Starting phenix.real_space_refine on Fri May 16 20:51:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8swv_40822/05_2025/8swv_40822.cif Found real_map, /net/cci-nas-00/data/ceres_data/8swv_40822/05_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_40822/05_2025/8swv_40822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8swv_40822/05_2025/8swv_40822.map" model { file = "/net/cci-nas-00/data/ceres_data/8swv_40822/05_2025/8swv_40822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8swv_40822/05_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-5687/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: 9.16, 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: 4.38 Conformation dependent library (CDL) restraints added in 1.6 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: 2.16 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: 5.66 Time building geometry restraints manager: 4.94 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: 20.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 33.040 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.030 ------------------------------------------------------------------------------- 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 : 1.520 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: 0.3195 time to fit residues: 169.5783 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 : 1.400 ------------------------------------------------------------------------------- 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 = 0.154797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.132429 restraints weight = 18820.343| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.35 r_work: 0.3296 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 10.789 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 : 3.29 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 3.43771 ( 147) link_ALPHA1-6 : bond 0.01081 ( 2) link_ALPHA1-6 : angle 1.42967 ( 6) link_BETA1-4 : bond 0.00802 ( 10) link_BETA1-4 : angle 3.04809 ( 30) link_ALPHA1-3 : bond 0.01412 ( 2) link_ALPHA1-3 : angle 2.19151 ( 6) hydrogen bonds : bond 0.05768 ( 578) hydrogen bonds : angle 5.40568 ( 1617) SS BOND : bond 0.00488 ( 33) SS BOND : angle 1.08189 ( 66) covalent geometry : bond 0.00386 (15112) covalent geometry : angle 0.65474 (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 : 1.404 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: 0.8829 (tt0) cc_final: 0.8570 (tt0) REVERT: B 542 ARG cc_start: 0.8959 (ttp-170) cc_final: 0.8722 (ttp-170) REVERT: C 633 LYS cc_start: 0.8619 (mmtp) cc_final: 0.8330 (mttp) REVERT: E 248 THR cc_start: 0.8554 (p) cc_final: 0.8280 (p) REVERT: E 315 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7288 (mt0) REVERT: F 35 TRP cc_start: 0.9000 (m100) cc_final: 0.8680 (m-90) REVERT: F 142 MET cc_start: 0.8916 (mmm) cc_final: 0.8669 (tpt) REVERT: F 475 MET cc_start: 0.8700 (mmt) cc_final: 0.8259 (mmt) REVERT: F 504 ARG cc_start: 0.7573 (tpm170) cc_final: 0.6897 (tpp80) outliers start: 24 outliers final: 17 residues processed: 272 average time/residue: 0.2986 time to fit residues: 115.3595 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 : 1.423 ------------------------------------------------------------------------------- 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: 0.0970 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: 1.9990 chunk 85 optimal weight: 0.2980 chunk 118 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 258 GLN A 280 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 GLN E 352 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.153452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.131340 restraints weight = 18688.695| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.30 r_work: 0.3261 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15208 