_start: 0.8819 (tt0) cc_final: 0.8561 (tt0) REVERT: A 347 LYS cc_start: 0.8497 (ttpp) cc_final: 0.8236 (tttp) REVERT: E 33 ASN cc_start: 0.6830 (t0) cc_final: 0.6612 (t0) REVERT: E 315 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7356 (mt0) REVERT: D 595 ILE cc_start: 0.8783 (tt) cc_final: 0.8581 (tt) REVERT: D 634 GLU cc_start: 0.7464 (tp30) cc_final: 0.6926 (mm-30) REVERT: F 35 TRP cc_start: 0.8972 (m100) cc_final: 0.8772 (m-90) REVERT: F 87 GLU cc_start: 0.8569 (tp30) cc_final: 0.7841 (mm-30) REVERT: F 142 MET cc_start: 0.8901 (mmm) cc_final: 0.8041 (mmt) REVERT: F 229 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8500 (mtmt) REVERT: F 504 ARG cc_start: 0.7657 (tpm170) cc_final: 0.7073 (tpp80) outliers start: 19 outliers final: 14 residues processed: 258 average time/residue: 0.4574 time to fit residues: 168.8985 Evaluate side-chains 239 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 225 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 126 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 179 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 130 GLN C 590 GLN C 607 ASN F 72 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.140601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.118351 restraints weight = 19295.386| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.29 r_work: 0.3095 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15208 Z= 0.242 Angle : 0.691 9.221 20787 Z= 0.337 Chirality : 0.047 0.277 2559 Planarity : 0.004 0.035 2542 Dihedral : 6.538 60.265 3255 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.56 % Allowed : 9.83 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.21), residues: 1574 helix: 1.18 (0.27), residues: 419 sheet: 0.47 (0.24), residues: 439 loop : -0.39 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 45 HIS 0.005 0.001 HIS A 216 PHE 0.023 0.003 PHE F 53 TYR 0.013 0.002 TYR F 486 ARG 0.006 0.001 ARG A 360 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 49) link_NAG-ASN : angle 2.61217 ( 147) link_ALPHA1-6 : bond 0.00999 ( 2) link_ALPHA1-6 : angle 1.63746 ( 6) link_BETA1-4 : bond 0.00561 ( 10) link_BETA1-4 : angle 1.91373 ( 30) link_ALPHA1-3 : bond 0.00992 ( 2) link_ALPHA1-3 : angle 1.91805 ( 6) hydrogen bonds : bond 0.05013 ( 578) hydrogen bonds : angle 4.94883 ( 1617) SS BOND : bond 0.00400 ( 33) SS BOND : angle 1.21876 ( 66) covalent geometry : bond 0.00584 (15112) covalent geometry : angle 0.65046 (20532) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 233 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ILE cc_start: 0.7328 (tt) cc_final: 0.6987 (pt) REVERT: A 191 TYR cc_start: 0.8969 (m-80) cc_final: 0.8756 (m-10) REVERT: A 211 GLU cc_start: 0.8893 (tt0) cc_final: 0.8572 (tt0) REVERT: E 156 GLU cc_start: 0.7468 (pm20) cc_final: 0.7233 (pm20) REVERT: E 248 THR cc_start: 0.8554 (p) cc_final: 0.8323 (p) REVERT: E 308 ARG cc_start: 0.8354 (ttp-170) cc_final: 0.8137 (ttm170) REVERT: E 315 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7367 (mt0) REVERT: E 342 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6152 (tt) REVERT: D 595 ILE cc_start: 0.8836 (tt) cc_final: 0.8612 (tt) REVERT: D 634 GLU cc_start: 0.7596 (tp30) cc_final: 0.7000 (mm-30) REVERT: F 35 TRP cc_start: 0.9062 (m100) cc_final: 0.8830 (m-90) REVERT: F 269 GLU cc_start: 0.7680 (pt0) cc_final: 0.7326 (tp30) REVERT: F 327 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7899 (mtm-85) REVERT: F 504 ARG cc_start: 0.7662 (tpm170) cc_final: 0.7091 (tpp80) outliers start: 37 outliers final: 27 residues processed: 258 average time/residue: 0.4426 time to fit residues: 162.9478 Evaluate side-chains 244 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 467 