Starting phenix.real_space_refine on Sat Aug 23 21:38:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8swv_40822/08_2025/8swv_40822.cif Found real_map, /net/cci-nas-00/data/ceres_data/8swv_40822/08_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_40822/08_2025/8swv_40822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8swv_40822/08_2025/8swv_40822.map" model { file = "/net/cci-nas-00/data/ceres_data/8swv_40822/08_2025/8swv_40822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8swv_40822/08_2025/8swv_40822.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.01, per 1000 atoms: 0.20 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: 1.12 Conformation dependent library (CDL) restraints added in 562.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.72 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: 2.26 Time building geometry restraints manager: 1.50 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 607)) selection = (chain 'E' and (resid 34 through 155 or resid 160 through 176 or resid 189 throu \ gh 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 607) \ ) } ncs_group { reference = (chain 'B' and resid 521 through 702) selection = chain 'C' selection = (chain 'D' and (resid 521 through 547 or resid 572 through 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: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.610 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.050 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (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 ARG 0.007 0.001 ARG F 503 TYR 0.064 0.007 TYR A 191 PHE 0.036 0.007 PHE A 383 TRP 0.045 0.009 TRP A 35 HIS 0.016 0.002 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.02198 (15112) covalent geometry : angle 1.64743 (20532) SS BOND : bond 0.02205 ( 33) SS BOND : angle 2.72285 ( 66) hydrogen bonds : bond 0.15783 ( 578) hydrogen bonds : angle 7.00547 ( 1617) link_ALPHA1-3 : bond 0.08991 ( 2) link_ALPHA1-3 : angle 4.52923 ( 6) 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_NAG-ASN : bond 0.07702 ( 49) link_NAG-ASN : angle 2.87819 ( 147) *********************** 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 : 0.493 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: 0.6637 (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: 0.7551 (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: 0.1186 time to fit residues: 62.9585 Evaluate side-chains 244 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 242 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN C 590 GLN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN E 203 GLN D 630 GLN F 85 HIS F 203 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.152623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.130400 restraints weight = 18744.085| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.32 r_work: 0.3267 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2272 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= 0.177 Angle : 0.736 13.646 20787 Z= 0.362 Chirality : 0.049 0.437 2559 Planarity : 0.004 0.045 2542 Dihedral : 8.100 81.420 3255 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.72 % Favored : 98.22 % Rotamer: Outliers : 1.45 % Allowed : 6.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.21), residues: 1574 helix: 1.06 (0.27), residues: 417 sheet: 0.89 (0.24), residues: 450 loop : 0.15 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 170 TYR 0.013 0.002 TYR C 643 PHE 0.035 0.003 PHE B 522 TRP 0.020 0.002 TRP E 479 HIS 0.007 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00397 (15112) covalent geometry : angle 0.66157 (20532) SS BOND : bond 0.00268 ( 33) SS BOND : angle 1.16426 ( 66) hydrogen bonds : bond 0.05973 ( 578) hydrogen bonds : angle 5.42159 ( 1617) link_ALPHA1-3 : bond 0.01563 ( 2) link_ALPHA1-3 : angle 1.83036 ( 6) link_ALPHA1-6 : bond 0.01124 ( 2) link_ALPHA1-6 : angle 1.39461 ( 6) link_BETA1-4 : bond 0.00840 ( 10) link_BETA1-4 : angle 3.11788 ( 30) link_NAG-ASN : bond 0.00536 ( 49) link_NAG-ASN : angle 3.54776 ( 147) *********************** 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 280 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 259 time to evaluate : 0.370 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: 0.7159 (tt) cc_final: 0.6858 (pt) REVERT: A 211 GLU cc_start: 0.8830 (tt0) cc_final: 0.8562 (tt0) REVERT: C 633 LYS cc_start: 0.8626 (mmtp) cc_final: 0.8338 (mttp) REVERT: E 248 THR cc_start: 0.8562 (p) cc_final: 