Starting phenix.real_space_refine on Sat May 17 08:59:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fyi_29579/05_2025/8fyi_29579.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fyi_29579/05_2025/8fyi_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_29579/05_2025/8fyi_29579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fyi_29579/05_2025/8fyi_29579.map" model { file = "/net/cci-nas-00/data/ceres_data/8fyi_29579/05_2025/8fyi_29579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fyi_29579/05_2025/8fyi_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-5687/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: 10.19, per 1000 atoms: 0.66 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: 4.46 Conformation dependent library (CDL) restraints added in 1.9 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: 1.93 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: 5.80 Time building geometry restraints manager: 5.05 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: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 38.470 Find NCS groups from input model: 0.770 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.040 ------------------------------------------------------------------------------- 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 15732 Z= 0.214 Angle : 0.720 14.570 21421 Z= 0.354 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 39) link_NAG-ASN : angle 2.72550 ( 117) link_BETA1-4 : bond 0.00583 ( 11) link_BETA1-4 : angle 2.00881 ( 33) hydrogen bonds : bond 0.20612 ( 483) hydrogen bonds : angle 8.11890 ( 1317) SS BOND : bond 0.00390 ( 35) SS BOND : angle 1.55679 ( 70) covalent geometry : bond 0.00452 (15646) covalent geometry : angle 0.68426 (21201) Misc. bond : bond 0.00093 ( 1) *********************** 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 : 1.854 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: 0.2563 time to fit residues: 87.8404 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 : 1.796 ------------------------------------------------------------------------------- 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: 2.9990 chunk 93 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 142 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 165 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 575 GLN F 590 GLN F 611 ASN Z 40 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105335 restraints weight = 22825.213| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.71 r_work: 0.3158 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15732 Z= 0.203 Angle : 0.641 12.608 21421 Z= 0.311 Chirality : 0.048 0.528 2553 Planarity : 0.004 0.064 2619 Dihedral : 8.782 64.089 3119 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.23 % Allowed : 20.27 % Favored : 76.51 % 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: -1.08 (0.20), residues: 1792 helix: 0.85 (0.27), residues: 393 sheet: -1.17 (0.22), residues: 552 loop : -1.06 (0.20), residues: 847 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 0.012 0.001 PHE C 159 TYR 0.014 0.002 TYR A 191 ARG 0.005 0.000 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 39) link_NAG-ASN : angle 2.53236 ( 117) link_BETA1-4 : bond 0.00467 ( 11) link_BETA1-4 : angle 2.19013 ( 33) hydrogen bonds : bond 0.04458 ( 483) hydrogen bonds : angle 5.85620 ( 1317) SS BOND : bond 0.00340 ( 35) SS BOND : angle 1.30342 ( 70) covalent geometry : bond 0.00477 (15646) covalent geometry : angle 0.60531 (21201) Misc. bond : bond 0.00091 ( 1) *********************** 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 283 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 230 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7233 (ttm170) REVERT: B 348 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7577 (tm-30) REVERT: C 230 ASP cc_start: 0.8363 (t70) cc_final: 0.8088 (t70) REVERT: Z 136 LYS cc_start: 0.7515 (mptt) cc_final: 0.7297 (pttm) REVERT: Z 165 GLN cc_start: 0.8040 (mt0) cc_final: 0.7737 (tm-30) outliers start: 53 outliers final: 33 residues processed: 265 average time/residue: 0.2654 time to fit residues: 106.8834 Evaluate side-chains 245 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 1.687 ------------------------------------------------------------------------------- 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 95 MET 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 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 182 VAL Chi-restraints excluded: chain B residue 195 ASN 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 23 SER 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 129 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 