Starting phenix.real_space_refine on Sun Nov 17 23:08:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swv_40822/11_2024/8swv_40822.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swv_40822/11_2024/8swv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swv_40822/11_2024/8swv_40822.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swv_40822/11_2024/8swv_40822.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swv_40822/11_2024/8swv_40822.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swv_40822/11_2024/8swv_40822.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 9272 2.51 5 N 2549 2.21 5 O 2947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14870 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3371 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Chain breaks: 6 Chain: "B" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 948 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "C" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 948 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "E" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3250 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 18, 'TRANS': 391} Chain breaks: 6 Chain: "D" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 962 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "F" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3395 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 18, 'TRANS': 410} Chain breaks: 5 Chain: "H" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 610 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'TRANS': 121} Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 122 Planarities with less than four sites: {'UNK:plan-1': 122} Unresolved non-hydrogen planarities: 122 Chain: "L" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 525 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'TRANS': 104} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 105 Planarities with less than four sites: {'UNK:plan-1': 105} Unresolved non-hydrogen planarities: 105 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 10.06, per 1000 atoms: 0.68 Number of scatterers: 14870 At special positions: 0 Unit cell: (130.937, 138.154, 121.658, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 2947 8.00 N 2549 7.00 C 9272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.10 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.11 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 149 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.01 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS E 501 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.07 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.06 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS F 501 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 73 " distance=2.02 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.05 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.02 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 149 " distance=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.02 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA K 3 " - " MAN K 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 295 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 339 " " NAG A 604 " - " ASN A 363 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 88 " " NAG A 607 " - " ASN A 241 " " NAG A 608 " - " ASN A 148 " " NAG A 609 " - " ASN A 197 " " NAG A 610 " - " ASN A 234 " " NAG A 611 " - " ASN A 332 " " NAG A 612 " - " ASN A 137 " " NAG A 613 " - " ASN A 152 " " NAG A 614 " - " ASN A 289 " " NAG A 615 " - " ASN A 355 " " NAG A 616 " - " ASN A 386 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 618 " " NAG C 701 " - " ASN C 637 " " NAG C 702 " - " ASN C 618 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG D 703 " - " ASN D 618 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 197 " " NAG E 603 " - " ASN E 332 " " NAG E 604 " - " ASN E 339 " " NAG E 605 " - " ASN E 295 " " NAG E 606 " - " ASN E 241 " " NAG E 607 " - " ASN E 448 " " NAG E 608 " - " ASN E 289 " " NAG E 609 " - " ASN E 301 " " NAG E 610 " - " ASN E 152 " " NAG E 611 " - " ASN E 88 " " NAG F 601 " - " ASN F 289 " " NAG F 602 " - " ASN F 295 " " NAG F 603 " - " ASN F 386 " " NAG F 604 " - " ASN F 133 " " NAG F 605 " - " ASN F 152 " " NAG F 606 " - " ASN F 332 " " NAG F 607 " - " ASN F 392 " " NAG G 1 " - " ASN A 448 " " NAG I 1 " - " ASN A 262 " " NAG J 1 " - " ASN A 301 " " NAG K 1 " - " ASN E 262 " " NAG M 1 " - " ASN F 363 " " NAG N 1 " - " ASN F 262 " " NAG O 1 " - " ASN F 197 " Time building additional restraints: 4.54 Conformation dependent library (CDL) restraints added in 1.6 seconds 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3494 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 34 sheets defined 26.8% alpha, 39.