0.8294 (p) REVERT: E 315 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7304 (mt0) REVERT: E 432 GLN cc_start: 0.8272 (mp10) cc_final: 0.7273 (mt0) REVERT: F 35 TRP cc_start: 0.9029 (m100) cc_final: 0.8709 (m-90) REVERT: F 142 MET cc_start: 0.8916 (mmm) cc_final: 0.8677 (tpt) REVERT: F 475 MET cc_start: 0.8692 (mmt) cc_final: 0.8253 (mmt) REVERT: F 504 ARG cc_start: 0.7596 (tpm170) cc_final: 0.7380 (tpp-160) outliers start: 21 outliers final: 16 residues processed: 269 average time/residue: 0.1173 time to fit residues: 45.1232 Evaluate side-chains 236 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 220 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 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 129 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 81 optimal weight: 0.1980 chunk 52 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- 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 B 607 ASN C 590 GLN E 352 HIS ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.148433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.126184 restraints weight = 19194.009| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.30 r_work: 0.3220 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15208 Z= 0.213 Angle : 0.700 9.227 20787 Z= 0.342 Chirality : 0.048 0.286 2559 Planarity : 0.004 0.039 2542 Dihedral : 7.251 69.768 3255 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.35 % Allowed : 8.17 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.21), residues: 1574 helix: 1.02 (0.27), residues: 424 sheet: 0.51 (0.23), residues: 454 loop : -0.23 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 469 TYR 0.013 0.002 TYR A 191 PHE 0.026 0.003 PHE E 376 TRP 0.017 0.002 TRP E 479 HIS 0.005 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00501 (15112) covalent geometry : angle 0.65167 (20532) SS BOND : bond 0.00322 ( 33) SS BOND : angle 1.14748 ( 66) hydrogen bonds : bond 0.05171 ( 578) hydrogen bonds : angle 5.08598 ( 1617) link_ALPHA1-3 : bond 0.01089 ( 2) link_ALPHA1-3 : angle 1.65906 ( 6) link_ALPHA1-6 : bond 0.01081 ( 2) link_ALPHA1-6 : angle 1.53210 ( 6) link_BETA1-4 : bond 0.00646 ( 10) link_BETA1-4 : angle 2.16027 ( 30) link_NAG-ASN : bond 0.00452 ( 49) link_NAG-ASN : angle 2.87102 ( 147) *********************** 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: 34 poor density : 240 time to evaluate : 0.496 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: 0.7970 (OUTLIER) cc_final: 0.7185 (tm130) REVERT: A 170 ARG cc_start: 0.8488 (tpt-90) cc_final: 0.8108 (ttp-170) REVERT: A 176 ILE cc_start: 0.7365 (tt) cc_final: 0.7093 (pt) REVERT: A 211 GLU cc_start: 0.8816 (tt0) cc_final: 0.8510 (tt0) REVERT: B 530 MET cc_start: 0.9174 (mtp) cc_final: 0.8946 (mtm) REVERT: E 248 THR cc_start: 0.8628 (p) cc_final: 0.8265 (p) REVERT: E 315 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7401 (mt0) REVERT: E 342 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6151 (tt) REVERT: E 370 GLU cc_start: 0.7929 (mp0) cc_final: 0.7719 (mp0) REVERT: D 595 ILE cc_start: 0.8818 (tt) cc_final: 0.8584 (tt) REVERT: D 617 ARG cc_start: 0.8110 (mtt90) cc_final: 0.7891 (mtt180) REVERT: D 634 GLU cc_start: 0.7689 (tp30) cc_final: 0.7213 (mm-30) REVERT: F 35 TRP cc_start: 0.9022 (m100) cc_final: 0.8806 (m-90) outliers start: 34 outliers final: 22 residues processed: 264 average time/residue: 0.1139 time to fit residues: 42.3534 Evaluate side-chains 246 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 396 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain E residue 90 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 77 THR 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 135 THR 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 50 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 590 GLN ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.141886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.119554 restraints weight = 19159.414| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.30 r_work: 0.3146 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15208 Z= 0.168 Angle : 0.642 12.693 20787 Z= 0.312 Chirality : 0.046 0.282 2559 Planarity : 0.003 0.040 2542 Dihedral : 6.725 64.664 3255 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.08 % Allowed : 9.34 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.21), residues: 1574 helix: 1.28 (0.28), residues: 412 sheet: 0.44 (0.24), residues: 436 loop : -0.33 