Starting phenix.real_space_refine on Tue Dec 31 10:59:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fyi_29579/12_2024/8fyi_29579.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fyi_29579/12_2024/8fyi_29579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fyi_29579/12_2024/8fyi_29579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fyi_29579/12_2024/8fyi_29579.map" model { file = "/net/cci-nas-00/data/ceres_data/8fyi_29579/12_2024/8fyi_29579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fyi_29579/12_2024/8fyi_29579.cif" } resolution = 3.4 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= 0.001 sd= 0.021 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 106 5.16 5 C 9625 2.51 5 N 2621 2.21 5 O 3012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15364 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3407 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 20, 'TRANS': 410} Chain breaks: 6 Chain: "B" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3433 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 20, 'TRANS': 413} Chain breaks: 5 Chain: "C" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3433 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 20, 'TRANS': 413} Chain breaks: 5 Chain: "D" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 982 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "E" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 982 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "F" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 982 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "Z" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} 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: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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: "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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 9.86, per 1000 atoms: 0.64 Number of scatterers: 15364 At special positions: 0 Unit cell: (125.632, 123.968, 143.936, 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 106 16.00 O 3012 8.00 N 2621 7.00 C 9625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.05 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 16 " - pdb=" SG CYS Z 84 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 130 " - pdb=" SG CYS Z 159 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " BMA H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 3 " - " NAG I 4 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " BMA K 2 " " NAG L 1 " - " NAG L 2 " " 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 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 234 " " NAG A 606 " - " ASN A 262 " " NAG A 608 " - " ASN A 276 " " NAG A 609 " - " ASN A 295 " " NAG A 610 " - " ASN A 301 " " NAG A 611 " - " ASN A 392 " " NAG A 612 " - " ASN A 448 " " NAG B 601 " - " ASN B 88 " " NAG B 602 " - " ASN B 133 " " NAG B 603 " - " ASN B 160 " " NAG B 604 " - " ASN B 197 " " NAG B 605 " - " ASN B 234 " " NAG B 606 " - " ASN B 262 " " NAG B 608 " - " ASN B 276 " " NAG B 609 " - " ASN B 295 " " NAG B 610 " - " ASN B 301 " " NAG B 611 " - " ASN B 363 " " NAG B 612 " - " ASN B 392 " " NAG B 613 " - " ASN B 448 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 160 " " NAG C 603 " - " ASN C 197 " " NAG C 604 " - " ASN C 234 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 363 " " NAG C 609 " - " ASN C 392 " " NAG C 610 " - " ASN C 448 " " NAG G 1 " - " ASN A 156 " " NAG I 1 " - " ASN A 386 " " NAG I 3 " - " ASN A 363 " " NAG J 1 " - " ASN B 156 " " NAG L 1 " - " ASN B 386 " " NAG M 1 " - " ASN C 156 " " NAG N 1 " - " ASN C 262 " " NAG O 1 " - " ASN C 386 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3448 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 32 sheets defined 24.7% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.242A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 354 removed outlier: 4.182A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.682A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 98 through 115 removed outlier: 4.117A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 474 through 481 removed outlier: 3.811A pdb=" N ASN B 478 " --> pdb=" O ASP B 474 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 115 removed