179 optimal weight: 30.0000 chunk 17 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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** Z 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.133561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.104326 restraints weight = 22781.961| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.64 r_work: 0.3149 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15732 Z= 0.229 Angle : 0.650 12.350 21421 Z= 0.314 Chirality : 0.048 0.483 2553 Planarity : 0.004 0.057 2619 Dihedral : 7.377 54.258 3116 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.53 % Allowed : 21.18 % Favored : 75.29 % 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: -1.08 (0.20), residues: 1792 helix: 0.82 (0.27), residues: 393 sheet: -1.13 (0.22), residues: 556 loop : -1.08 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 479 HIS 0.003 0.001 HIS C 374 PHE 0.019 0.002 PHE F 522 TYR 0.013 0.002 TYR A 484 ARG 0.004 0.000 ARG E 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 39) link_NAG-ASN : angle 2.51409 ( 117) link_BETA1-4 : bond 0.00380 ( 11) link_BETA1-4 : angle 2.14748 ( 33) hydrogen bonds : bond 0.04341 ( 483) hydrogen bonds : angle 5.55448 ( 1317) SS BOND : bond 0.00460 ( 35) SS BOND : angle 1.22946 ( 70) covalent geometry : bond 0.00540 (15646) covalent geometry : angle 0.61601 (21201) Misc. bond : bond 0.00096 ( 1) *********************** 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 281 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 223 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7004 (pt) REVERT: B 348 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7684 (tm-30) REVERT: C 164 GLU cc_start: 0.7992 (pm20) cc_final: 0.7778 (pm20) REVERT: D 632 ASP cc_start: 0.9050 (t70) cc_final: 0.8706 (t0) REVERT: D 634 GLU cc_start: 0.8258 (tm-30) cc_final: 0.8031 (mt-10) REVERT: E 617 ARG cc_start: 0.8272 (mtm-85) cc_final: 0.7603 (mtm-85) REVERT: E 625 ASN cc_start: 0.8367 (m110) cc_final: 0.8051 (m-40) REVERT: Z 136 LYS cc_start: 0.7563 (mptt) cc_final: 0.7281 (pttm) REVERT: Z 162 LEU cc_start: 0.8225 (tt) cc_final: 0.7646 (mt) REVERT: Z 165 GLN cc_start: 0.8191 (mt0) cc_final: 0.7719 (mp10) outliers start: 58 outliers final: 41 residues processed: 262 average time/residue: 0.2522 time to fit residues: 101.3022 Evaluate side-chains 258 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 216 time to evaluate : 1.748 ------------------------------------------------------------------------------- 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 95 MET Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 447 SER 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 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 Z residue 23 SER Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 160 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 81 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 64 GLN Z 163 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106910 restraints weight = 22763.950| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.70 r_work: 0.3181 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15732 Z= 0.121 Angle : 0.571 12.849 21421 Z= 0.276 Chirality : 0.046 0.446 2553 Planarity : 0.003 0.057 2619 Dihedral : 6.228 59.955 3116 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.29 % Allowed : 22.09 % Favored : 74.62 % 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: -1.00 (0.23), residues: 539 loop : -1.00 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 96 HIS 0.002 0.000 HIS A 249 PHE 0.016 0.001 PHE F 522 TYR 0.010 0.001 TYR C 39 ARG 0.003 0.000 ARG E 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 39) link_NAG-ASN : angle 2.28881 ( 117) link_BETA1-4 : bond 0.00417 ( 11) link_BETA1-4 : angle 1.93819 ( 33) hydrogen bonds : bond 0.03651 ( 483) hydrogen bonds : angle 5.14453 ( 1317) SS BOND : bond 0.00224 ( 35) SS BOND : angle 1.16017 ( 70) covalent geometry : bond 0.00277 (15646) covalent geometry : angle 0.53924 (21201) Misc. bond : bond 0.00078 ( 1) *********************** 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 293 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 239 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8357 (tpt) cc_final: 0.8015 (tpt) REVERT: A 304 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.7176 (ttm170) REVERT: B 348 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7551 (tm-30) REVERT: B 475 MET cc_start: 0.8201 (mmm) cc_final: 0.7967 (mmm) REVERT: B 492 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8153 (mm-30) REVERT: C 230 ASP cc_start: 0.8322 (t70) cc_final: 0.8012 (t70) REVERT: C 377 ASN cc_start: 0.8920 (p0) cc_final: 