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 170 TYR 0.010 0.001 TYR F 486 PHE 0.021 0.002 PHE E 376 TRP 0.017 0.001 TRP F 479 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00391 (15112) covalent geometry : angle 0.59344 (20532) SS BOND : bond 0.00312 ( 33) SS BOND : angle 1.11079 ( 66) hydrogen bonds : bond 0.04697 ( 578) hydrogen bonds : angle 4.97504 ( 1617) link_ALPHA1-3 : bond 0.01183 ( 2) link_ALPHA1-3 : angle 2.15757 ( 6) link_ALPHA1-6 : bond 0.01080 ( 2) link_ALPHA1-6 : angle 1.78608 ( 6) link_BETA1-4 : bond 0.00510 ( 10) link_BETA1-4 : angle 1.87826 ( 30) link_NAG-ASN : bond 0.00403 ( 49) link_NAG-ASN : angle 2.74467 ( 147) *********************** 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 259 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.8445 (tpt-90) cc_final: 0.8015 (ttp-170) REVERT: A 176 ILE cc_start: 0.7354 (tt) cc_final: 0.7014 (pt) REVERT: A 211 GLU cc_start: 0.8880 (tt0) cc_final: 0.8546 (tt0) REVERT: B 530 MET cc_start: 0.9105 (mtp) cc_final: 0.8838 (mtm) REVERT: B 621 GLU cc_start: 0.7774 (tt0) cc_final: 0.7476 (tt0) REVERT: E 248 THR cc_start: 0.8621 (p) cc_final: 0.8236 (p) REVERT: E 315 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7416 (mt0) REVERT: E 342 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6069 (tt) REVERT: E 370 GLU cc_start: 0.8004 (mp0) cc_final: 0.7768 (mp0) REVERT: E 475 MET cc_start: 0.7723 (mmm) cc_final: 0.7241 (mmm) REVERT: E 486 TYR cc_start: 0.9146 (m-80) cc_final: 0.8833 (m-80) REVERT: D 595 ILE cc_start: 0.8796 (tt) cc_final: 0.8574 (tt) REVERT: D 617 ARG cc_start: 0.8177 (mtt90) cc_final: 0.7960 (mtt180) REVERT: D 634 GLU cc_start: 0.7575 (tp30) cc_final: 0.6944 (mm-30) REVERT: F 35 TRP cc_start: 0.9040 (m100) cc_final: 0.8829 (m-90) REVERT: F 504 ARG cc_start: 0.7616 (tpm170) cc_final: 0.7088 (tpp80) outliers start: 30 outliers final: 25 residues processed: 249 average time/residue: 0.1436 time to fit residues: 50.7759 Evaluate side-chains 238 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain C residue 595 ILE 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 22 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 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 = 0.3405 r_free = 0.3405 target = 0.132436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.108651 restraints weight = 19624.256| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.53 r_work: 0.2994 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 15208 Z= 0.340 Angle : 0.812 9.399 20787 Z= 0.394 Chirality : 0.051 0.309 2559 Planarity : 0.004 0.038 2542 Dihedral : 7.281 61.340 3255 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.98 % Allowed : 9.76 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.20), residues: 1574 helix: 0.73 (0.27), residues: 425 sheet: 0.19 (0.24), residues: 411 loop : -0.64 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 360 TYR 0.016 0.002 TYR E 484 PHE 0.028 0.003 PHE E 376 TRP 0.019 0.002 TRP F 69 HIS 0.006 0.002 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00817 (15112) covalent geometry : angle 0.76680 (20532) SS BOND : bond 0.00550 ( 33) SS BOND : angle 1.59985 ( 66) hydrogen bonds : bond 0.05748 ( 578) hydrogen bonds : angle 5.25487 ( 1617) link_ALPHA1-3 : bond 0.01037 ( 2) link_ALPHA1-3 : angle 2.06476 ( 6) link_ALPHA1-6 : bond 0.00990 ( 2) link_ALPHA1-6 : angle 1.63303 ( 6) link_BETA1-4 : bond 0.00533 ( 10) link_BETA1-4 : angle 2.17961 ( 30) link_NAG-ASN : bond 0.00576 ( 49) link_NAG-ASN : angle 2.94638 ( 147) *********************** 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 274 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 231 time to evaluate : 0.481 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: A 95 MET cc_start: 0.8840 (ptm) cc_final: 0.8631 (ttp) REVERT: A 190 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7586 (mm-30) REVERT: A 211 GLU cc_start: 0.8678 (tt0) cc_final: 0.8283 (tt0) REVERT: B 530 MET cc_start: 0.8985 (mtp) cc_final: 0.8733 (mtm) REVERT: C 625 ASN cc_start: 0.8273 (m-40) cc_final: 0.7996 (t0) REVERT: E 156 GLU cc_start: 0.7312 (pm20) cc_final: 0.6413 (pt0) REVERT: E 248 THR cc_start: 0.8762 (p) cc_final: 0.8399 (p) REVERT: E 276 ASN cc_start: 0.8003 (t0) cc_final: 0.7671 (t0) REVERT: E 315 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7357 (mt0) REVERT: E 342 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6159 (tt) REVERT: D 617 ARG cc_start: 0.8158 (mtt90) cc_final: 0.7498 (mtt180) REVERT: D 