outlier: 4.175A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.763A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 377 through 381 Processing helix chain 'C' and resid 386 through 390 removed outlier: 4.499A pdb=" N GLY C 389 " --> pdb=" O ASN C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 480 removed outlier: 3.526A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.920A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 595 removed outlier: 3.546A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 624 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 662 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 543 removed outlier: 3.814A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 596 removed outlier: 3.602A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 623 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 662 removed outlier: 3.552A pdb=" N ILE E 642 " --> pdb=" O TYR E 638 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.282A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 536 Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.157A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 595 removed outlier: 3.707A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 removed outlier: 3.501A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 618 through 623' Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 662 removed outlier: 3.766A pdb=" N ALA F 662 " --> pdb=" O GLN F 658 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 62 removed outlier: 3.628A pdb=" N TRP Z 62 " --> pdb=" O ARG Z 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 75 through 79 removed outlier: 3.680A pdb=" N SER Z 79 " --> pdb=" O ILE Z 76 " (cutoff:3.500A) Processing helix chain 'Z' and resid 150 through 154 removed outlier: 3.764A pdb=" N SER Z 154 " --> pdb=" O LEU Z 151 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.274A pdb=" N VAL A 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.791A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.514A 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 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 67 removed outlier: 7.346A pdb=" N HIS A 66 " --> pdb=" O SER A 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.509A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 177 removed outlier: 3.827A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 302 removed outlier: 7.226A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 329 through 334 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.603A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.007A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR E 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.338A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.574A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 169 through 177 removed outlier: 3.508A pdb=" N CYS B 131 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS B 189 " --> pdb=" O CYS B 131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 200 through 203 removed outlier: 6.217A pdb=" N ALA B 200 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR B 435 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 271 through 274 removed outlier: 6.203A pdb=" N ILE B 358 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE B 468 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 374 through 378 removed outlier: 3.812A pdb=" N CYS B 378 " --> pdb=" O GLU B 381 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU B 381 " --> pdb=" O CYS B 378 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 304 through 312 removed outlier: 3.568A pdb=" N ILE B 309 " --> pdb=" O GLN B 315 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.780A pdb=" N VAL F 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N VAL C 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR F 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N TYR C 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N CYS F 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.694A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 169 through 177 removed outlier: 3.814A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.046A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 261 current: chain 'C' and resid 284 through 302 removed outlier: 