0.8575 (p0) REVERT: C 499 THR cc_start: 0.7018 (m) cc_final: 0.6776 (m) REVERT: D 542 ARG cc_start: 0.8676 (ptm-80) cc_final: 0.8425 (ttp80) REVERT: D 632 ASP cc_start: 0.8895 (t70) cc_final: 0.8561 (t0) REVERT: D 634 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7602 (tm-30) REVERT: E 617 ARG cc_start: 0.8056 (mtm-85) cc_final: 0.7500 (mtm-85) REVERT: Z 64 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7928 (pt0) REVERT: Z 162 LEU cc_start: 0.8245 (tt) cc_final: 0.7753 (mt) REVERT: Z 165 GLN cc_start: 0.8137 (mt0) cc_final: 0.7684 (tm-30) outliers start: 54 outliers final: 35 residues processed: 274 average time/residue: 0.2488 time to fit residues: 103.5302 Evaluate side-chains 253 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 1.669 ------------------------------------------------------------------------------- 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 103 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 126 CYS 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 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 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 Z residue 64 GLN 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 119 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 607 ASN Z 129 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105285 restraints weight = 22871.816| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.69 r_work: 0.3159 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15732 Z= 0.179 Angle : 0.599 13.644 21421 Z= 0.289 Chirality : 0.046 0.445 2553 Planarity : 0.003 0.057 2619 Dihedral : 5.883 56.930 3116 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.26 % Allowed : 21.42 % Favored : 74.32 % 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: -0.90 (0.20), residues: 1792 helix: 0.95 (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 0.013 0.001 TRP C 96 HIS 0.002 0.001 HIS B 374 PHE 0.013 0.001 PHE F 522 TYR 0.013 0.001 TYR B 486 ARG 0.004 0.000 ARG Z 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 39) link_NAG-ASN : angle 2.30619 ( 117) link_BETA1-4 : bond 0.00372 ( 11) link_BETA1-4 : angle 1.86497 ( 33) hydrogen bonds : bond 0.03735 ( 483) hydrogen bonds : angle 5.05523 ( 1317) SS BOND : bond 0.00277 ( 35) SS BOND : angle 1.10641 ( 70) covalent geometry : bond 0.00424 (15646) covalent geometry : angle 0.56900 (21201) Misc. bond : bond 0.00080 ( 1) *********************** 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 286 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 216 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8596 (m100) cc_final: 0.8380 (m100) REVERT: A 161 MET cc_start: 0.8378 (tpt) cc_final: 0.8081 (tpt) REVERT: A 304 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7180 (ttm170) REVERT: A 326 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.6937 (pt) REVERT: B 348 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7574 (tm-30) REVERT: B 475 MET cc_start: 0.8266 (mmm) cc_final: 0.8014 (mmm) REVERT: B 492 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8180 (mm-30) REVERT: D 542 ARG cc_start: 0.8689 (ptm-80) cc_final: 0.8408 (ttp80) REVERT: D 632 ASP cc_start: 0.8921 (t70) cc_final: 0.8567 (t0) REVERT: D 634 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7618 (tm-30) REVERT: E 619 LEU cc_start: 0.8574 (mt) cc_final: 0.8365 (mt) REVERT: F 528 SER cc_start: 0.8178 (m) cc_final: 0.7967 (p) REVERT: F 590 GLN cc_start: 0.8250 (tp40) cc_final: 0.7901 (tp40) REVERT: Z 162 LEU cc_start: 0.8276 (tt) cc_final: 0.7658 (mt) REVERT: Z 165 GLN cc_start: 0.8157 (mt0) cc_final: 0.7647 (tm-30) REVERT: Z 167 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7850 (mtpt) outliers start: 70 outliers final: 52 residues processed: 267 average time/residue: 0.2513 time to fit residues: 103.0542 Evaluate side-chains 271 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 216 time to evaluate : 1.819 ------------------------------------------------------------------------------- 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 304 ARG Chi-restraints excluded: chain A residue 326 ILE 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 195 ASN Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 243 SER 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 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 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 76 ILE Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 167 LYS 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 125 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 178 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.136568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.107386 