634 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7000 (tp30) REVERT: F 35 TRP cc_start: 0.8997 (m100) cc_final: 0.8702 (m-90) REVERT: F 478 ASN cc_start: 0.8991 (OUTLIER) cc_final: 0.8089 (m-40) REVERT: F 504 ARG cc_start: 0.7663 (tpm170) cc_final: 0.7120 (tpp80) outliers start: 43 outliers final: 34 residues processed: 258 average time/residue: 0.1377 time to fit residues: 50.4561 Evaluate side-chains 261 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 208 VAL 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 A residue 442 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 613 THR 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 D residue 634 GLU Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 478 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 0 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 139 optimal weight: 0.3980 chunk 170 optimal weight: 6.9990 chunk 147 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 590 GLN ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.136743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.113402 restraints weight = 19242.294| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.46 r_work: 0.3064 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15208 Z= 0.138 Angle : 0.622 15.858 20787 Z= 0.301 Chirality : 0.045 0.284 2559 Planarity : 0.003 0.035 2542 Dihedral : 6.541 56.925 3255 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.94 % Allowed : 11.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.21), residues: 1574 helix: 1.37 (0.28), residues: 406 sheet: 0.20 (0.24), residues: 416 loop : -0.64 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 170 TYR 0.021 0.001 TYR E 486 PHE 0.027 0.002 PHE F 53 TRP 0.015 0.001 TRP F 479 HIS 0.003 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00312 (15112) covalent geometry : angle 0.57575 (20532) SS BOND : bond 0.00309 ( 33) SS BOND : angle 0.99592 ( 66) hydrogen bonds : bond 0.04498 ( 578) hydrogen bonds : angle 4.96367 ( 1617) link_ALPHA1-3 : bond 0.01066 ( 2) link_ALPHA1-3 : angle 2.05480 ( 6) link_ALPHA1-6 : bond 0.00991 ( 2) link_ALPHA1-6 : angle 1.54144 ( 6) link_BETA1-4 : bond 0.00510 ( 10) link_BETA1-4 : angle 1.54599 ( 30) link_NAG-ASN : bond 0.00381 ( 49) link_NAG-ASN : angle 2.67673 ( 147) *********************** 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 249 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8752 (ptm) cc_final: 0.8523 (ttp) REVERT: A 170 ARG cc_start: 0.8135 (tpt-90) cc_final: 0.7876 (ttp-170) REVERT: A 176 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7068 (pt) REVERT: A 211 GLU cc_start: 0.8683 (tt0) cc_final: 0.8270 (tt0) REVERT: A 322 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8129 (t0) REVERT: E 156 GLU cc_start: 0.7357 (pm20) cc_final: 0.6302 (pt0) REVERT: E 248 THR cc_start: 0.8572 (p) cc_final: 0.8267 (p) REVERT: E 315 GLN cc_start: 0.7872 (mm-40) cc_final: 0.7415 (mt0) REVERT: E 342 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.5922 (tt) REVERT: D 617 ARG cc_start: 0.8099 (mtt90) cc_final: 0.7869 (mtt180) REVERT: D 634 GLU cc_start: 0.7432 (tp30) cc_final: 0.6877 (mm-30) REVERT: F 35 TRP cc_start: 0.8930 (m100) cc_final: 0.8725 (m-90) REVERT: F 478 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8163 (m-40) REVERT: F 504 ARG cc_start: 0.7679 (tpm170) cc_final: 0.7128 (tpp80) outliers start: 28 outliers final: 19 residues processed: 242 average time/residue: 0.1382 time to fit residues: 47.4147 Evaluate side-chains 238 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 215 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain E residue 68 VAL 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 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 120 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 478 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 76 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 154 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 166 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 176 optimal weight: 5.9990 chunk 85 optimal weight: 0.0980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 607 ASN C 590 GLN F 72 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.137349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.113985 restraints weight = 19136.592| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.47 r_work: 0.3087 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15208 Z= 0.144 Angle : 