Z= 0.130 Angle : 0.601 8.134 20787 Z= 0.295 Chirality : 0.044 0.267 2559 Planarity : 0.003 0.040 2542 Dihedral : 6.869 69.979 3255 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.80 % Allowed : 7.96 % 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: 0.72 (0.21), residues: 1574 helix: 1.29 (0.28), residues: 415 sheet: 0.66 (0.23), residues: 462 loop : -0.04 (0.23), residues: 697 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 0.024 0.002 PHE E 391 TYR 0.010 0.001 TYR D 638 ARG 0.004 0.000 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 49) link_NAG-ASN : angle 2.66249 ( 147) link_ALPHA1-6 : bond 0.00984 ( 2) link_ALPHA1-6 : angle 1.55880 ( 6) link_BETA1-4 : bond 0.00771 ( 10) link_BETA1-4 : angle 1.97920 ( 30) link_ALPHA1-3 : bond 0.01212 ( 2) link_ALPHA1-3 : angle 1.50106 ( 6) hydrogen bonds : bond 0.04561 ( 578) hydrogen bonds : angle 4.95914 ( 1617) SS BOND : bond 0.00208 ( 33) SS BOND : angle 0.84660 ( 66) covalent geometry : bond 0.00287 (15112) covalent geometry : angle 0.55270 (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 274 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 1.704 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: 0.7932 (OUTLIER) cc_final: 0.7211 (tm130) REVERT: A 170 ARG cc_start: 0.8472 (tpt-90) cc_final: 0.8093 (ttp-170) REVERT: A 176 ILE cc_start: 0.7272 (tt) cc_final: 0.7042 (pt) REVERT: A 211 GLU cc_start: 0.8794 (tt0) cc_final: 0.8544 (tt0) REVERT: E 315 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7324 (mt0) REVERT: E 370 GLU cc_start: 0.7967 (mp0) cc_final: 0.7749 (mp0) REVERT: D 530 MET cc_start: 0.8937 (mtp) cc_final: 0.8733 (mtp) REVERT: D 595 ILE cc_start: 0.8762 (tt) cc_final: 0.8549 (tt) REVERT: D 601 LYS cc_start: 0.9332 (mttm) cc_final: 0.9104 (mttm) REVERT: D 634 GLU cc_start: 0.7477 (tp30) cc_final: 0.6779 (mm-30) REVERT: D 654 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7575 (mm-30) REVERT: F 35 TRP cc_start: 0.8987 (m100) cc_final: 0.8781 (m-90) REVERT: F 87 GLU cc_start: 0.8558 (tp30) cc_final: 0.7822 (mm-30) REVERT: F 142 MET cc_start: 0.8904 (mmm) cc_final: 0.8025 (mmt) REVERT: F 255 VAL cc_start: 0.9235 (t) cc_final: 0.8792 (m) REVERT: F 475 MET cc_start: 0.8595 (mmt) cc_final: 0.8065 (mmt) REVERT: F 504 ARG cc_start: 0.7630 (tpm170) cc_final: 0.7393 (tpp-160) outliers start: 26 outliers final: 18 residues processed: 263 average time/residue: 0.2912 time to fit residues: 108.6849 Evaluate side-chains 242 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 223 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 16 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.152619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.130520 restraints weight = 18772.058| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.32 r_work: 0.3248 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15208 Z= 0.131 Angle : 0.601 13.743 20787 Z= 0.292 Chirality : 0.044 0.263 2559 Planarity : 0.003 0.039 2542 Dihedral : 6.385 64.303 3255 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.45 % Allowed : 9.41 % Favored : 89.13 % 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: 0.67 (0.21), residues: 1574 helix: 1.36 (0.28), residues: 415 sheet: 0.63 (0.23), residues: 453 loop : -0.13 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 69 HIS 0.002 0.001 HIS A 216 PHE 0.024 0.002 PHE F 53 TYR 0.013 0.001 TYR F 486 ARG 0.006 0.000 ARG F 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 49) link_NAG-ASN : angle 2.63198 ( 147) link_ALPHA1-6 : bond 0.00756 ( 2) link_ALPHA1-6 : angle 1.53949 ( 6) link_BETA1-4 : bond 0.00567 ( 10) link_BETA1-4 : angle 1.81750 ( 30) link_ALPHA1-3 : bond 0.01072 ( 2) link_ALPHA1-3 : angle 1.99824 ( 6) hydrogen bonds : bond 0.04305 ( 578) hydrogen bonds : angle 4.83192 ( 1617) SS BOND : bond 0.00263 ( 33) SS BOND : angle 1.01316 ( 