3.912A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 322 through 323 current: chain 'C' and resid 393 through 395 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 393 through 395 current: chain 'C' and resid 465 through 470 Processing sheet with id=AC8, first strand: chain 'C' and resid 305 through 312 removed outlier: 7.202A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 382 through 383 removed outlier: 4.259A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Z' and resid 2 through 5 removed outlier: 3.803A pdb=" N LYS Z 2 " --> pdb=" O GLU Z 92 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Z' and resid 13 through 15 removed outlier: 3.561A pdb=" N LEU Z 14 " --> pdb=" O LEU Z 69 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Z' and resid 27 through 29 removed outlier: 6.659A pdb=" N TRP Z 28 " --> pdb=" O ILE Z 36 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Z' and resid 99 through 102 Processing sheet with id=AD5, first strand: chain 'Z' and resid 139 through 140 removed outlier: 3.762A pdb=" N GLY Z 140 " --> pdb=" O VAL Z 128 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL Z 128 " --> pdb=" O GLY Z 140 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1317 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: 5.59 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4896 1.35 - 1.48: 3914 1.48 - 1.61: 6694 1.61 - 1.75: 0 1.75 - 1.88: 142 Bond restraints: 15646 Sorted by residual: bond pdb=" C1 NAG C 605 " pdb=" O5 NAG C 605 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.48e+00 bond pdb=" CB CYS C 331 " pdb=" SG CYS C 331 " ideal model delta sigma weight residual 1.808 1.879 -0.071 3.30e-02 9.18e+02 4.58e+00 bond pdb=" C LYS C 117 " pdb=" N PRO C 118 " ideal model delta sigma weight residual 1.334 1.348 -0.015 8.40e-03 1.42e+04 3.13e+00 bond pdb=" CB CYS C 296 " pdb=" SG CYS C 296 " ideal model delta sigma weight residual 1.808 1.752 0.056 3.30e-02 9.18e+02 2.92e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.83e+00 ... (remaining 15641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 21060 2.91 - 5.83: 116 5.83 - 8.74: 20 8.74 - 11.66: 3 11.66 - 14.57: 2 Bond angle restraints: 21201 Sorted by residual: angle pdb=" C SER F 612 " pdb=" CA SER F 612 " pdb=" CB SER F 612 " ideal model delta sigma weight residual 116.54 110.53 6.01 1.15e+00 7.56e-01 2.73e+01 angle pdb=" CB MET B 475 " pdb=" CG MET B 475 " pdb=" SD MET B 475 " ideal model delta sigma weight residual 112.70 127.27 -14.57 3.00e+00 1.11e-01 2.36e+01 angle pdb=" CA CYS C 296 " pdb=" CB CYS C 296 " pdb=" SG CYS C 296 " ideal model delta sigma weight residual 114.40 125.19 -10.79 2.30e+00 1.89e-01 2.20e+01 angle pdb=" CA CYS C 501 " pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " ideal model delta sigma weight residual 114.40 123.26 -8.86 2.30e+00 1.89e-01 1.48e+01 angle pdb=" CB GLN B 348 " pdb=" CG GLN B 348 " pdb=" CD GLN B 348 " ideal model delta sigma weight residual 112.60 119.14 -6.54 1.70e+00 3.46e-01 1.48e+01 ... (remaining 21196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.58: 9201 22.58 - 45.15: 803 45.15 - 67.73: 119 67.73 - 90.31: 39 90.31 - 112.88: 15 Dihedral angle restraints: 10177 sinusoidal: 4868 harmonic: 5309 Sorted by residual: dihedral pdb=" CB CYS B 501 " pdb=" SG CYS B 501 " pdb=" SG CYS E 605 " pdb=" CB CYS E 605 " ideal model delta sinusoidal sigma weight residual 93.00 8.34 84.66 1 1.00e+01 1.00e-02 8.71e+01 dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual -86.00 -14.23 -71.77 1 1.00e+01 1.00e-02 6.60e+01 dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 196 " pdb=" CB CYS B 196 " ideal model delta sinusoidal sigma weight residual 93.00 160.06 -67.06 1 1.00e+01 1.00e-02 5.86e+01 ... (remaining 10174 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 2532 0.149 - 0.297: 19 0.297 - 0.446: 0 0.446 - 0.594: 1 0.594 - 0.743: 1 Chirality restraints: 2553 Sorted by residual: chirality pdb=" C1 NAG C 610 " pdb=" ND2 ASN C 448 " pdb=" C2 NAG C 610 " pdb=" O5 NAG C 610 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" C1 NAG B 612 " pdb=" ND2 ASN B 392 " pdb=" C2 NAG B 612 " pdb=" O5 NAG B 612 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.00e+00 chirality pdb=" C5 BMA H 2 " pdb=" C4 BMA H 2 " pdb=" C6 BMA H 2 " pdb=" O5 BMA H 2 