restraints weight = 22637.162| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.69 r_work: 0.3188 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15732 Z= 0.121 Angle : 0.561 13.961 21421 Z= 0.269 Chirality : 0.045 0.424 2553 Planarity : 0.003 0.057 2619 Dihedral : 5.483 54.852 3116 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.71 % Allowed : 22.64 % Favored : 73.65 % 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: 1.11 (0.28), residues: 399 sheet: -0.86 (0.22), residues: 542 loop : -1.00 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 96 HIS 0.002 0.001 HIS A 249 PHE 0.013 0.001 PHE C 159 TYR 0.010 0.001 TYR A 484 ARG 0.003 0.000 ARG Z 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 39) link_NAG-ASN : angle 2.17201 ( 117) link_BETA1-4 : bond 0.00404 ( 11) link_BETA1-4 : angle 1.64867 ( 33) hydrogen bonds : bond 0.03374 ( 483) hydrogen bonds : angle 4.83583 ( 1317) SS BOND : bond 0.00205 ( 35) SS BOND : angle 1.16584 ( 70) covalent geometry : bond 0.00281 (15646) covalent geometry : angle 0.53177 (21201) Misc. bond : bond 0.00074 ( 1) *********************** 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 293 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 232 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8601 (m100) cc_final: 0.8398 (m100) REVERT: A 37 THR cc_start: 0.9413 (m) cc_final: 0.9185 (p) REVERT: A 161 MET cc_start: 0.8375 (tpt) cc_final: 0.8073 (tpt) REVERT: A 304 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7169 (ttm170) REVERT: A 326 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.6836 (pt) REVERT: A 464 THR cc_start: 0.7967 (p) cc_final: 0.7745 (t) REVERT: B 161 MET cc_start: 0.8507 (tpp) cc_final: 0.8111 (ttm) REVERT: B 348 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7434 (tm-30) REVERT: B 392 ASN cc_start: 0.7431 (t0) cc_final: 0.6886 (p0) REVERT: B 475 MET cc_start: 0.8259 (mmm) cc_final: 0.7868 (mmm) REVERT: B 492 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8186 (mm-30) REVERT: C 230 ASP cc_start: 0.8331 (t70) cc_final: 0.8029 (t70) REVERT: C 377 ASN cc_start: 0.8893 (p0) cc_final: 0.8497 (p0) REVERT: D 542 ARG cc_start: 0.8657 (ptm-80) cc_final: 0.8397 (ttp80) REVERT: D 632 ASP cc_start: 0.8883 (t70) cc_final: 0.8518 (t0) REVERT: D 634 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7665 (tm-30) REVERT: D 652 GLN cc_start: 0.7309 (mt0) cc_final: 0.7086 (mt0) REVERT: E 617 ARG cc_start: 0.8126 (mtm-85) cc_final: 0.7454 (mtm-85) REVERT: F 590 GLN cc_start: 0.8205 (tp40) cc_final: 0.7873 (tp40) REVERT: Z 162 LEU cc_start: 0.8202 (tt) cc_final: 0.7828 (mp) REVERT: Z 165 GLN cc_start: 0.8165 (mt0) cc_final: 0.7652 (tm-30) outliers start: 61 outliers final: 49 residues processed: 273 average time/residue: 0.2562 time to fit residues: 106.5509 Evaluate side-chains 267 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 216 time to evaluate : 1.820 ------------------------------------------------------------------------------- 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 326 ILE 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 213 ILE Chi-restraints excluded: chain B residue 243 SER 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 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 D residue 658 GLN 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 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 107 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 125 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS F 543 ASN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.135795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106596 restraints weight = 22922.927| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.63 r_work: 0.3212 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15732 Z= 0.153 Angle : 0.575 14.535 21421 Z= 0.277 Chirality : 0.045 0.421 2553 Planarity : 0.003 0.057 2619 Dihedral : 5.377 54.598 3116 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.41 % Allowed : 23.07 % 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: -0.75 (0.20), residues: 1792 helix: 1.09 (0.28), residues: 399 sheet: -0.83 (0.22), residues: 552 loop : -0.97 (0.21), residues: 841 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 0.008 0.001 PHE F 522 TYR 0.017 0.001 TYR B 486 ARG 0.002 0.000 ARG Z 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 39) link_NAG-ASN : angle 2.22625 ( 117) link_BETA1-4 : bond 0.00364 ( 11) link_BETA1-4 : angle 1.65290 ( 33) hydrogen bonds : bond 0.03466 ( 483) hydrogen bonds : angle 4.80718 ( 1317) SS BOND : bond 0.00268 ( 35) SS BOND : angle 1.07794 ( 70) covalent geometry : bond 0.00361 (15646) covalent geometry : angle 0.54679 (21201) Misc. bond : bond 0.00083 ( 1) *********************** 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 271 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 215 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8644 (m100) cc_final: 0.8422 (m100) REVERT: A 95 MET cc_start: 0.9230 (ttp) cc_final: 0.9016 (ttp) REVERT: A 161 MET cc_start: 0.8616 (tpt) cc_final: 0.8312 (tpt) REVERT: A 304 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.7309 (ttm170) REVERT: A 326 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.6883 (pt) REVERT: A 464 THR cc_start: 0.8116 (p) cc_final: 0.7860 (t) REVERT: B 348 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7612 (tm-30) REVERT: B 475 MET cc_start: 0.8524 (mmm) cc_final: 0.8111 (mmm) REVERT: B 492 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8366 (mm-30) REVERT: C 377 ASN cc_start: 0.9040 (p0) cc_final: 0.8687 (p0) REVERT: D 542 ARG cc_start: 0.8867 (ptm-80) cc_final: 0.8587 (ttp80) REVERT: D 632 ASP cc_start: 0.8944 (t70) cc_final: 0.8625 (t0) REVERT: D 634 GLU cc_start: 0.8492 (tm-30) cc_final: 0.7878 (tm-30) REVERT: D 639 THR cc_start: 0.8449 (p) cc_final: 0.8199 (p) REVERT: E 617 ARG cc_start: 0.8311 (mtm-85) cc_final: 0.7578 (mtm-85) REVERT: E 619 LEU cc_start: 0.8523 (mt) cc_final: 0.8265 (mt) REVERT: F 590 GLN cc_start: 0.8397 (tp40) cc_final: 0.8009 (tp40) REVERT: Z 165 GLN cc_start: 0.8151 (mt0) cc_final: 0.7868 (mp10) outliers start: 56 outliers final: 47 residues processed: 256 average time/residue: 0.2406 time to fit residues: 94.0257 Evaluate side-chains 266 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 217 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 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 326 ILE 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 213 ILE 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 461 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 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 D residue 658 GLN 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 161 VAL 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 111 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 GLN F 543 ASN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.102771 restraints weight = 22778.871| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.58 r_work: 0.3151 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 15732 Z= 0.286 Angle : 0.683 13.803 21421 Z= 0.329 Chirality : 0.049 0.465 2553 Planarity : 0.004 0.057 2619 Dihedral : 5.908 53.480 3116 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.08 % Allowed : 23.01 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.20), residues: 1792 helix: 0.60 (0.27), residues: 411 sheet: -1.01 (0.23), residues: 542 loop : -1.08 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 316 HIS 0.004 0.001 HIS C 374 PHE 0.014 0.002 PHE C 317 TYR 0.020 0.002 TYR A 484 ARG 0.004 0.000 ARG C 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 39) link_NAG-ASN : angle 2.56124 ( 117) link_BETA1-4 : bond 0.00353 ( 11) link_BETA1-4 : angle 1.81623 ( 33) hydrogen bonds : bond 0.04068 ( 483) hydrogen bonds : angle 5.07637 ( 1317) SS BOND : bond 0.00387 ( 35) SS BOND : angle 1.27183 ( 70) covalent geometry : bond 0.00681 (15646) covalent geometry : angle 0.65186 (21201) Misc. bond : bond 0.00108 ( 1) *********************** 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 296 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 229 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9279 (ttp) cc_final: 0.8989 (ttp) REVERT: A 122 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8641 (mp) REVERT: A 304 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.7327 (ttm170) REVERT: B 348 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7745 (tm-30) REVERT: B 475 MET cc_start: 0.8560 (mmm) cc_final: 0.8179 (mmm) REVERT: B 492 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8357 (mm-30) REVERT: C 161 MET cc_start: 0.8588 (tpt) cc_final: 0.8201 (tpt) REVERT: C 230 ASP cc_start: 0.8519 (t70) cc_final: 0.8243 (t70) REVERT: D 542 ARG cc_start: 0.8982 (ptm-80) cc_final: 0.8637 (ttp80) REVERT: D 632 ASP cc_start: 0.9013 (t70) cc_final: 0.8687 (t0) REVERT: D 634 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8355 (tm-30) REVERT: D 639 THR cc_start: 0.8532 (p) cc_final: 0.8293 (p) REVERT: D 657 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7641 (tm-30) REVERT: E 625 ASN cc_start: 0.8373 (m110) cc_final: 0.7942 (m110) REVERT: F 590 GLN cc_start: 0.8417 (tp40) cc_final: 0.7890 (tp40) REVERT: Z 73 ASN cc_start: 0.8933 (t0) cc_final: 0.8704 (t0) REVERT: Z 165 GLN cc_start: 0.8261 (mt0) cc_final: 0.7927 (mp10) outliers start: 