0.607 12.163 20787 Z= 0.294 Chirality : 0.045 0.294 2559 Planarity : 0.003 0.036 2542 Dihedral : 6.318 59.677 3255 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.80 % Allowed : 11.83 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.21), residues: 1574 helix: 1.46 (0.28), residues: 408 sheet: 0.38 (0.25), residues: 402 loop : -0.65 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 170 TYR 0.018 0.001 TYR E 486 PHE 0.025 0.002 PHE F 53 TRP 0.017 0.001 TRP A 427 HIS 0.002 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00334 (15112) covalent geometry : angle 0.56393 (20532) SS BOND : bond 0.00341 ( 33) SS BOND : angle 1.03636 ( 66) hydrogen bonds : bond 0.04311 ( 578) hydrogen bonds : angle 4.82632 ( 1617) link_ALPHA1-3 : bond 0.01078 ( 2) link_ALPHA1-3 : angle 1.91101 ( 6) link_ALPHA1-6 : bond 0.00962 ( 2) link_ALPHA1-6 : angle 1.56539 ( 6) link_BETA1-4 : bond 0.00521 ( 10) link_BETA1-4 : angle 1.52174 ( 30) link_NAG-ASN : bond 0.00359 ( 49) link_NAG-ASN : angle 2.53314 ( 147) *********************** 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 250 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 224 time to evaluate : 0.448 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 211 GLU cc_start: 0.8693 (tt0) cc_final: 0.8282 (tt0) REVERT: A 322 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8163 (t0) REVERT: A 475 MET cc_start: 0.8683 (tpp) cc_final: 0.8481 (tpp) REVERT: C 530 MET cc_start: 0.9206 (mtp) cc_final: 0.9001 (mtp) REVERT: E 142 MET cc_start: 0.7604 (mmm) cc_final: 0.7336 (mmm) REVERT: E 156 GLU cc_start: 0.7291 (pm20) cc_final: 0.6249 (pt0) REVERT: E 276 ASN cc_start: 0.7750 (t0) cc_final: 0.7413 (t0) REVERT: E 315 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7385 (mt0) REVERT: E 342 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.5885 (tt) REVERT: E 348 GLN cc_start: 0.7449 (mm110) cc_final: 0.7242 (mm-40) REVERT: E 475 MET cc_start: 0.7571 (mmm) cc_final: 0.6834 (mmm) REVERT: F 142 MET cc_start: 0.8609 (mmm) cc_final: 0.7980 (mmt) REVERT: F 504 ARG cc_start: 0.7609 (tpm170) cc_final: 0.7005 (tpp80) outliers start: 26 outliers final: 23 residues processed: 242 average time/residue: 0.1232 time to fit residues: 42.4895 Evaluate side-chains 242 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 217 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain E residue 68 VAL 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 342 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 595 ILE 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 120 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 166 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 153 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 102 optimal weight: 0.0670 chunk 61 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 590 GLN E 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.136101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.112518 restraints weight = 19317.578| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.51 r_work: 0.3050 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15208 Z= 0.176 Angle : 0.620 11.321 20787 Z= 0.301 Chirality : 0.045 0.290 2559 Planarity : 0.003 0.038 2542 Dihedral : 6.314 59.404 3255 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.08 % Allowed : 12.80 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.21), residues: 1574 helix: 1.58 (0.28), residues: 396 sheet: 0.35 (0.25), residues: 404 loop : -0.71 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 170 TYR 0.018 0.001 TYR E 486 PHE 0.017 0.002 PHE E 376 TRP 0.019 0.001 TRP A 427 HIS 0.003 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00417 (15112) covalent geometry : angle 0.58077 (20532) SS BOND : bond 0.00372 ( 33) SS BOND : angle 1.07205 ( 66) hydrogen bonds : bond 0.04456 ( 578) hydrogen bonds : angle 4.83133 ( 1617) link_ALPHA1-3 : bond 0.01019 ( 2) link_ALPHA1-3 : angle 1.84756 ( 6) link_ALPHA1-6 : bond 0.00987 ( 2) link_ALPHA1-6 : angle 1.56481 ( 6) link_BETA1-4 : bond 0.00502 ( 10) link_BETA1-4 : angle 1.57886 ( 30) link_NAG-ASN : bond 0.00346 ( 49) link_NAG-ASN : angle 2.43497 ( 147) *********************** 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 258 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.8144 (tpt-90) cc_final: 0.7834 (ttp-170) REVERT: A 211 GLU cc_start: 0.8651 (tt0) cc_final: 0.8275 (tt0) REVERT: A 322 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8178 (t0) REVERT: C 530 MET