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 2550 not shown) Planarity restraints: 2658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 75 " 0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO B 76 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 75 " 0.036 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO A 76 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 448 " 0.020 2.00e-02 2.50e+03 1.97e-02 4.83e+00 pdb=" CG ASN C 448 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN C 448 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 448 " -0.019 2.00e-02 2.50e+03 pdb=" C1 NAG C 610 " 0.019 2.00e-02 2.50e+03 ... (remaining 2655 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1348 2.74 - 3.28: 14452 3.28 - 3.82: 24907 3.82 - 4.36: 28874 4.36 - 4.90: 51384 Nonbonded interactions: 120965 Sorted by model distance: nonbonded pdb=" O SER A 264 " pdb=" NE2 GLN A 287 " model vdw 2.200 3.120 nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 373 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR C 297 " pdb=" O ILE C 443 " model vdw 2.249 3.040 nonbonded pdb=" NH1 ARG C 273 " pdb=" OE1 GLN C 287 " model vdw 2.251 3.120 nonbonded pdb=" NZ LYS E 655 " pdb=" OE1 GLN E 658 " model vdw 2.252 3.120 ... (remaining 120960 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 367 or resid 369 through 504 or resid 601 throu \ gh 610)) selection = (chain 'B' and (resid 34 through 367 or resid 369 through 428 or resid 432 throu \ gh 504 or resid 601 through 610)) selection = (chain 'C' and (resid 34 through 367 or resid 369 through 428 or resid 432 throu \ gh 504 or resid 601 through 610)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'H' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'O' and resid 1) } 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: 2.620 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: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 36.410 Find NCS groups from input model: 0.760 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: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 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 : 0.005 0.071 15646 Z= 0.289 Angle : 0.684 14.570 21201 Z= 0.346 Chirality : 0.051 0.743 2553 Planarity : 0.004 0.086 2619 Dihedral : 16.635 112.883 6624 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.18 % Allowed : 21.97 % Favored : 77.85 % 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: -1.26 (0.20), residues: 1792 helix: 0.36 (0.27), residues: 415 sheet: -1.16 (0.23), residues: 539 loop : -1.12 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 96 HIS 0.003 0.000 HIS C 374 PHE 0.022 0.001 PHE C 53 TYR 0.011 0.001 TYR A 435 ARG 0.005 0.000 ARG E 617 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 224 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 475 MET cc_start: 0.8569 (mmm) cc_final: 0.8345 (mmm) REVERT: Z 136 LYS cc_start: 0.7529 (mptt) cc_final: 0.7250 (pttm) REVERT: Z 165 GLN cc_start: 0.8064 (mt0) cc_final: 0.7689 (tm-30) outliers start: 3 outliers final: 3 residues processed: 226 average time/residue: 0.2632 time to fit residues: 90.1102 Evaluate side-chains 213 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 210 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain E residue 627 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 165 optimal weight: 10.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 575 GLN D 577 GLN F 590 GLN F 611 ASN Z 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15646 Z= 0.248 Angle : 0.579 9.270 21201 Z= 0.290 Chirality : 0.047 0.516 2553 Planarity : 0.004 0.065 2619 Dihedral : 8.890 66.409 3119 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.62 % Allowed : 20.39 % Favored : 76.99 % 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: -1.05 (0.20), residues: 1792 helix: 0.70 (0.27), residues: 417 sheet: -1.06 (0.22), residues: 554 loop : -1.07 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 96 HIS 0.003 0.001 HIS C 374 PHE 0.010 0.001 PHE C 159 TYR 0.013 0.002 TYR A 191 ARG 0.005 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 348 GLN cc_start: 0.7922 (tm-30) cc_final: 0.7653 (tm-30) REVERT: D 632 ASP cc_start: 0.8860 (t70) cc_final: 0.8563 (t0) REVERT: Z 40 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8705 (tp-100) REVERT: Z 136 LYS cc_start: 0.7512 (mptt) cc_final: 0.7274 (pttm) REVERT: Z 165 GLN cc_start: 0.8074 (mt0) cc_final: 0.7771 (tm-30) outliers start: 43 outliers final: 24 residues processed: 255 average time/residue: 0.2570 time to fit residues: 100.1350 Evaluate side-chains 236 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain Z residue 40 GLN Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 142 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 45 optimal weight: 0.0030 chunk 165 optimal weight: 10.0000 chunk 178 optimal weight: 30.0000 chunk 147 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 overall best weight: 2.