67 outliers final: 49 residues processed: 278 average time/residue: 0.2382 time to fit residues: 100.8941 Evaluate side-chains 268 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 217 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 208 VAL 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 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 174 SER Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 213 ILE 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 75 VAL 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 447 SER Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 658 GLN 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 543 ASN 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 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 70 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 120 optimal weight: 0.0770 chunk 67 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN F 543 ASN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.135953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106677 restraints weight = 22526.323| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.70 r_work: 0.3177 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15732 Z= 0.117 Angle : 0.585 14.752 21421 Z= 0.282 Chirality : 0.046 0.431 2553 Planarity : 0.003 0.057 2619 Dihedral : 5.463 54.686 3116 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.04 % Allowed : 24.35 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.20), residues: 1792 helix: 1.05 (0.28), residues: 399 sheet: -0.85 (0.22), residues: 552 loop : -0.96 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 96 HIS 0.002 0.000 HIS A 249 PHE 0.026 0.001 PHE F 522 TYR 0.010 0.001 TYR A 191 ARG 0.009 0.000 ARG E 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 39) link_NAG-ASN : angle 2.31490 ( 117) link_BETA1-4 : bond 0.00406 ( 11) link_BETA1-4 : angle 1.54844 ( 33) hydrogen bonds : bond 0.03434 ( 483) hydrogen bonds : angle 4.81474 ( 1317) SS BOND : bond 0.00303 ( 35) SS BOND : angle 1.21472 ( 70) covalent geometry : bond 0.00271 (15646) covalent geometry : angle 0.55457 (21201) Misc. bond : bond 0.00064 ( 1) *********************** 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 277 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8443 (tpt) cc_final: 0.8063 (tpt) REVERT: A 304 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7212 (ttm170) REVERT: A 464 THR cc_start: 0.7999 (p) cc_final: 0.7754 (t) REVERT: B 348 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7453 (tm-30) REVERT: B 475 MET cc_start: 0.8249 (mmm) cc_final: 0.7823 (mmm) REVERT: B 492 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8105 (mm-30) REVERT: C 161 MET cc_start: 0.8295 (tpt) cc_final: 0.7969 (tpt) REVERT: D 542 ARG cc_start: 0.8679 (ptm-80) cc_final: 0.8439 (ttp80) REVERT: D 634 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8194 (tm-30) REVERT: D 639 THR cc_start: 0.8385 (p) cc_final: 0.8135 (p) REVERT: F 590 GLN cc_start: 0.8168 (tp40) cc_final: 0.7661 (tp40) REVERT: Z 73 ASN cc_start: 0.8844 (t0) cc_final: 0.8630 (t0) REVERT: Z 165 GLN cc_start: 0.8159 (mt0) cc_final: 0.7855 (mp10) outliers start: 50 outliers final: 42 residues processed: 259 average time/residue: 0.2535 time to fit residues: 99.3881 Evaluate side-chains 261 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 1.808 ------------------------------------------------------------------------------- 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 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 125 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 501 CYS 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 443 ILE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 658 GLN 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 622 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 Chi-restraints excluded: chain Z residue 95 LEU 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 146 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 0.0040 chunk 81 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 2 optimal weight: 0.3980 overall best weight: 0.7794 ------------------------------------------------------------------------------- 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 ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.136309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.107074 restraints weight = 22747.552| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.73 r_work: 0.3181 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15732 Z= 0.122 Angle : 0.578 14.800 21421 Z= 0.277 Chirality : 0.045 0.415 2553 Planarity : 0.003 0.056 2619 Dihedral : 5.223 54.881 3116 