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 116 removed outlier: 3.923A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 4.081A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 664 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 543 removed outlier: 3.734A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 596 Processing helix chain 'C' and resid 611 through 615 Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.837A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 664 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.510A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 3.796A pdb=" N ARG E 143 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.391A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.862A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 572 through 596 Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 662 Processing helix chain 'F' and resid 67 through 73 Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.004A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 335 through 354 removed outlier: 4.028A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 429 removed outlier: 4.431A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 480 Processing helix chain 'H' and resid 63 through 68 removed outlier: 4.692A pdb=" N UNK H 68 " --> pdb=" O UNK H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 78 No H-bonds generated for 'chain 'H' and resid 76 through 78' Processing helix chain 'H' and resid 89 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.493A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.817A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 173 through 175 Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.505A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 10.258A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 10.953A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.586A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.817A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.586A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 10.953A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.258A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.240A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 603 through 609 removed outlier: 8.180A pdb=" N CYS C 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TYR E 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N THR C 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N VAL E 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL C 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.668A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB5, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB6, first strand: chain 'E' and resid 161 through 169 Processing sheet with id=AB7, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.459A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.650A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 10.305A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.632A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.564A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.315A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.650A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 10.305A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.632A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.564A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.315A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.169A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 603 through 609 removed outlier: 7.925A pdb=" N CYS D 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N TYR F 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR D 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL F 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL D 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AC4, first strand: chain 'F' and resid 75 through 76 removed outlier: 4.195A pdb=" N VAL F 75 " --> pdb=" O CYS F 54 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AC6, first strand: chain 'F' and resid 161 through 169 Processing sheet with id=AC7, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.567A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 259 through 261 removed outlier: 10.319A pdb=" N VAL F 442 " --> pdb=" O CYS F 296 " (cutoff:3.500A) removed outlier: 11.009A pdb=" N CYS F 296 " --> pdb=" O VAL F 442 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.453A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.679A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N ASN F 448 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N GLU F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 271 through 273 removed outlier: 6.935A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N GLU F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N ASN F 448 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.679A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.453A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.009A pdb=" N CYS F 296 " --> pdb=" O VAL F 442 " (cutoff:3.500A) removed outlier: 10.319A pdb=" N VAL F 442 " --> pdb=" O