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 15646 Z= 0.439 Angle : 0.660 12.321 21201 Z= 0.328 Chirality : 0.049 0.496 2553 Planarity : 0.004 0.057 2619 Dihedral : 7.542 53.645 3116 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.96 % Allowed : 20.63 % Favored : 75.41 % 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: -1.16 (0.20), residues: 1792 helix: 0.58 (0.27), residues: 405 sheet: -1.07 (0.22), residues: 546 loop : -1.14 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 610 HIS 0.005 0.001 HIS C 374 PHE 0.018 0.002 PHE F 522 TYR 0.016 0.002 TYR A 484 ARG 0.003 0.000 ARG E 617 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 215 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8537 (tpt) cc_final: 0.8200 (tpt) REVERT: A 304 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.7374 (ttm170) REVERT: B 348 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7739 (tm-30) REVERT: B 475 MET cc_start: 0.8584 (mmm) cc_final: 0.8181 (mmm) REVERT: C 164 GLU cc_start: 0.7991 (pm20) cc_final: 0.7779 (pm20) REVERT: E 617 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7565 (mtm-85) REVERT: E 625 ASN cc_start: 0.8329 (m110) cc_final: 0.8081 (m-40) REVERT: Z 64 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7967 (pt0) REVERT: Z 136 LYS cc_start: 0.7494 (mptt) cc_final: 0.7267 (pttm) REVERT: Z 162 LEU cc_start: 0.8283 (tt) cc_final: 0.7529 (mt) REVERT: Z 165 GLN cc_start: 0.8267 (mt0) cc_final: 0.7650 (mp10) outliers start: 65 outliers final: 43 residues processed: 259 average time/residue: 0.2634 time to fit residues: 103.4404 Evaluate side-chains 254 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 209 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 64 GLN Chi-restraints excluded: chain Z residue 76 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 85 optimal weight: 0.0470 chunk 18 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 166 optimal weight: 7.9990 chunk 175 optimal weight: 0.2980 chunk 86 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN C 195 ASN D 607 ASN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 64 GLN Z 163 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 15646 Z= 0.158 Angle : 0.535 12.900 21201 Z= 0.267 Chirality : 0.046 0.446 2553 Planarity : 0.003 0.057 2619 Dihedral : 6.346 59.894 3116 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.41 % Allowed : 21.73 % Favored : 74.86 % 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: -0.89 (0.20), residues: 1792 helix: 1.00 (0.28), residues: 399 sheet: -0.97 (0.22), residues: 538 loop : -1.02 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 610 HIS 0.002 0.000 HIS A 249 PHE 0.017 0.001 PHE F 522 TYR 0.011 0.001 TYR C 39 ARG 0.003 0.000 ARG E 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 228 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8579 (m100) cc_final: 0.8339 (m100) REVERT: A 161 MET cc_start: 0.8531 (tpt) cc_final: 0.8193 (tpt) REVERT: A 304 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.7271 (ttm170) REVERT: B 348 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7645 (tm-30) REVERT: B 475 MET cc_start: 0.8420 (mmm) cc_final: 0.8060 (mmm) REVERT: B 492 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8210 (mm-30) REVERT: C 377 ASN cc_start: 0.8954 (p0) cc_final: 0.8653 (p0) REVERT: D 632 ASP cc_start: 0.8952 (t70) cc_final: 0.8614 (t0) REVERT: E 617 ARG cc_start: 0.8059 (mtm-85) cc_final: 0.7600 (mtm-85) REVERT: Z 165 GLN cc_start: 0.8068 (mt0) cc_final: 0.7744 (tm-30) REVERT: Z 167 LYS cc_start: 0.8711 (mtpt) cc_final: 0.8323 (mmmt) outliers start: 56 outliers final: 33 residues processed: 268 average time/residue: 0.2695 time to fit residues: 108.9645 