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 105 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 590 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.138954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.115446 restraints weight = 19085.018| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.48 r_work: 0.3091 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15208 Z= 0.136 Angle : 0.593 16.102 20787 Z= 0.286 Chirality : 0.044 0.269 2559 Planarity : 0.003 0.036 2542 Dihedral : 6.050 54.839 3255 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.52 % Allowed : 11.56 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 1574 helix: 1.49 (0.28), residues: 410 sheet: 0.62 (0.25), residues: 397 loop : -0.42 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 427 HIS 0.003 0.001 HIS E 216 PHE 0.020 0.002 PHE F 53 TYR 0.021 0.001 TYR E 486 ARG 0.006 0.000 ARG F 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 49) link_NAG-ASN : angle 2.52499 ( 147) link_ALPHA1-6 : bond 0.01004 ( 2) link_ALPHA1-6 : angle 1.51445 ( 6) link_BETA1-4 : bond 0.00530 ( 10) link_BETA1-4 : angle 1.48198 ( 30) link_ALPHA1-3 : bond 0.01131 ( 2) link_ALPHA1-3 : angle 2.05411 ( 6) hydrogen bonds : bond 0.04251 ( 578) hydrogen bonds : angle 4.75873 ( 1617) SS BOND : bond 0.00364 ( 33) SS BOND : angle 0.98660 ( 66) covalent geometry : bond 0.00311 (15112) covalent geometry : angle 0.54925 (20532) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 235 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8699 (ptm) cc_final: 0.8476 (ttp) REVERT: A 170 ARG cc_start: 0.8174 (tpt-90) cc_final: 0.7906 (ttp-170) REVERT: A 176 ILE cc_start: 0.7156 (tt) cc_final: 0.6880 (pt) REVERT: A 211 GLU cc_start: 0.8695 (tt0) cc_final: 0.8328 (tt0) REVERT: A 322 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8141 (t0) REVERT: A 347 LYS cc_start: 0.8446 (ttpp) cc_final: 0.8141 (tttp) REVERT: E 33 ASN cc_start: 0.6786 (t0) cc_final: 0.6439 (t0) REVERT: E 315 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7341 (mt0) REVERT: E 444 ARG cc_start: 0.7235 (ttm-80) cc_final: 0.6908 (ttm-80) REVERT: E 475 MET cc_start: 0.7582 (mmm) cc_final: 0.7020 (mmm) REVERT: D 595 ILE cc_start: 0.8695 (tt) cc_final: 0.8483 (tt) REVERT: D 634 GLU cc_start: 0.7464 (tp30) cc_final: 0.7018 (mm-30) REVERT: F 504 ARG cc_start: 0.7571 (tpm170) cc_final: 0.6966 (tpp80) outliers start: 22 outliers final: 19 residues processed: 251 average time/residue: 0.3162 time to fit residues: 111.3681 Evaluate side-chains 241 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 221 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 166 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 128 optimal weight: 3.9990 chunk 155 optimal weight: 0.4980 chunk 158 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 478 ASN C 543 ASN C 590 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.136686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.112853 restraints weight = 19295.011| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.53 r_work: 0.3059 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15208 Z= 0.190 Angle : 0.637 14.005 20787 Z= 0.308 Chirality : 0.045 0.292 2559 Planarity : 0.003 0.044 2542 Dihedral : 6.200 59.894 3255 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.01 % Allowed : 11.90 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.21), residues: 1574 helix: 1.35 (0.27), residues: 416 sheet: 0.55 (0.24), residues: 409 loop : -0.51 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 69 HIS 0.003 0.001 HIS A 216 PHE 0.021 0.002 PHE F 53 TYR 0.022 0.002 TYR A 191 ARG 0.006 0.001 ARG F 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 49) link_NAG-ASN : angle 2.51770 ( 147) link_ALPHA1-6 : bond 0.00976 ( 2) link_ALPHA1-6 : angle 1.57194 ( 6) link_BETA1-4 : bond 0.00513 ( 10) link_BETA1-4 : angle 1.62308 ( 30) link_ALPHA1-3 : bond 0.01196 ( 2) link_ALPHA1-3 : angle 1.96011 ( 6) hydrogen bonds : bond 0.04566 ( 578) hydrogen bonds : angle 4.80278 ( 1617) SS BOND : bond 0.00409 ( 33) SS BOND : angle 1.16203 ( 66) covalent geometry : bond 0.00453 (15112) covalent geometry : angle 0.59588 (20532) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8766 (ptm) cc_final: 0.8556 (ttp) REVERT: A 176 ILE cc_start: 0.7296 (tt) cc_final: 0.7021 (pt) REVERT: A 211 GLU cc_start: 0.8687 (tt0) cc_final: 0.8307 (tt0) REVERT: A 322 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8146 (t0) REVERT: C 621 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7453 (mp0) REVERT: E 315 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7357 (mt0) REVERT: E 342 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.5889 (tt) REVERT: D 634 GLU cc_start: 0.7666 (tp30) cc_final: 0.7073 (mm-30) REVERT: F 504 ARG cc_start: 0.7578 (tpm170) cc_final: 0.6985 (tpp80) outliers start: 29 outliers final: 24 residues processed: 237 average time/residue: 0.3190 time to fit residues: 106.3502 Evaluate side-chains 237 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 166 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 131 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 chunk 147 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 150 optimal weight: 0.0770 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 590 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.139376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.115941 restraints weight = 19085.510| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.47 r_work: 0.3091 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15208 Z= 0.116 Angle : 0.561 11.629 20787 Z= 0.273 Chirality : 0.043 0.269 2559 Planarity : 0.003 0.044 2542 Dihedral : 5.876 59.279 3255 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.59 % Allowed : 12.11 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.21), residues: 1574 helix: 1.79 (0.28), residues: 395 sheet: 0.52 (0.24), residues: 404 loop : -0.52 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 69 HIS 0.002 0.001 HIS E 216 PHE 0.022 0.002 PHE F 53 TYR 0.017 0.001 TYR A 191 ARG 0.007 0.000 ARG F 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 49) link_NAG-ASN : angle 2.29342 ( 147) link_ALPHA1-6 : bond 0.00989 ( 2) link_ALPHA1-6 : angle 1.57655 ( 6) link_BETA1-4 : bond 0.00525 ( 10) link_BETA1-4 : angle 1.38211 ( 30) link_ALPHA1-3 : bond 0.01045 ( 2) link_ALPHA1-3 : angle 1.86725 ( 6) hydrogen bonds : bond 0.03997 ( 578) hydrogen bonds : angle 4.67684 ( 1617) SS BOND : bond 0.00324 ( 33) SS BOND : angle 0.89456 ( 66) covalent geometry : bond 0.00261 (15112) covalent geometry : angle 0.52341 (20532) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8703 (ptm) cc_final: 0.8503 (ttp) REVERT: A 170 ARG cc_start: 0.8051 (tpt-90) cc_final: 0.7799 (ttp-170) REVERT: A 176 ILE cc_start: 0.7252 (tt) cc_final: 0.6935 (pt) REVERT: A 211 GLU cc_start: 0.8683 (tt0) cc_final: 0.8295 (tt0) REVERT: B 617 ARG cc_start: 0.8740 (ttm-80) cc_final: 0.7750 (ttm170) REVERT: C 621 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7418 (mp0) REVERT: C 626 MET cc_start: 0.8795 (ttm) cc_final: 0.8302 (ttt) REVERT: E 276 ASN cc_start: 0.7683 (t0) cc_final: 0.7330 (t0) REVERT: E 315 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7373 (mt0) REVERT: E 348 GLN cc_start: 0.7289 (mm110) cc_final: 0.6730 (mm110) REVERT: E 475 MET cc_start: 0.7526 (mmm) cc_final: 0.6821 (mmm) REVERT: D 634 GLU cc_start: 0.7658 (tp30) cc_final: 0.7395 (tt0) REVERT: F 142 MET cc_start: 0.8538 (mmm) cc_final: 0.7939 (mmt) REVERT: F 504 ARG cc_start: 0.7574 (tpm170) cc_final: 0.6939 (tpp80) outliers start: 23 outliers final: 22 residues processed: 242 average time/residue: 0.3287 time to fit residues: 113.7633 Evaluate side-chains 240 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 126 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 166 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 590 GLN E 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.145935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.123440 restraints weight = 18775.232| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.36 r_work: 0.3101 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15208 Z= 0.135 Angle : 0.586 14.577 20787 Z= 0.285 Chirality : 0.044 0.271 2559 Planarity : 0.003 0.044 2542 Dihedral : 5.831 56.907 3255 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.87 % Allowed : 12.18 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1574 helix: 1.79 (0.28), residues: 395 sheet: 0.51 (0.25), residues: 400 loop : -0.53 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 427 HIS 0.003 0.001 HIS E 216 PHE 0.023 0.002 PHE F 53 TYR 0.014 0.001 TYR F 486 ARG 0.003 0.000 ARG B 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 49) link_NAG-ASN : angle 2.24665 ( 147) link_ALPHA1-6 : bond 0.00999 ( 2) link_ALPHA1-6 : angle 1.58359 ( 6) link_BETA1-4 : bond 0.00499 ( 10) link_BETA1-4 : angle 1.40783 ( 30) link_ALPHA1-3 : bond 0.01002 ( 2) link_ALPHA1-3 : angle 1.77922 ( 6) hydrogen bonds : bond 0.04043 ( 578) hydrogen bonds : angle 4.60660 ( 1617) SS BOND : bond 0.00388 ( 33) SS BOND : angle 1.37878 ( 66) covalent geometry : bond 0.00313 (15112) covalent geometry : angle 0.54869 (20532) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 227 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.8133 (tpt-90) cc_final: 0.7664 (ttp80) REVERT: A 176 ILE cc_start: 0.7059 (tt) cc_final: 0.6748 (pt) REVERT: A 211 GLU cc_start: 0.8766 (tt0) cc_final: 0.8380 (tt0) REVERT: A 322 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8355 (t0) REVERT: B 542 ARG cc_start: 0.8962 (ttp-170) cc_final: 0.8683 (ttp-170) REVERT: C 621 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7497 (mp0) REVERT: E 276 ASN cc_start: 0.7578 (t0) cc_final: 0.7186 (t0) REVERT: E 315 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7269 (mt0) REVERT: E 475 MET cc_start: 0.7560 (mmm) cc_final: 0.6713 (mmm) REVERT: D 626 MET cc_start: 0.8345 (ttm) cc_final: 0.8023 (mtp) REVERT: D 634 GLU cc_start: 0.7641 (tp30) cc_final: 0.7440 (tt0) REVERT: F 142 MET cc_start: 0.8609 (mmm) cc_final: 0.7996 (mmt) REVERT: F 504 ARG cc_start: 0.7719 (tpm170) cc_final: 0.6947 (tpp80) outliers start: 27 outliers final: 20 residues processed: 243 average time/residue: 0.3081 time to fit residues: 107.0200 Evaluate side-chains 244 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 126 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 157 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 141 optimal weight: 0.0170 chunk 22 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 151 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN C 590 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.140105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.116380 restraints weight = 19216.360| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.53 r_work: 0.3103 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15208 Z= 0.114 Angle : 0.560 15.637 20787 Z= 0.272 Chirality : 0.043 0.257 2559 Planarity : 0.003 0.045 2542 Dihedral : 5.596 54.827 3255 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.45 % Allowed : 12.73 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.21), residues: 1574 helix: 1.93 (0.28), residues: 391 sheet: 0.41 (0.24), residues: 418 loop : -0.50 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 427 HIS 0.002 0.001 HIS E 216 PHE 0.024 0.001 PHE F 53 TYR 0.010 0.001 TYR A 191 ARG 0.008 0.000 ARG F 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00342 ( 49) link_NAG-ASN : angle 2.20367 ( 147) link_ALPHA1-6 : bond 0.01014 ( 2) link_ALPHA1-6 : angle 1.59449 ( 6) link_BETA1-4 : bond 0.00517 ( 10) link_BETA1-4 : angle 1.30860 ( 30) link_ALPHA1-3 : bond 0.00978 ( 2) link_ALPHA1-3 : angle 1.76087 ( 6) hydrogen bonds : bond 0.03777 ( 578) hydrogen bonds : angle 4.52521 ( 1617) SS BOND : bond 0.00281 ( 33) SS BOND : angle 1.04200 ( 66) covalent geometry : bond 0.00257 (15112) covalent geometry : angle 0.52455 (20532) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.8006 (tpt-90) cc_final: 0.7598 (ttp80) REVERT: A 211 GLU cc_start: 0.8689 (tt0) cc_final: 0.8284 (tt0) REVERT: A 322 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8201 (t0) REVERT: A 347 LYS cc_start: 0.8455 (ttpp) cc_final: 0.8158 (tttp) REVERT: B 542 ARG cc_start: 0.8939 (ttp-170) cc_final: 0.8706 (ttp-170) REVERT: C 621 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7530 (mp0) REVERT: E 276 ASN cc_start: 0.7677 (t0) cc_final: 0.7316 (t0) REVERT: E 315 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7366 (mt0) REVERT: E 475 MET cc_start: 0.7460 (mmm) cc_final: 0.6670 (mmm) REVERT: D 634 GLU cc_start: 0.7616 (tp30) cc_final: 0.7400 (tt0) REVERT: F 142 MET cc_start: 0.8588 (mmm) cc_final: 0.7992 (mmt) REVERT: F 504 ARG cc_start: 0.7567 (tpm170) cc_final: 0.6892 (tpp80) outliers start: 21 outliers final: 20 residues processed: 243 average time/residue: 0.2969 time to fit residues: 103.4062 Evaluate side-chains 247 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 226 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 126 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 151 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 112 optimal weight: 0.3980 chunk 161 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 59 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 590 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.140252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.116995 restraints weight = 19103.321| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.46 r_work: 0.3107 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 15208 Z= 0.141 Angle : 0.774 59.199 20787 Z= 0.434 Chirality : 0.044 0.492 2559 Planarity : 0.003 0.045 2542 Dihedral : 5.603 54.828 3255 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.66 % Allowed : 12.80 % Favored : 85.54 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.21), residues: 1574 helix: 1.94 (0.28), residues: 391 sheet: 0.41 (0.24), residues: 418 loop : -0.50 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 427 HIS 0.002 0.001 HIS E 216 PHE 0.022 0.001 PHE F 53 TYR 0.011 0.001 TYR E 484 ARG 0.007 0.000 ARG F 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 49) link_NAG-ASN : angle 2.19400 ( 147) link_ALPHA1-6 : bond 0.01016 ( 2) link_ALPHA1-6 : angle 1.59496 ( 6) link_BETA1-4 : bond 0.00519 ( 10) link_BETA1-4 : angle 1.30883 ( 30) link_ALPHA1-3 : bond 0.00972 ( 2) link_ALPHA1-3 : angle 1.75511 ( 6) hydrogen bonds : bond 0.03790 ( 578) hydrogen bonds : angle 4.52720 ( 1617) SS BOND : bond 0.00270 ( 33) SS BOND : angle 1.01453 ( 66) covalent geometry : bond 0.00317 (15112) covalent geometry : angle 0.75123 (20532) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8094.10 seconds wall clock time: 142 minutes 22.59 seconds (8542.59 seconds total)