CYS F 296 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N PHE F 468 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.593A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 13 through 14 removed outlier: 5.862A pdb=" N UNK H 13 " --> pdb=" O UNK H 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'H' and resid 60 through 62 removed outlier: 5.672A pdb=" N UNK H 49 " --> pdb=" O UNK H 40 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N UNK H 40 " --> pdb=" O UNK H 49 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N UNK H 96 " --> pdb=" O UNK H 116 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N UNK H 116 " --> pdb=" O UNK H 96 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N UNK H 98 " --> pdb=" O UNK H 114 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AD6, first strand: chain 'L' and resid 43 through 46 removed outlier: 6.547A pdb=" N UNK L 33 " --> pdb=" O UNK L 45 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 43 through 46 removed outlier: 6.547A pdb=" N UNK L 33 " --> pdb=" O UNK L 45 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1617 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.42 Time building geometry restraints manager: 5.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2906 1.32 - 1.45: 4525 1.45 - 1.59: 7459 1.59 - 1.72: 92 1.72 - 1.86: 130 Bond restraints: 15112 Sorted by residual: bond pdb=" NE ARG E 469 " pdb=" CZ ARG E 469 " ideal model delta sigma weight residual 1.326 1.402 -0.076 1.10e-02 8.26e+03 4.80e+01 bond pdb=" NE ARG E 504 " pdb=" CZ ARG E 504 " ideal model delta sigma weight residual 1.326 1.397 -0.071 1.10e-02 8.26e+03 4.22e+01 bond pdb=" NE1 TRP F 427 " pdb=" CE2 TRP F 427 " ideal model delta sigma weight residual 1.370 1.300 0.070 1.10e-02 8.26e+03 3.99e+01 bond pdb=" CD2 TRP D 571 " pdb=" CE3 TRP D 571 " ideal model delta sigma weight residual 1.398 1.497 -0.099 1.60e-02 3.91e+03 3.84e+01 bond pdb=" NE ARG F 504 " pdb=" CZ ARG F 504 " ideal model delta sigma weight residual 1.326 1.394 -0.068 1.10e-02 8.26e+03 3.84e+01 ... (remaining 15107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 17847 2.38 - 4.76: 2361 4.76 - 7.14: 286 7.14 - 9.52: 36 9.52 - 11.90: 2 Bond angle restraints: 20532 Sorted by residual: angle pdb=" N GLU F 370 " pdb=" CA GLU F 370 " pdb=" C GLU F 370 " ideal model delta sigma weight residual 114.62 103.65 10.97 1.14e+00 7.69e-01 9.26e+01 angle pdb=" C GLU E 492 " pdb=" N PRO E 493 " pdb=" CA PRO E 493 " ideal model delta sigma weight residual 119.56 128.24 -8.68 1.02e+00 9.61e-01 7.24e+01 angle pdb=" C ARG F 298 " pdb=" N PRO F 299 " pdb=" CA PRO F 299 " ideal model delta sigma weight residual 119.56 127.71 -8.15 1.01e+00 9.80e-01 6.52e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.56 127.53 -7.97 1.01e+00 9.80e-01 6.23e+01 angle pdb=" N GLU A 87 " pdb=" CA GLU A 87 " pdb=" C GLU A 87 " ideal model delta sigma weight residual 111.28 119.81 -8.53 1.09e+00 8.42e-01 6.13e+01 ... (remaining 20527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.18: 9648 21.18 - 42.37: 167 42.37 - 63.55: 59 63.55 - 84.74: 33 84.74 - 105.92: 14 Dihedral angle restraints: 9921 sinusoidal: 4560 harmonic: 5361 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -131.42 45.42 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -127.65 41.65 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -127.02 41.02 1 1.00e+01 1.00e-02 2.36e+01 ... (remaining 9918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1770 0.103 - 0.205: 495 0.205 - 0.308: 165 0.308 - 0.411: 90 0.411 - 0.513: 39 Chirality restraints: 2559 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.10e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.49e+01 ... (remaining 2556 not shown) Planarity restraints: 2591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 339 " 0.111 2.00e-02 2.50e+03 1.18e-01 1.73e+02 pdb=" CG ASN E 339 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN E 339 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN E 339 " -0.184 2.00e-02 2.50e+03 pdb=" C1 NAG E 604 " 0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 133 " 0.090 2.00e-02 2.50e+03 9.24e-02 1.07e+02 pdb=" CG ASN F 133 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN F 133 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN F 133 " -0.142 2.00e-02 2.50e+03 pdb=" C1 NAG F 604 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 133 " 0.078 2.00e-02 2.50e+03 8.21e-02 8.43e+01 pdb=" CG ASN E 133 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN E 133 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN E 133 " -0.129 2.00e-02 2.50e+03 pdb=" C1 NAG E 601 " 0.098 2.00e-02 2.50e+03 ... (remaining 2588 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2033 2.74 - 3.28: 13222 3.28 - 3.82: 22720 3.82 - 4.36: 28825 4.36 - 4.90: 47467 Nonbonded interactions: 114267 Sorted by model distance: nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.201 3.040 nonbonded pdb=" OG1 THR E 37 " pdb=" OG1 THR E 499 " model vdw 2.274 3.040 