Evaluate side-chains 246 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 76 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 2 optimal weight: 0.0070 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN D 607 ASN Z 64 GLN Z 129 GLN Z 163 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15646 Z= 0.258 Angle : 0.559 13.576 21201 Z= 0.278 Chirality : 0.046 0.440 2553 Planarity : 0.003 0.057 2619 Dihedral : 5.847 56.283 3116 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.77 % Allowed : 21.67 % Favored : 74.56 % 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: -0.86 (0.20), residues: 1792 helix: 1.01 (0.28), residues: 399 sheet: -0.91 (0.23), residues: 536 loop : -1.03 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 96 HIS 0.002 0.001 HIS B 374 PHE 0.015 0.001 PHE F 522 TYR 0.017 0.002 TYR B 486 ARG 0.004 0.000 ARG Z 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 218 time to evaluate : 1.856 Fit side-chains revert: symmetry clash REVERT: A 304 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7296 (ttm170) REVERT: B 348 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7744 (tm-30) REVERT: B 475 MET cc_start: 0.8453 (mmm) cc_final: 0.8066 (mmm) REVERT: B 492 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8234 (mm-30) REVERT: D 542 ARG cc_start: 0.8555 (ptm-80) cc_final: 0.8321 (ttp80) REVERT: D 632 ASP cc_start: 0.8907 (t70) cc_final: 0.8572 (t0) REVERT: E 617 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7615 (mtm-85) REVERT: F 590 GLN cc_start: 0.8293 (tp40) cc_final: 0.7956 (tp40) REVERT: Z 165 GLN cc_start: 0.8130 (mt0) cc_final: 0.7767 (tm-30) REVERT: Z 167 LYS cc_start: 0.8684 (mtpt) cc_final: 0.8280 (mmmt) outliers start: 62 outliers final: 48 residues processed: 262 average time/residue: 0.2544 time to fit residues: 102.3454 Evaluate side-chains 258 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 209 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 64 GLN Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 172 ILE Chi-restraints excluded: chain Z residue 175 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 176 optimal weight: 20.0000 chunk 146 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Z 64 GLN Z 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15646 Z= 0.235 Angle : 0.555 14.075 21201 Z= 0.275 Chirality : 0.046 0.436 2553 Planarity : 0.003 0.057 2619 Dihedral : 5.666 54.504 3116 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.65 % Allowed : 22.76 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.80 (0.20), residues: 1792 helix: 1.08 (0.28), residues: 396 sheet: -0.90 (0.22), residues: 552 loop : -0.98 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 96 HIS 0.002 0.001 HIS B 374 PHE 0.020 0.001 PHE C 53 TYR 0.011 0.001 TYR C 39 ARG 0.003 0.000 ARG Z 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 214 time to evaluate : 1.733 Fit side-chains revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8597 (m100) cc_final: 0.8390 (m100) REVERT: A 304 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.7300 (ttm170) REVERT: B 348 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7625 (tm-30) REVERT: B 475 MET cc_start: 0.8446 (mmm) cc_final: 0.8018 (mmm) REVERT: B 492 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8217 (mm-30) REVERT: D 542 ARG cc_start: 0.8554 (ptm-80) cc_final: 0.8321 (ttp80) REVERT: D 632 ASP cc_start: 0.8901 (t70) cc_final: 0.8607 (t0) REVERT: D 639 THR cc_start: 0.8426 (p) cc_final: 0.8165 (p) REVERT: F 590 GLN cc_start: 0.8300 (tp40) cc_final: 0.7975 (tp40) REVERT: Z 56 ASP cc_start: 0.8347 (t0) cc_final: 0.8143 (t0) REVERT: Z 165 GLN cc_start: 0.8164 (mt0) cc_final: 0.7782 (tm-30) REVERT: Z 167 LYS cc_start: 0.8677 (mtpt) cc_final: 0.8216 (mmmt) outliers start: 60 outliers final: 49 residues processed: 257 average time/residue: 0.2621 time to fit residues: 102.7644 Evaluate side-chains 259 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 87 GLU Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 172 ILE Chi-restraints excluded: chain Z residue 175 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Z 163 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15646 Z= 0.242 Angle : 0.550 14.496 21201 Z= 0.273 Chirality : 0.046 0.430 2553 Planarity : 0.003 0.056 2619 Dihedral : 5.518 54.449 3116 