66) covalent geometry : bond 0.00295 (15112) covalent geometry : angle 0.55354 (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 263 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 242 time to evaluate : 1.612 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 83 GLU cc_start: 0.8055 (tt0) cc_final: 0.7684 (tt0) REVERT: A 170 ARG cc_start: 0.8437 (tpt-90) cc_final: 0.8068 (ttp-170) REVERT: A 176 ILE cc_start: 0.7278 (tt) cc_final: 0.7045 (pt) REVERT: A 211 GLU cc_start: 0.8828 (tt0) cc_final: 0.8571 (tt0) REVERT: B 530 MET cc_start: 0.9160 (mtp) cc_final: 0.8905 (mtm) REVERT: E 33 ASN cc_start: 0.6837 (t0) cc_final: 0.6598 (t0) REVERT: E 315 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7354 (mt0) REVERT: E 370 GLU cc_start: 0.7940 (mp0) cc_final: 0.7725 (mp0) REVERT: E 475 MET cc_start: 0.7513 (mmm) cc_final: 0.7024 (mmm) REVERT: D 595 ILE cc_start: 0.8782 (tt) cc_final: 0.8573 (tt) REVERT: D 634 GLU cc_start: 0.7389 (tp30) cc_final: 0.6847 (mm-30) REVERT: F 35 TRP cc_start: 0.9001 (m100) cc_final: 0.8799 (m-90) REVERT: F 87 GLU cc_start: 0.8563 (tp30) cc_final: 0.7830 (mm-30) REVERT: F 142 MET cc_start: 0.8898 (mmm) cc_final: 0.8026 (mmt) REVERT: F 229 LYS cc_start: 0.8715 (mtpt) cc_final: 0.8468 (mtmt) REVERT: F 255 VAL cc_start: 0.9238 (t) cc_final: 0.8832 (m) outliers start: 21 outliers final: 18 residues processed: 254 average time/residue: 0.2911 time to fit residues: 105.4271 Evaluate side-chains 245 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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 396 ILE 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 544 LEU 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 E residue 236 THR 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 123 THR Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 166 SER 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: 0.3980 chunk 40 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 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: 0.5980 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.136432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.113079 restraints weight = 19235.231| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.41 r_work: 0.3161 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.005 0.049 15208 Z= 0.202 Angle : 0.651 10.273 20787 Z= 0.318 Chirality : 0.046 0.273 2559 Planarity : 0.004 0.036 2542 Dihedral : 6.389 59.201 3255 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.42 % Allowed : 9.55 % Favored : 88.03 % 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: 0.47 (0.21), residues: 1574 helix: 1.26 (0.28), residues: 419 sheet: 0.61 (0.24), residues: 425 loop : -0.36 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 69 HIS 0.004 0.001 HIS A 216 PHE 0.024 0.002 PHE F 53 TYR 0.015 0.002 TYR E 484 ARG 0.005 0.001 ARG A 360 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 49) link_NAG-ASN : angle 2.51524 ( 147) link_ALPHA1-6 : bond 0.01039 ( 2) link_ALPHA1-6 : angle 1.62011 ( 6) link_BETA1-4 : bond 0.00525 ( 10) link_BETA1-4 : angle 1.78362 ( 30) link_ALPHA1-3 : bond 0.01067 ( 2) link_ALPHA1-3 : angle 1.94006 ( 6) hydrogen bonds : bond 0.04750 ( 578) hydrogen bonds : angle 4.90207 ( 1617) SS BOND : bond 0.00355 ( 33) SS BOND : angle 1.15810 ( 66) covalent geometry : bond 0.00483 (15112) covalent geometry : angle 0.61098 (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: 35 poor density : 235 time to evaluate : 1.237 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: 0.7377 (tt) cc_final: 0.7131 (pt) REVERT: A 191 TYR cc_start: 0.8876 (m-80) cc_final: 0.8675 (m-10) REVERT: A 211 GLU cc_start: 0.8725 (tt0) cc_final: 0.8407 (tt0) REVERT: B 530 MET cc_start: 0.9045 (mtp) cc_final: 0.8765 (mtm) REVERT: E 156 GLU cc_start: 0.7436 (pm20) cc_final: 0.7216 (pm20) REVERT: E 276 ASN cc_start: 