nonbonded pdb=" OG1 THR F 37 " pdb=" OG1 THR F 499 " model vdw 2.304 3.040 nonbonded pdb=" OD2 ASP C 632 " pdb=" NZ LYS E 46 " model vdw 2.385 3.120 nonbonded pdb=" N ILE E 213 " pdb=" O ILE E 213 " model vdw 2.398 2.496 ... (remaining 114262 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 34 through 56 or resid 66 through 353 or resid 363 through \ 456 or resid 470 through 504 or resid 601 through 607)) selection = (chain 'E' and (resid 34 through 155 or resid 160 through 176 or resid 189 throu \ gh 504 or resid 601 through 607)) selection = (chain 'F' and (resid 34 through 56 or resid 66 through 155 or resid 160 through \ 176 or resid 189 through 353 or resid 363 through 456 or resid 470 through 504 \ or resid 601 through 607)) } ncs_group { reference = (chain 'B' and (resid 521 through 664 or resid 701 through 702)) selection = chain 'C' selection = (chain 'D' and (resid 521 through 547 or resid 572 through 664 or resid 701 thro \ ugh 702)) } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'O' } ncs_group { reference = (chain 'H' and resid 19 through 123) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 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: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 37.910 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.120 ------------------------------------------------------------------------------- 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 15112 Z= 1.376 Angle : 1.647 11.902 20532 Z= 1.064 Chirality : 0.134 0.513 2559 Planarity : 0.009 0.049 2542 Dihedral : 11.213 105.922 6328 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.03 % Favored : 97.90 % Rotamer: Outliers : 0.21 % Allowed : 0.35 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.20), residues: 1574 helix: -0.01 (0.25), residues: 417 sheet: 1.10 (0.23), residues: 461 loop : 0.56 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.009 TRP A 35 HIS 0.016 0.002 HIS F 374 PHE 0.036 0.007 PHE A 383 TYR 0.064 0.007 TYR A 191 ARG 0.007 0.001 ARG F 503 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 374 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.6851 (m-30) cc_final: 0.6636 (m-30) REVERT: A 211 GLU cc_start: 0.7976 (tt0) cc_final: 0.7745 (tt0) REVERT: E 113 ASP cc_start: 0.7277 (m-30) cc_final: 0.7037 (m-30) REVERT: E 248 THR cc_start: 0.8098 (p) cc_final: 0.7765 (p) REVERT: E 315 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7552 (mt0) REVERT: E 482 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7168 (mm-30) REVERT: F 35 TRP cc_start: 0.8913 (m100) cc_final: 0.8661 (m-90) REVERT: F 142 MET cc_start: 0.8786 (mmm) cc_final: 0.8474 (mmt) REVERT: F 419 ARG cc_start: 0.8278 (mmm-85) cc_final: 0.8033 (mmm160) REVERT: F 478 ASN cc_start: 0.8204 (m-40) cc_final: 0.7890 (m-40) outliers start: 3 outliers final: 2 residues processed: 376 average time/residue: 0.3130 time to fit residues: 164.7634 Evaluate side-chains 245 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 243 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain D residue 618 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN C 590 GLN E 137 ASN E 203 GLN D 630 GLN F 85 HIS F 203 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15112 Z= 0.248 Angle : 0.655 9.942 20532 Z= 0.340 Chirality : 0.048 0.400 2559 Planarity : 0.004 0.044 2542 Dihedral : 8.014 80.061 3255 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.65 % Favored : 98.28 % Rotamer: Outliers : 1.66 % Allowed : 6.09 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.21), residues: 1574 helix: 1.02 (0.27), residues: 417 sheet: 0.81 (0.23), residues: 454 loop : 0.12 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 479 HIS 0.008 0.001 HIS E 352 PHE 0.035 0.003 PHE B 522 TYR 0.012 0.001 TYR C 643 ARG 0.004 0.001 ARG E 444 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 260 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8714 (t0) cc_final: 0.8466 (t0) REVERT: C 633 LYS cc_start: 0.8405 (mmtp) cc_final: 0.8125 (mttp) REVERT: E 248 THR cc_start: 0.8211 (p) cc_final: 0.7945 (p) REVERT: E 315 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7506 (mt0) REVERT: F 475 MET cc_start: 0.8623 (mmt) cc_final: 0.8276 (mmt) REVERT: F 504 ARG cc_start: 0.7259 (tpm170) cc_final: 0.6860 (tpp80) outliers start: 24 outliers final: 17 residues processed: 272 average time/residue: 0.3433 time to fit residues: 132.5581 Evaluate side-chains 238 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 467 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN A 258 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15112 Z= 0.339 Angle : 0.658 7.871 20532 Z= 0.334 Chirality : 0.047 0.288 2559 Planarity : 0.004 0.038 2542 Dihedral : 7.275 70.587 3255 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.28 % Allowed : 8.37 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1574 helix: 0.91 (0.27), residues: 427 sheet: 0.50 (0.24), residues: 448 loop : -0.21 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 479 HIS 