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.71 % Allowed : 22.76 % Favored : 73.52 % 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: -0.78 (0.20), residues: 1792 helix: 1.09 (0.28), residues: 396 sheet: -0.87 (0.22), residues: 552 loop : -0.98 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 96 HIS 0.003 0.001 HIS B 374 PHE 0.017 0.001 PHE C 53 TYR 0.010 0.001 TYR C 39 ARG 0.004 0.000 ARG E 617 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 218 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8608 (m100) cc_final: 0.8406 (m100) REVERT: A 304 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.7333 (ttm170) REVERT: B 348 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7677 (tm-30) REVERT: B 475 MET cc_start: 0.8481 (mmm) cc_final: 0.8004 (mmm) REVERT: B 492 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8201 (mm-30) REVERT: C 377 ASN cc_start: 0.8964 (p0) cc_final: 0.8629 (p0) REVERT: D 542 ARG cc_start: 0.8572 (ptm-80) cc_final: 0.8368 (ttp80) REVERT: D 632 ASP cc_start: 0.8919 (t70) cc_final: 0.8630 (t0) REVERT: D 639 THR cc_start: 0.8444 (p) cc_final: 0.8173 (p) REVERT: F 590 GLN cc_start: 0.8288 (tp40) cc_final: 0.7908 (tp40) REVERT: Z 56 ASP cc_start: 0.8355 (t0) cc_final: 0.8140 (t0) REVERT: Z 165 GLN cc_start: 0.8133 (mt0) cc_final: 0.7774 (tm-30) outliers start: 61 outliers final: 49 residues processed: 261 average time/residue: 0.2584 time to fit residues: 102.8499 Evaluate side-chains 272 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 172 ILE Chi-restraints excluded: chain Z residue 175 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 34 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS F 543 ASN Z 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15646 Z= 0.229 Angle : 0.549 13.712 21201 Z= 0.272 Chirality : 0.046 0.426 2553 Planarity : 0.003 0.056 2619 Dihedral : 5.419 54.596 3116 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.65 % Allowed : 23.31 % Favored : 73.04 % 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: -0.75 (0.20), residues: 1792 helix: 1.10 (0.28), residues: 396 sheet: -0.81 (0.22), residues: 552 loop : -0.96 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP F 610 HIS 0.002 0.001 HIS B 374 PHE 0.016 0.001 PHE C 53 TYR 0.010 0.001 TYR A 484 ARG 0.005 0.000 ARG E 617 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 224 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8675 (mp) REVERT: A 304 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7335 (ttm170) REVERT: A 464 THR cc_start: 0.8125 (p) cc_final: 0.7910 (t) REVERT: B 348 GLN cc_start: 0.8048 (tm-30) cc_final: 0.7601 (tm-30) REVERT: B 475 MET cc_start: 0.8490 (mmm) cc_final: 0.7996 (mmm) REVERT: B 492 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8201 (mm-30) REVERT: C 230 ASP cc_start: 0.8287 (t70) cc_final: 0.8008 (t70) REVERT: D 632 ASP cc_start: 0.8921 (t70) cc_final: 0.8628 (t0) REVERT: D 639 THR cc_start: 0.8428 (p) cc_final: 0.8162 (p) REVERT: F 590 GLN cc_start: 0.8253 (tp40) cc_final: 0.7792 (tp40) REVERT: Z 165 GLN cc_start: 0.8138 (mt0) cc_final: 0.7782 (tm-30) outliers start: 60 outliers final: 50 residues processed: 265 average time/residue: 0.2533 time to fit residues: 102.3264 Evaluate side-chains 263 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 211 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 172 ILE Chi-restraints excluded: chain Z residue 175 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 50 optimal weight: 0.1980 chunk 147 optimal weight: 0.6980 chunk 154 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Z 163 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15646 Z= 0.221 Angle : 0.550 14.885 21201 Z= 0.271 Chirality : 0.045 0.421 2553 Planarity : 0.003 0.056 2619 Dihedral : 5.324 54.615 3116 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.65 % Allowed : 23.31 % Favored : 73.04 % 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: 1792 helix: 1.12 (0.28), residues: 396 sheet: -0.78 (0.22), residues: 552 loop : -0.97 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP F 610 HIS 0.002 0.001 HIS B 374 PHE 0.015 0.001 PHE C 53 TYR 0.010 0.001 TYR C 39 ARG 0.006 0.000 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 218 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8639 (mp) REVERT: A 302 ASN cc_start: 