0.7906 (t0) cc_final: 0.7596 (t0) REVERT: E 315 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7398 (mt0) REVERT: E 342 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.5996 (tt) REVERT: E 475 MET cc_start: 0.7548 (mmm) cc_final: 0.7063 (mmm) REVERT: D 634 GLU cc_start: 0.7456 (tp30) cc_final: 0.7083 (mm-30) REVERT: F 35 TRP cc_start: 0.8984 (m100) cc_final: 0.8767 (m-90) REVERT: F 122 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.7952 (mp) REVERT: F 142 MET cc_start: 0.8775 (mmm) cc_final: 0.7928 (mmt) REVERT: F 269 GLU cc_start: 0.7500 (pt0) cc_final: 0.7250 (tp30) REVERT: F 426 MET cc_start: 0.8077 (mmm) cc_final: 0.7871 (mmm) REVERT: F 504 ARG cc_start: 0.7509 (tpm170) cc_final: 0.7066 (tpp80) outliers start: 35 outliers final: 26 residues processed: 258 average time/residue: 0.3510 time to fit residues: 126.9350 Evaluate side-chains 243 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 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 396 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 544 LEU 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 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 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 122 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 105 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.138547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.114735 restraints weight = 19080.760| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.50 r_work: 0.3079 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15208 Z= 0.152 Angle : 0.603 8.950 20787 Z= 0.293 Chirality : 0.044 0.271 2559 Planarity : 0.003 0.038 2542 Dihedral : 6.142 58.336 3255 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.15 % Allowed : 10.93 % 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: 0.52 (0.21), residues: 1574 helix: 1.54 (0.28), residues: 406 sheet: 0.58 (0.24), residues: 414 loop : -0.41 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 427 HIS 0.003 0.001 HIS E 216 PHE 0.020 0.002 PHE F 53 TYR 0.022 0.001 TYR E 486 ARG 0.006 0.000 ARG F 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 49) link_NAG-ASN : angle 2.50220 ( 147) link_ALPHA1-6 : bond 0.01028 ( 2) link_ALPHA1-6 : angle 1.56870 ( 6) link_BETA1-4 : bond 0.00557 ( 10) link_BETA1-4 : angle 1.57108 ( 30) link_ALPHA1-3 : bond 0.01081 ( 2) link_ALPHA1-3 : angle 2.02180 ( 6) hydrogen bonds : bond 0.04361 ( 578) hydrogen bonds : angle 4.80845 ( 1617) SS BOND : bond 0.00405 ( 33) SS BOND : angle 1.13602 ( 66) covalent geometry : bond 0.00355 (15112) covalent geometry : angle 0.55958 (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 258 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 227 time to evaluate : 1.443 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 170 ARG cc_start: 0.8200 (tpt-90) cc_final: 0.7932 (ttp-170) REVERT: A 176 ILE cc_start: 0.7270 (tt) cc_final: 0.6966 (pt) REVERT: A 211 GLU cc_start: 0.8688 (tt0) cc_final: 0.8327 (tt0) REVERT: A 322 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8149 (t0) REVERT: B 530 MET cc_start: 0.9018 (mtp) cc_final: 0.8680 (mtm) REVERT: E 33 ASN cc_start: 0.6698 (t0) cc_final: 0.6222 (t0) REVERT: E 156 GLU cc_start: 0.7355 (pm20) cc_final: 0.7011 (pm20) REVERT: E 315 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7284 (mt0) REVERT: E 342 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.5915 (tt) REVERT: E 421 LYS cc_start: 0.8667 (tttt) cc_final: 0.8423 (tttp) REVERT: E 475 MET cc_start: 0.7445 (mmm) cc_final: 0.6812 (mmm) REVERT: D 530 MET cc_start: 0.8565 (mtt) cc_final: 0.8330 (mtt) REVERT: D 634 GLU cc_start: 0.7571 (tp30) cc_final: 0.6981 (mm-30) REVERT: F 35 TRP cc_start: 0.8911 (m100) cc_final: 0.8702 (m-90) REVERT: F 122 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.7820 (mp) REVERT: F 142 MET cc_start: 0.8691 (mmm) cc_final: 0.7854 (mmt) REVERT: F 269 GLU cc_start: 0.7456 (pt0) cc_final: 0.7115 (tp30) REVERT: F 426 MET cc_start: 0.8085 (mmm) cc_final: 0.7805 (mmm) REVERT: F 504 ARG cc_start: 0.7628 (tpm170) cc_final: 0.7069 (tpp80) outliers start: 31 outliers final: 24 residues processed: 247 average time/residue: 0.3189 time to fit residues: 112.7749 Evaluate side-chains 245 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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 322 ASP Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain E residue 90 THR 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 E residue 236 THR 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 83 GLU Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 LEU 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: 4.9990 chunk 155 optimal weight: 0.0060 chunk 158 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 76 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- 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 590 GLN F 72 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.138947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.115303 restraints weight = 19119.515| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.49 r_work: 0.3096 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15208 Z= 0.138 Angle : 0.581 16.383 20787 Z= 0.281 Chirality : 0.044 0.265 2559 Planarity : 0.003 0.046 2542 Dihedral : 5.928 59.901 3255 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.15 % Allowed : 11.14 % Favored : 86.71 % 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: 0.51 (0.21), residues: 1574 helix: 1.62 (0.28), residues: 406 sheet: 0.55 (0.24), residues: 414 loop : -0.46 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 427 HIS 0.003 0.001 HIS E 216 PHE 0.022 0.002 PHE F 53 TYR 0.023 0.001 TYR A 191 ARG 0.006 0.000 ARG F 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 49) link_NAG-ASN : angle 2.38908 ( 147) link_ALPHA1-6 : bond 0.01006 ( 2) link_ALPHA1-6 : angle 1.57045 ( 6) link_BETA1-4 : bond 0.00524 ( 10) link_BETA1-4 : angle 1.46240 ( 30) link_ALPHA1-3 : bond 0.01099 ( 2) link_ALPHA1-3 : angle 1.88351 ( 6) hydrogen bonds : bond 0.04133 ( 578) hydrogen bonds : angle 4.72850 ( 1617) SS BOND : bond 0.00340 ( 33) SS BOND : angle 1.03689 ( 66) covalent geometry : bond 0.00319 (15112) covalent geometry : angle 0.54135 (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 256 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.6817 (tm130) REVERT: A 176 ILE cc_start: 0.7217 (tt) cc_final: 0.7008 (pt) REVERT: A 211 GLU cc_start: 0.8682 (tt0) cc_final: 0.8309 (tt0) REVERT: B 530 MET cc_start: 0.9007 (mtp) cc_final: 0.8690 (mtm) REVERT: E 156 GLU cc_start: 0.7262 (pm20) cc_final: 0.6277 (pt0) REVERT: E 276 ASN cc_start: 0.7688 (t0) cc_final: 0.7327 (t0) REVERT: E 315 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7359 (mt0) REVERT: E 421 LYS cc_start: 0.8618 (tttt) cc_final: 0.8368 (tttp) REVERT: E 475 MET cc_start: 0.7434 (mmm) cc_final: 0.6752 (mmm) REVERT: D 634 GLU cc_start: 0.7562 (tp30) cc_final: 0.6934 (mm-30) REVERT: F 122 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7844 (mp) REVERT: F 142 MET cc_start: 0.8729 (mmm) cc_final: 0.7930 (mmt) REVERT: F 232 LYS cc_start: 0.8616 (mmtp) cc_final: 0.8284 (mmtm) REVERT: F 269 GLU cc_start: 0.7448 (pt0) cc_final: 0.6995 (tp30) REVERT: F 426 MET cc_start: 0.8094 (mmm) cc_final: 0.7798 (mmm) REVERT: F 504 ARG cc_start: 0.7660 (tpm170) cc_final: 0.6967 (tpp80) outliers start: 31 outliers final: 26 residues processed: 246 average time/residue: 0.2961 time to fit residues: 103.4114 Evaluate side-chains 249 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 1.609 ------------------------------------------------------------------------------- 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 