cc_start: 0.9191 (mtp) cc_final: 0.8986 (mtp) REVERT: E 156 GLU cc_start: 0.7329 (pm20) cc_final: 0.6241 (pt0) REVERT: E 276 ASN cc_start: 0.7736 (t0) cc_final: 0.7396 (t0) REVERT: E 315 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7422 (mt0) REVERT: E 342 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.5873 (tt) REVERT: E 348 GLN cc_start: 0.7555 (mm110) cc_final: 0.7242 (mm-40) REVERT: F 142 MET cc_start: 0.8632 (mmm) cc_final: 0.7950 (mmt) REVERT: F 478 ASN cc_start: 0.8834 (OUTLIER) cc_final: 0.8137 (m-40) REVERT: F 504 ARG cc_start: 0.7564 (tpm170) cc_final: 0.6966 (tpp80) outliers start: 30 outliers final: 23 residues processed: 246 average time/residue: 0.1273 time to fit residues: 44.4509 Evaluate side-chains 247 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain E residue 68 VAL 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 342 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 595 ILE 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 123 THR Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 478 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 82 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN C 590 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.136785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.113246 restraints weight = 19334.165| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.50 r_work: 0.3067 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4121 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= 0.157 Angle : 0.605 15.374 20787 Z= 0.293 Chirality : 0.044 0.285 2559 Planarity : 0.003 0.038 2542 Dihedral : 6.205 58.148 3255 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.08 % Allowed : 12.94 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.21), residues: 1574 helix: 1.62 (0.28), residues: 396 sheet: 0.33 (0.25), residues: 406 loop : -0.72 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 170 TYR 0.018 0.001 TYR E 486 PHE 0.022 0.002 PHE F 53 TRP 0.020 0.001 TRP A 427 HIS 0.003 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00369 (15112) covalent geometry : angle 0.56875 (20532) SS BOND : bond 0.00349 ( 33) SS BOND : angle 0.99687 ( 66) hydrogen bonds : bond 0.04290 ( 578) hydrogen bonds : angle 4.77305 ( 1617) link_ALPHA1-3 : bond 0.01004 ( 2) link_ALPHA1-3 : angle 1.83469 ( 6) link_ALPHA1-6 : bond 0.01011 ( 2) link_ALPHA1-6 : angle 1.58587 ( 6) link_BETA1-4 : bond 0.00498 ( 10) link_BETA1-4 : angle 1.50440 ( 30) link_NAG-ASN : bond 0.00328 ( 49) link_NAG-ASN : angle 2.34096 ( 147) *********************** 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 247 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 0.390 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 130 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.6384 (tm130) REVERT: A 211 GLU cc_start: 0.8613 (tt0) cc_final: 0.8258 (tt0) REVERT: A 322 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8177 (t0) REVERT: B 636 SER cc_start: 0.8919 (t) cc_final: 0.8603 (m) REVERT: C 530 MET cc_start: 0.9204 (mtp) cc_final: 0.8999 (mtp) REVERT: C 621 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7587 (mp0) REVERT: E 156 GLU cc_start: 0.7352 (pm20) cc_final: 0.6250 (pt0) REVERT: E 276 ASN cc_start: 0.7804 (t0) cc_final: 0.7458 (t0) REVERT: E 315 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7422 (mt0) REVERT: E 342 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.5875 (tt) REVERT: E 475 MET cc_start: 0.7541 (mmm) cc_final: 0.6793 (mmm) REVERT: F 142 MET cc_start: 0.8641 (mmm) cc_final: 0.7984 (mmt) REVERT: F 478 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8106 (m-40) REVERT: F 504 ARG cc_start: 0.7599 (tpm170) cc_final: 0.6934 (tpp80) outliers start: 30 outliers final: 24 residues processed: 235 average time/residue: 0.1297 time to fit residues: 43.1409 Evaluate side-chains 241 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 393 SER 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 C residue 636 SER Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain E residue 68 VAL 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 342 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 595 ILE 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 123 THR Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 478 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 19 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 chunk 21 optimal weight: 0.0370 chunk 103 