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.68 % Allowed : 24.47 % Favored : 72.85 % 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: -0.69 (0.20), residues: 1792 helix: 1.12 (0.28), residues: 399 sheet: -0.75 (0.22), residues: 552 loop : -0.95 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 96 HIS 0.002 0.000 HIS A 249 PHE 0.029 0.001 PHE F 522 TYR 0.012 0.001 TYR A 484 ARG 0.010 0.000 ARG E 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 39) link_NAG-ASN : angle 2.29906 ( 117) link_BETA1-4 : bond 0.00411 ( 11) link_BETA1-4 : angle 1.53336 ( 33) hydrogen bonds : bond 0.03307 ( 483) hydrogen bonds : angle 4.71533 ( 1317) SS BOND : bond 0.00284 ( 35) SS BOND : angle 1.10033 ( 70) covalent geometry : bond 0.00283 (15646) covalent geometry : angle 0.54793 (21201) Misc. bond : bond 0.00081 ( 1) ********************** 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 277 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 233 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 THR cc_start: 0.9407 (m) cc_final: 0.9177 (p) REVERT: A 95 MET cc_start: 0.9073 (ttp) cc_final: 0.8784 (ttp) REVERT: A 302 ASN cc_start: 0.8390 (t0) cc_final: 0.8141 (t0) REVERT: A 304 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.7214 (ttm170) REVERT: A 464 THR cc_start: 0.8013 (p) cc_final: 0.7775 (t) REVERT: B 84 ILE cc_start: 0.8691 (mt) cc_final: 0.8473 (mt) REVERT: B 348 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7467 (tm-30) REVERT: B 392 ASN cc_start: 0.7489 (t0) cc_final: 0.6942 (p0) REVERT: B 475 MET cc_start: 0.8340 (mmm) cc_final: 0.7942 (mmm) REVERT: B 492 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8145 (mm-30) REVERT: C 161 MET cc_start: 0.8212 (tpt) cc_final: 0.7954 (mmm) REVERT: D 542 ARG cc_start: 0.8693 (ptm-80) cc_final: 0.8474 (ttp80) REVERT: D 634 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8242 (tm-30) REVERT: D 639 THR cc_start: 0.8370 (p) cc_final: 0.8150 (p) REVERT: D 652 GLN cc_start: 0.7873 (pt0) cc_final: 0.7508 (mt0) REVERT: F 590 GLN cc_start: 0.8190 (tp40) cc_final: 0.7686 (tp40) REVERT: Z 73 ASN cc_start: 0.8844 (t0) cc_final: 0.8629 (t0) REVERT: Z 165 GLN cc_start: 0.8087 (mt0) cc_final: 0.7814 (mp10) outliers start: 44 outliers final: 39 residues processed: 262 average time/residue: 0.2789 time to fit residues: 112.3695 Evaluate side-chains 263 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 1.610 ------------------------------------------------------------------------------- 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 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 125 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 658 GLN 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 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 Chi-restraints excluded: chain Z residue 95 LEU 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 58 optimal weight: 0.0980 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 117 optimal weight: 0.2980 chunk 74 optimal weight: 0.0870 chunk 160 optimal weight: 0.0020 chunk 104 optimal weight: 5.9990 chunk 175 optimal weight: 0.5980 chunk 174 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 overall best weight: 0.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN B 249 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN F 543 ASN F 577 GLN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.139875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.110904 restraints weight = 22409.575| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.69 r_work: 0.3247 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 15732 Z= 0.093 Angle : 0.553 14.664 21421 Z= 0.268 Chirality : 0.044 0.395 2553 Planarity : 0.004 0.056 2619 Dihedral : 4.880 55.595 3116 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.13 % Allowed : 25.32 % Favored : 72.55 % 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: -0.57 (0.20), residues: 1792 helix: 1.21 (0.27), residues: 417 sheet: -0.63 (0.23), residues: 540 loop : -0.96 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 96 HIS 0.003 0.000 HIS A 249 PHE 0.018 0.001 PHE F 522 TYR 0.009 0.001 TYR B 486 ARG 0.009 0.000 ARG E 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 39) link_NAG-ASN : angle 2.02783 ( 117) link_BETA1-4 : bond 0.00506 ( 11) link_BETA1-4 : angle 1.41313 ( 33) hydrogen bonds : bond 0.03028 ( 483) hydrogen bonds : angle 4.51840 ( 1317) SS BOND : bond 0.00251 ( 35) SS BOND : angle 0.99415 ( 70) covalent geometry : bond 0.00204 (15646) covalent geometry : angle 0.52900 (21201) Misc. bond : bond 0.00074 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7602.73 seconds wall clock time: 132 minutes 46.35 seconds (7966.35 seconds total)