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 544 LEU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain E residue 90 THR 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 E residue 236 THR 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 117 LYS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 LEU 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 346 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 131 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.137842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.114358 restraints weight = 19187.494| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.47 r_work: 0.3085 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15208 Z= 0.165 Angle : 0.606 16.266 20787 Z= 0.294 Chirality : 0.044 0.281 2559 Planarity : 0.003 0.046 2542 Dihedral : 5.942 59.870 3255 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.15 % Allowed : 11.07 % Favored : 86.78 % 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: 0.47 (0.21), residues: 1574 helix: 1.62 (0.28), residues: 406 sheet: 0.52 (0.24), residues: 415 loop : -0.50 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 427 HIS 0.003 0.001 HIS E 216 PHE 0.022 0.002 PHE F 53 TYR 0.016 0.001 TYR A 191 ARG 0.007 0.000 ARG F 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 49) link_NAG-ASN : angle 2.34045 ( 147) link_ALPHA1-6 : bond 0.00983 ( 2) link_ALPHA1-6 : angle 1.57255 ( 6) link_BETA1-4 : bond 0.00481 ( 10) link_BETA1-4 : angle 1.49300 ( 30) link_ALPHA1-3 : bond 0.01042 ( 2) link_ALPHA1-3 : angle 1.85425 ( 6) hydrogen bonds : bond 0.04234 ( 578) hydrogen bonds : angle 4.74628 ( 1617) SS BOND : bond 0.00418 ( 33) SS BOND : angle 1.51839 ( 66) covalent geometry : bond 0.00392 (15112) covalent geometry : angle 0.56581 (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 255 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 1.652 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 170 ARG cc_start: 0.8078 (tpt-90) cc_final: 0.7835 (ttp-170) REVERT: A 176 ILE cc_start: 0.7239 (tt) cc_final: 0.7000 (pt) REVERT: A 211 GLU cc_start: 0.8686 (tt0) cc_final: 0.8309 (tt0) REVERT: B 530 MET cc_start: 0.8987 (mtp) cc_final: 0.8672 (mtm) REVERT: E 276 ASN cc_start: 0.7737 (t0) cc_final: 0.7364 (t0) REVERT: E 315 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7381 (mt0) REVERT: E 342 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.5899 (tt) REVERT: E 421 LYS cc_start: 0.8647 (tttt) cc_final: 0.8401 (tttp) REVERT: E 475 MET cc_start: 0.7444 (mmm) cc_final: 0.6764 (mmm) REVERT: E 486 TYR cc_start: 0.9170 (m-80) cc_final: 0.8819 (m-80) REVERT: D 634 GLU cc_start: 0.7620 (tp30) cc_final: 0.6993 (mm-30) REVERT: F 122 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.7938 (mp) REVERT: F 142 MET cc_start: 0.8724 (mmm) cc_final: 0.7937 (mmt) REVERT: F 232 LYS cc_start: 0.8683 (mmtp) cc_final: 0.8334 (mmtm) REVERT: F 269 GLU cc_start: 0.7465 (pt0) cc_final: 0.7011 (tp30) REVERT: F 426 MET cc_start: 0.8119 (mmm) cc_final: 0.7806 (mmm) REVERT: F 504 ARG cc_start: 0.7649 (tpm170) cc_final: 0.6984 (tpp80) outliers start: 31 outliers final: 27 residues processed: 242 average time/residue: 0.2925 time to fit residues: 100.1147 Evaluate side-chains 252 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 396 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain E residue 90 THR 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 E residue 236 THR 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 77 THR 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 122 LEU 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 346 VAL 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: 0.6980 chunk 106 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 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 130 GLN A 195 ASN C 590 GLN E 85 