0.8528 (t0) cc_final: 0.8290 (t0) REVERT: A 304 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.7339 (ttm170) REVERT: A 464 THR cc_start: 0.8134 (p) cc_final: 0.7927 (t) REVERT: B 84 ILE cc_start: 0.8779 (mt) cc_final: 0.8559 (mt) REVERT: B 348 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7616 (tm-30) REVERT: B 475 MET cc_start: 0.8499 (mmm) cc_final: 0.8003 (mmm) REVERT: B 492 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8192 (mm-30) REVERT: D 632 ASP cc_start: 0.8918 (t70) cc_final: 0.8632 (t0) REVERT: D 639 THR cc_start: 0.8411 (p) cc_final: 0.8175 (p) REVERT: F 590 GLN cc_start: 0.8262 (tp40) cc_final: 0.7786 (tp40) REVERT: Z 73 ASN cc_start: 0.8790 (t0) cc_final: 0.8572 (t0) REVERT: Z 165 GLN cc_start: 0.8191 (mt0) cc_final: 0.7892 (mp10) outliers start: 60 outliers final: 51 residues processed: 259 average time/residue: 0.2614 time to fit residues: 102.1254 Evaluate side-chains 270 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 217 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 172 ILE Chi-restraints excluded: chain Z residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 1.9990 chunk 172 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 0.2980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 GLN F 543 ASN Z 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15646 Z= 0.238 Angle : 0.560 14.739 21201 Z= 0.276 Chirality : 0.046 0.422 2553 Planarity : 0.003 0.056 2619 Dihedral : 5.273 54.561 3116 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.77 % Allowed : 23.55 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.20), residues: 1792 helix: 1.11 (0.28), residues: 396 sheet: -0.77 (0.22), residues: 552 loop : -0.94 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 610 HIS 0.003 0.001 HIS A 249 PHE 0.015 0.001 PHE C 53 TYR 0.010 0.001 TYR C 39 ARG 0.005 0.000 ARG E 617 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 224 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.7899 (m-90) cc_final: 0.7549 (m-90) REVERT: A 302 ASN cc_start: 0.8533 (t0) cc_final: 0.8296 (t0) REVERT: A 304 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.7347 (ttm170) REVERT: A 464 THR cc_start: 0.8147 (p) cc_final: 0.7940 (t) REVERT: B 84 ILE cc_start: 0.8782 (mt) cc_final: 0.8563 (mt) REVERT: B 348 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7621 (tm-30) REVERT: B 475 MET cc_start: 0.8513 (mmm) cc_final: 0.8034 (mmm) REVERT: B 492 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8192 (mm-30) REVERT: C 230 ASP cc_start: 0.8264 (t70) cc_final: 0.8059 (t70) REVERT: D 632 ASP cc_start: 0.8915 (t70) cc_final: 0.8605 (t0) REVERT: D 634 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7558 (tm-30) REVERT: D 639 THR cc_start: 0.8414 (p) cc_final: 0.8152 (p) REVERT: F 590 GLN cc_start: 0.8272 (tp40) cc_final: 0.7781 (tp40) REVERT: Z 73 ASN cc_start: 0.8794 (t0) cc_final: 0.8577 (t0) REVERT: Z 165 GLN cc_start: 0.8164 (mt0) cc_final: 0.7865 (mp10) outliers start: 62 outliers final: 53 residues processed: 268 average time/residue: 0.2597 time to fit residues: 106.2449 Evaluate side-chains 268 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 214 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 95 LEU Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 172 ILE Chi-restraints excluded: chain Z residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 163 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.132853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103455 restraints weight = 22711.626| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.65 r_work: 0.3143 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15646 Z= 0.341 Angle : 0.608 15.016 21201 Z= 0.300 Chirality : 0.047 0.441 2553 Planarity : 0.004 0.057 2619 Dihedral : 5.528 54.063 3116 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.35 % Allowed : 24.28 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.85 (0.20), residues: 1792 helix: 0.77 (0.27), residues: 408 sheet: -0.79 (0.23), residues: 534 loop : -1.00 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 610 HIS 0.003 0.001 HIS C 85 PHE 0.015 0.002 PHE C 53 TYR 0.016 0.002 TYR A 484 ARG 0.007 0.000 ARG D 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3664.93 seconds wall clock time: 67 minutes 58.25 seconds (4078.25 seconds total)