0.005 0.001 HIS A 216 PHE 0.026 0.003 PHE E 376 TYR 0.013 0.002 TYR A 191 ARG 0.006 0.001 ARG B 617 *********************** 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 277 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8776 (t0) cc_final: 0.8522 (t0) REVERT: A 130 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7608 (tm130) REVERT: E 248 THR cc_start: 0.8331 (p) cc_final: 0.7896 (p) REVERT: E 342 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6333 (tt) REVERT: E 486 TYR cc_start: 0.8673 (m-80) cc_final: 0.8459 (m-80) outliers start: 33 outliers final: 24 residues processed: 265 average time/residue: 0.3363 time to fit residues: 125.8256 Evaluate side-chains 239 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 1.504 ------------------------------------------------------------------------------- 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 176 ILE 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 443 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain C residue 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 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 269 GLU 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 164 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 478 ASN C 590 GLN ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 15112 Z= 0.327 Angle : 0.637 14.319 20532 Z= 0.321 Chirality : 0.047 0.287 2559 Planarity : 0.004 0.039 2542 Dihedral : 6.896 65.197 3255 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.56 % Allowed : 9.48 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.21), residues: 1574 helix: 1.08 (0.27), residues: 418 sheet: 0.21 (0.23), residues: 459 loop : -0.36 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 69 HIS 0.004 0.001 HIS A 216 PHE 0.029 0.002 PHE F 53 TYR 0.011 0.001 TYR F 486 ARG 0.006 0.000 ARG F 170 *********************** 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 253 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 1.571 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 99 ASN cc_start: 0.8780 (t0) cc_final: 0.8500 (t0) REVERT: A 475 MET cc_start: 0.8768 (tpp) cc_final: 0.8384 (tpp) REVERT: E 248 THR cc_start: 0.8252 (p) cc_final: 0.7838 (p) REVERT: E 342 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6376 (tt) REVERT: E 475 MET cc_start: 0.7535 (mmm) cc_final: 0.7303 (mmm) REVERT: E 486 TYR cc_start: 0.8693 (m-80) cc_final: 0.8446 (m-80) REVERT: F 142 MET cc_start: 0.8271 (tpt) cc_final: 0.7686 (mmt) outliers start: 37 outliers final: 29 residues processed: 241 average time/residue: 0.3050 time to fit residues: 104.3394 Evaluate side-chains 240 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU 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 A residue 396 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain 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 155 THR Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 467 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 147 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN C 590 GLN C 607 ASN ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15112 Z= 0.244 Angle : 0.578 10.840 20532 Z= 0.294 Chirality : 0.045 0.276 2559 Planarity : 0.003 0.036 2542 Dihedral : 6.491 59.609 3255 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.08 % Allowed : 10.59 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.21), residues: 1574 helix: 1.52 (0.28), residues: 394 sheet: 0.31 (0.24), residues: 422 loop : -0.44 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 69 HIS 0.003 0.001 HIS A 216 PHE 0.028 0.002 PHE F 53 TYR 0.015 0.001 TYR F 486 ARG 0.010 0.000 ARG B 617 *********************** 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 255 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 1.671 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 99 ASN cc_start: 0.8711 (t0) cc_final: 0.8410 (t0) REVERT: A 359 ILE cc_start: 0.8850 (mt) cc_final: 0.8606 (mt) REVERT: E 156 GLU cc_start: 0.7062 (pm20) cc_final: 0.6786 (pt0) REVERT: E 342 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6179 (tt) REVERT: E 475 MET cc_start: 0.7537 (mmm) cc_final: 0.7263 (mmm) REVERT: F 142 MET cc_start: 0.8265 (tpt) cc_final: 0.7729 (mmt) outliers start: 30 outliers final: 25 residues processed: 246 average time/residue: 0.3348 time to fit residues: 117.2344 Evaluate side-chains 239 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 1.469 ------------------------------------------------------------------------------- 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 346 VAL Chi-restraints excluded: chain A residue 355 ASN 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 613 THR Chi-restraints excluded: chain B residue 618 ASN 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 77 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 346 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 59 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN C 590 GLN F 72 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15112 