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 171 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN C 590 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.137620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.114297 restraints weight = 19281.322| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.47 r_work: 0.3073 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15208 Z= 0.138 Angle : 0.605 15.450 20787 Z= 0.293 Chirality : 0.044 0.280 2559 Planarity : 0.003 0.039 2542 Dihedral : 6.051 57.213 3255 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.08 % Allowed : 13.22 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.21), residues: 1574 helix: 1.62 (0.28), residues: 401 sheet: 0.33 (0.25), residues: 408 loop : -0.69 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 170 TYR 0.017 0.001 TYR E 486 PHE 0.023 0.002 PHE F 53 TRP 0.018 0.001 TRP A 427 HIS 0.002 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00321 (15112) covalent geometry : angle 0.56488 (20532) SS BOND : bond 0.00337 ( 33) SS BOND : angle 1.61580 ( 66) hydrogen bonds : bond 0.04125 ( 578) hydrogen bonds : angle 4.70412 ( 1617) link_ALPHA1-3 : bond 0.01061 ( 2) link_ALPHA1-3 : angle 1.82897 ( 6) link_ALPHA1-6 : bond 0.00999 ( 2) link_ALPHA1-6 : angle 1.58136 ( 6) link_BETA1-4 : bond 0.00510 ( 10) link_BETA1-4 : angle 1.43826 ( 30) link_NAG-ASN : bond 0.00322 ( 49) link_NAG-ASN : angle 2.31036 ( 147) ********************** 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 252 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 0.445 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 130 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.6613 (tm130) REVERT: A 170 ARG cc_start: 0.8068 (tpt-90) cc_final: 0.7648 (ttp80) REVERT: A 211 GLU cc_start: 0.8611 (tt0) cc_final: 0.8254 (tt0) REVERT: A 322 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.8142 (t0) REVERT: B 636 SER cc_start: 0.8889 (t) cc_final: 0.8594 (m) REVERT: C 530 MET cc_start: 0.9213 (mtp) cc_final: 0.9001 (mtp) REVERT: C 621 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7584 (mp0) REVERT: E 156 GLU cc_start: 0.7313 (pm20) cc_final: 0.6199 (pt0) REVERT: E 276 ASN cc_start: 0.7706 (t0) cc_final: 0.7356 (t0) REVERT: E 315 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7422 (mt0) REVERT: E 342 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.5862 (tt) REVERT: E 475 MET cc_start: 0.7548 (mmm) cc_final: 0.6785 (mmm) REVERT: F 142 MET cc_start: 0.8594 (mmm) cc_final: 0.8006 (mmt) REVERT: F 504 ARG cc_start: 0.7580 (tpm170) cc_final: 0.6878 (tpp80) outliers start: 30 outliers final: 23 residues processed: 240 average time/residue: 0.1230 time to fit residues: 42.3698 Evaluate side-chains 245 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain E residue 68 VAL 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 595 ILE 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 120 VAL 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 1 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN C 590 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.136820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.113317 restraints weight = 19261.669| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.51 r_work: 0.3060 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15208 Z= 0.167 Angle : 0.617 15.224 20787 Z= 0.299 Chirality : 0.045 0.282 2559 Planarity : 0.003 0.039 2542 Dihedral : 6.062 56.705 3255 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.01 % Allowed : 13.49 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.21), residues: 1574 helix: 1.58 (0.28), residues: 401 sheet: 0.30 (0.25), residues: 408 loop : -0.70 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 170 TYR 0.017 0.001 TYR E 486 PHE 0.033 0.002 PHE E 376 TRP 0.018 0.001 TRP F 69 HIS 0.003 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00397 (15112) covalent geometry : angle 0.58007 (20532) SS BOND : bond 0.00390 ( 33) SS BOND : angle 1.30864 ( 66) hydrogen bonds : bond 0.04264 ( 578) hydrogen bonds : angle 4.71798 ( 1617) link_ALPHA1-3 : bond 0.00977 ( 2) link_ALPHA1-3 : angle 1.75738 ( 6) link_ALPHA1-6 : bond 0.01017 ( 2) link_ALPHA1-6 : angle 1.58397 ( 6) link_BETA1-4 : bond 0.00490 ( 10) link_BETA1-4 : angle 1.48659 ( 30) link_NAG-ASN : bond 0.00322 ( 49) link_NAG-ASN : angle 2.31004 ( 147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3026.64 seconds wall clock time: 52 minutes 39.44 seconds (3159.44 seconds total)