HIS D 630 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.139017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.115522 restraints weight = 19025.237| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.48 r_work: 0.3092 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3964 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= 0.134 Angle : 0.574 15.535 20787 Z= 0.279 Chirality : 0.043 0.265 2559 Planarity : 0.003 0.047 2542 Dihedral : 5.769 56.071 3255 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.80 % Allowed : 11.97 % Favored : 86.23 % 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: 0.47 (0.21), residues: 1574 helix: 1.68 (0.28), residues: 407 sheet: 0.47 (0.24), residues: 419 loop : -0.51 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 69 HIS 0.003 0.001 HIS E 216 PHE 0.023 0.002 PHE F 53 TYR 0.015 0.001 TYR F 486 ARG 0.003 0.000 ARG B 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 49) link_NAG-ASN : angle 2.29516 ( 147) link_ALPHA1-6 : bond 0.00999 ( 2) link_ALPHA1-6 : angle 1.56898 ( 6) link_BETA1-4 : bond 0.00508 ( 10) link_BETA1-4 : angle 1.39082 ( 30) link_ALPHA1-3 : bond 0.00986 ( 2) link_ALPHA1-3 : angle 1.78682 ( 6) hydrogen bonds : bond 0.04005 ( 578) hydrogen bonds : angle 4.63690 ( 1617) SS BOND : bond 0.00311 ( 33) SS BOND : angle 1.08011 ( 66) covalent geometry : bond 0.00313 (15112) covalent geometry : angle 0.53675 (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: 26 poor density : 228 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.8108 (tpt-90) cc_final: 0.7714 (ttp80) REVERT: A 176 ILE cc_start: 0.7253 (tt) cc_final: 0.6942 (pt) REVERT: A 211 GLU cc_start: 0.8685 (tt0) cc_final: 0.8296 (tt0) REVERT: A 322 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8180 (t0) REVERT: B 530 MET cc_start: 0.8933 (mtp) cc_final: 0.8604 (mtm) REVERT: E 276 ASN cc_start: 0.7654 (t0) cc_final: 0.7290 (t0) REVERT: E 315 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7346 (mt0) REVERT: E 342 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.5843 (tt) REVERT: E 421 LYS cc_start: 0.8595 (tttt) cc_final: 0.8338 (tttp) REVERT: E 475 MET cc_start: 0.7423 (mmm) cc_final: 0.6720 (mmm) REVERT: D 634 GLU cc_start: 0.7660 (tp30) cc_final: 0.7406 (tt0) REVERT: F 122 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7995 (mp) REVERT: F 142 MET cc_start: 0.8725 (mmm) cc_final: 0.7979 (mmt) REVERT: F 170 ARG cc_start: 0.8244 (tmm-80) cc_final: 0.8043 (ttp80) REVERT: F 232 LYS cc_start: 0.8657 (mmtp) cc_final: 0.8297 (mmtm) REVERT: F 269 GLU cc_start: 0.7483 (pt0) cc_final: 0.6998 (tp30) REVERT: F 426 MET cc_start: 0.8112 (mmm) cc_final: 0.7788 (mmm) REVERT: F 504 ARG cc_start: 0.7681 (tpm170) cc_final: 0.7008 (tpp80) outliers start: 26 outliers final: 22 residues processed: 241 average time/residue: 0.3036 time to fit residues: 103.0533 Evaluate side-chains 244 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 219 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 346 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain E residue 90 THR 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 120 VAL Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 157 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 172 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN C 543 ASN C 590 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.136678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.113081 restraints weight = 19379.181| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.51 r_work: 0.3073 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15208 Z= 0.178 Angle : 0.616 15.613 20787 Z= 0.298 Chirality : 0.045 0.280 2559 Planarity : 0.003 0.046 2542 Dihedral : 5.912 55.229 3255 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.87 % Allowed : 11.83 % 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: 