Z= 0.226 Angle : 0.567 15.529 20532 Z= 0.287 Chirality : 0.044 0.272 2559 Planarity : 0.003 0.037 2542 Dihedral : 6.203 56.981 3255 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.35 % Allowed : 11.21 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.21), residues: 1574 helix: 1.57 (0.28), residues: 397 sheet: 0.29 (0.24), residues: 422 loop : -0.47 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 69 HIS 0.003 0.001 HIS E 216 PHE 0.023 0.002 PHE F 53 TYR 0.014 0.001 TYR E 484 ARG 0.006 0.000 ARG F 170 *********************** 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 260 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8380 (ptm) cc_final: 0.7876 (ttp) REVERT: A 99 ASN cc_start: 0.8736 (t0) cc_final: 0.8422 (t0) REVERT: A 359 ILE cc_start: 0.8867 (mt) cc_final: 0.8605 (mt) REVERT: C 535 MET cc_start: 0.7444 (mtp) cc_final: 0.7199 (mtp) REVERT: E 156 GLU cc_start: 0.7119 (pm20) cc_final: 0.6535 (pt0) REVERT: E 342 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6201 (tt) REVERT: E 475 MET cc_start: 0.7461 (mmm) cc_final: 0.7154 (mmm) REVERT: F 142 MET cc_start: 0.8275 (tpt) cc_final: 0.7771 (mmt) outliers start: 34 outliers final: 28 residues processed: 252 average time/residue: 0.3373 time to fit residues: 120.7782 Evaluate side-chains 246 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 1.664 ------------------------------------------------------------------------------- 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 346 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 538 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 C residue 613 THR Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 346 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 170 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 176 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 543 ASN C 590 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15112 Z= 0.272 Angle : 0.584 16.080 20532 Z= 0.293 Chirality : 0.045 0.289 2559 Planarity : 0.003 0.043 2542 Dihedral : 6.248 59.023 3255 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.49 % Allowed : 11.90 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.21), residues: 1574 helix: 1.58 (0.28), residues: 397 sheet: 0.27 (0.24), residues: 418 loop : -0.57 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 427 HIS 0.003 0.001 HIS E 216 PHE 0.017 0.002 PHE E 376 TYR 0.014 0.001 TYR F 486 ARG 0.006 0.000 ARG F 170 *********************** 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 255 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 219 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8434 (ptm) cc_final: 0.7960 (ttp) REVERT: A 359 ILE cc_start: 0.8876 (mt) cc_final: 0.8618 (mt) REVERT: C 535 MET cc_start: 0.7420 (mtp) cc_final: 0.7160 (mtp) REVERT: E 156 GLU cc_start: 0.7080 (pm20) cc_final: 0.6568 (pt0) REVERT: E 342 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6192 (tt) REVERT: E 475 MET cc_start: 0.7471 (mmm) cc_final: 0.7159 (mmm) REVERT: F 142 MET cc_start: 0.8250 (tpt) cc_final: 0.7795 (mmt) outliers start: 36 outliers final: 30 residues processed: 244 average time/residue: 0.3498 time to fit residues: 121.8355 Evaluate side-chains 246 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 1.822 ------------------------------------------------------------------------------- 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 346 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 538 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 C residue 613 THR Chi-restraints excluded: chain C residue 660 LEU 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 236 THR Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain F residue 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 166 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 346 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 168 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15112 Z= 0.206 Angle : 0.545 14.972 20532 Z= 0.275 Chirality : 0.044 0.270 2559 Planarity : 0.003 0.044 2542 Dihedral : 6.025 59.028 3255 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.21), residues: 1574 helix: 1.65 (0.28), residues: 398 sheet: 0.34 (0.25), residues: 413 loop : -0.56 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 69 HIS 0.003 0.001 HIS E 216 PHE 0.024 0.002 PHE F 53 TYR 0.010 0.001 TYR E 484 ARG 0.007 0.000 ARG F 170 *********************** 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 251 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8410 (ptm) cc_final: 0.7939 (ttp) REVERT: A 359 ILE cc_start: 0.8845 (mt) cc_final: 0.8584 (mt) REVERT: E 156 GLU cc_start: 0.7051 (pm20) cc_final: 0.6545 (pt0) REVERT: E 475 MET cc_start: 0.7434 (mmm) cc_final: 0.7112 (mmm) REVERT: F 142 MET cc_start: 0.8237 (tpt) cc_final: 0.7862 (mmt) outliers start: 30 outliers final: 28 residues processed: 242 average time/residue: 0.3307 time to fit residues: 112.8004 Evaluate side-chains 243 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 660 LEU 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 D residue 536 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 346 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 0.0980 chunk 164 optimal weight: 7.9990 chunk 168 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15112 Z= 0.337 Angle : 0.626 14.689 20532 Z= 0.312 Chirality : 0.046 0.297 2559 Planarity : 0.004 0.042 2542 Dihedral : 6.366 57.891 3255 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.21 % Allowed : 12.