0.36 (0.21), residues: 1574 helix: 1.46 (0.28), residues: 418 sheet: 0.39 (0.24), residues: 425 loop : -0.52 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 69 HIS 0.003 0.001 HIS E 216 PHE 0.023 0.002 PHE F 53 TYR 0.012 0.001 TYR E 484 ARG 0.003 0.000 ARG B 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 49) link_NAG-ASN : angle 2.31360 ( 147) link_ALPHA1-6 : bond 0.00974 ( 2) link_ALPHA1-6 : angle 1.56284 ( 6) link_BETA1-4 : bond 0.00492 ( 10) link_BETA1-4 : angle 1.52017 ( 30) link_ALPHA1-3 : bond 0.00953 ( 2) link_ALPHA1-3 : angle 1.74296 ( 6) hydrogen bonds : bond 0.04336 ( 578) hydrogen bonds : angle 4.72323 ( 1617) SS BOND : bond 0.00372 ( 33) SS BOND : angle 1.26315 ( 66) covalent geometry : bond 0.00426 (15112) covalent geometry : angle 0.57920 (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 245 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 1.414 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 211 GLU cc_start: 0.8696 (tt0) cc_final: 0.8304 (tt0) REVERT: A 322 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8208 (t0) REVERT: B 530 MET cc_start: 0.8988 (mtp) cc_final: 0.8698 (mtm) REVERT: B 636 SER cc_start: 0.8823 (t) cc_final: 0.8533 (m) REVERT: E 276 ASN cc_start: 0.7682 (t0) cc_final: 0.7303 (t0) REVERT: E 315 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7431 (mt0) REVERT: E 342 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.5920 (tt) REVERT: E 421 LYS cc_start: 0.8631 (tttt) cc_final: 0.8374 (tttp) REVERT: E 475 MET cc_start: 0.7459 (mmm) cc_final: 0.6803 (mmm) REVERT: D 634 GLU cc_start: 0.7745 (tp30) cc_final: 0.7068 (mm-30) REVERT: F 122 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.7921 (mp) REVERT: F 142 MET cc_start: 0.8724 (mmm) cc_final: 0.7958 (mmt) REVERT: F 170 ARG cc_start: 0.8340 (tmm-80) cc_final: 0.8070 (ttp80) REVERT: F 504 ARG cc_start: 0.7654 (tpm170) cc_final: 0.7004 (tpp80) outliers start: 27 outliers final: 22 residues processed: 234 average time/residue: 0.2979 time to fit residues: 97.5985 Evaluate side-chains 241 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 396 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain E residue 90 THR 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 120 VAL Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 151 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 161 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.137378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.113835 restraints weight = 19145.173| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.49 r_work: 0.3064 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15208 Z= 0.154 Angle : 0.589 13.864 20787 Z= 0.286 Chirality : 0.044 0.275 2559 Planarity : 0.003 0.047 2542 Dihedral : 5.883 54.155 3255 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.87 % Allowed : 11.97 % Favored : 86.16 % 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: 0.35 (0.21), residues: 1574 helix: 1.49 (0.28), residues: 418 sheet: 0.35 (0.24), residues: 421 loop : -0.53 (0.22), residues: 735 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 0.024 0.002 PHE F 53 TYR 0.015 0.001 TYR F 486 ARG 0.005 0.000 ARG E 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 49) link_NAG-ASN : angle 2.27194 ( 147) link_ALPHA1-6 : bond 0.01081 ( 2) link_ALPHA1-6 : angle 1.63036 ( 6) link_BETA1-4 : bond 0.00506 ( 10) link_BETA1-4 : angle 1.43312 ( 30) link_ALPHA1-3 : bond 0.00973 ( 2) link_ALPHA1-3 : angle 1.77224 ( 6) hydrogen bonds : bond 0.04172 ( 578) hydrogen bonds : angle 4.68083 ( 1617) SS BOND : bond 0.00334 ( 33) SS BOND : angle 1.12775 ( 66) covalent geometry : bond 0.00363 (15112) covalent geometry : angle 0.55244 (20532) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7149.41 seconds wall clock time: 125 minutes 21.25 seconds (7521.25 seconds total)