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1574 helix: 1.43 (0.28), residues: 404 sheet: 0.33 (0.25), residues: 401 loop : -0.66 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 427 HIS 0.003 0.001 HIS E 216 PHE 0.021 0.002 PHE F 53 TYR 0.013 0.002 TYR E 484 ARG 0.006 0.001 ARG F 170 *********************** 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 255 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 1.729 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 95 MET cc_start: 0.8462 (ptm) cc_final: 0.7985 (ttp) REVERT: A 130 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7129 (tm130) REVERT: A 359 ILE cc_start: 0.8871 (mt) cc_final: 0.8608 (mt) REVERT: B 530 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8574 (ptm) REVERT: E 156 GLU cc_start: 0.7181 (pm20) cc_final: 0.6484 (pt0) REVERT: E 475 MET cc_start: 0.7579 (mmm) cc_final: 0.7323 (mmm) REVERT: F 142 MET cc_start: 0.8254 (tpt) cc_final: 0.7890 (mmt) outliers start: 32 outliers final: 29 residues processed: 245 average time/residue: 0.3316 time to fit residues: 116.4349 Evaluate side-chains 249 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 1.685 ------------------------------------------------------------------------------- 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 346 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 538 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 C residue 613 THR Chi-restraints excluded: chain C residue 660 LEU 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 D residue 536 THR 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 166 SER 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 173 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 182 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 145 optimal weight: 0.1980 chunk 15 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15112 Z= 0.194 Angle : 0.549 11.071 20532 Z= 0.277 Chirality : 0.044 0.281 2559 Planarity : 0.003 0.045 2542 Dihedral : 6.101 56.466 3255 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.73 % Allowed : 13.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1574 helix: 1.65 (0.28), residues: 400 sheet: 0.27 (0.24), residues: 418 loop : -0.64 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 69 HIS 0.002 0.001 HIS E 216 PHE 0.023 0.002 PHE F 53 TYR 0.029 0.001 TYR E 486 ARG 0.007 0.000 ARG F 170 ********************** 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 246 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8389 (ptm) cc_final: 0.7938 (ttp) REVERT: A 130 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7544 (tm130) REVERT: E 156 GLU cc_start: 0.7096 (pm20) cc_final: 0.6369 (pt0) REVERT: E 475 MET cc_start: 0.7512 (mmm) cc_final: 0.7229 (mmm) REVERT: F 142 MET cc_start: 0.8229 (tpt) cc_final: 0.7870 (mmt) outliers start: 25 outliers final: 24 residues processed: 239 average time/residue: 0.3441 time to fit residues: 117.3619 Evaluate side-chains 239 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 214 time to evaluate : 1.687 ------------------------------------------------------------------------------- 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 346 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain C residue 613 THR 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 D residue 536 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 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 154 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 60 optimal weight: 0.0010 chunk 149 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.138804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.115569 restraints weight = 19067.653| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.44 r_work: 0.3089 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15112 Z= 0.167 Angle : 0.532 15.529 20532 Z= 0.267 Chirality : 0.043 0.273 2559 Planarity : 0.003 0.043 2542 Dihedral : 5.910 55.681 3255 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.66 % Allowed : 14.12 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.21), residues: 1574 helix: 1.73 (0.28), residues: 400 sheet: 0.29 (0.24), residues: 415 loop : -0.65 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 69 HIS 0.002 0.001 HIS E 216 PHE 0.023 0.001 PHE F 53 TYR 0.026 0.001 TYR E 486 ARG 0.003 0.000 ARG A 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3373.63 seconds wall clock time: 74 minutes 55.24 seconds (4495.24 seconds total)