Starting phenix.real_space_refine on Sat Aug 23 23:47:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fyi_29579/08_2025/8fyi_29579.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fyi_29579/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fyi_29579/08_2025/8fyi_29579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fyi_29579/08_2025/8fyi_29579.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fyi_29579/08_2025/8fyi_29579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fyi_29579/08_2025/8fyi_29579.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.70, per 1000 atoms: 0.24 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: 1.20 Conformation dependent library (CDL) restraints added in 554.8 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.53 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: 2.47 Time building geometry restraints manager: 1.60 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 610)) selection = (chain 'B' and (resid 34 through 367 or resid 369 through 428 or resid 432 throu \ gh 610)) selection = (chain 'C' and (resid 34 through 367 or resid 369 through 428 or resid 432 throu \ gh 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: 3.780 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.520 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.050 ------------------------------------------------------------------------------- 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 : 10.34 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.005 0.000 ARG E 617 TYR 0.011 0.001 TYR A 435 PHE 0.022 0.001 PHE C 53 TRP 0.021 0.001 TRP C 96 HIS 0.003 0.000 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00452 (15646) covalent geometry : angle 0.68426 (21201) SS BOND : bond 0.00390 ( 35) SS BOND : angle 1.55679 ( 70) hydrogen bonds : bond 0.20612 ( 483) hydrogen bonds : angle 8.11890 ( 1317) Misc. bond : bond 0.00093 ( 1) link_BETA1-4 : bond 0.00583 ( 11) link_BETA1-4 : angle 2.00881 ( 33) link_NAG-ASN : bond 0.00373 ( 39) link_NAG-ASN : angle 2.72550 ( 117) *********************** 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 : 0.605 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: 0.1127 time to fit residues: 38.7840 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 : 0.436 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 149 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: 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 = 0.3688 r_free = 0.3688 target = 0.135423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.105934 restraints weight = 22807.194| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.70 r_work: 0.3174 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15732 Z= 0.184 Angle : 0.629 12.489 21421 Z= 0.305 Chirality : 0.048 0.522 2553 Planarity : 0.004 0.064 2619 Dihedral : 8.689 63.289 3119 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.92 % Allowed : 20.39 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.20), residues: 1792 helix: 0.90 (0.27), residues: 393 sheet: -1.11 (0.22), residues: 562 loop : -1.05 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 273 TYR 0.014 0.002 TYR A 191 PHE 0.012 0.001 PHE C 159 TRP 0.013 0.001 TRP C 96 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00430 (15646) covalent geometry : angle 0.59361 (21201) SS BOND : bond 0.00383 ( 35) SS BOND : angle 1.27832 ( 70) hydrogen bonds : bond 0.04333 ( 483) hydrogen bonds : angle 5.81717 ( 1317) Misc. bond : bond 0.00071 ( 1) link_BETA1-4 : bond 0.00464 ( 11) link_BETA1-4 : angle 2.19580 ( 33) link_NAG-ASN : bond 0.00431 ( 39) link_NAG-ASN : angle 2.51047 ( 117) *********************** 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 282 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 348 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7567 (tm-30) REVERT: C 230 ASP cc_start: 0.8337 (t70) cc_final: 0.8068 (t70) REVERT: D 632 ASP cc_start: 0.8845 (t70) cc_final: 0.8535 (t0) REVERT: Z 136 LYS cc_start: 0.7535 (mptt) cc_final: 0.7288 (pttm) REVERT: Z 165 GLN cc_start: 0.8047 (mt0) cc_final: 0.7740 (tm-30) outliers start: 48 outliers final: 29 residues processed: 266 average time/residue: 0.1052 time to fit residues: 43.2290 Evaluate side-chains 241 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 447 SER Chi-restraints excluded: chain B residue 103 GLN 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 53 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.135126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.105304 restraints weight = 23221.302| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.71 r_work: 0.3153 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15732 Z= 0.203 Angle : 0.631 12.129 21421 Z= 0.305 Chirality : 0.048 0.471 2553 Planarity : 0.004 0.057 2619 Dihedral : 7.308 57.258 3116 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.59 % Allowed : 20.82 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.20), residues: 1792 helix: 0.93 (0.28), residues: 393 sheet: -1.06 (0.22), residues: 555 loop : -1.05 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 617 TYR 0.013 0.002 TYR A 484 PHE 0.017 0.001 PHE F 522 TRP 0.021 0.001 TRP F 610 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00479 (15646) covalent geometry : angle 0.59789 (21201) SS BOND : bond 0.00322 ( 35) SS BOND : angle 1.17681 ( 70) hydrogen bonds : bond 0.04256 ( 483) hydrogen bonds : angle 5.51875 ( 1317) Misc. bond : bond 0.00091 ( 1) link_BETA1-4 : bond 0.00401 ( 11) link_BETA1-4 : angle 2.12999 ( 33) link_NAG-ASN : bond 0.00443 ( 39) link_NAG-ASN : angle 2.45289 ( 117) *********************** 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: 59 poor density : 222 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8638 (m100) cc_final: 0.8312 (m100) REVERT: A 161 MET cc_start: 0.8334 (tpt) cc_final: 0.7973 (tpt) REVERT: A 304 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.7246 (ttm170) REVERT: B 348 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7575 (tm-30) REVERT: B 475 MET cc_start: 0.8256 (mmm) cc_final: 0.7902 (mmm) REVERT: D 632 ASP cc_start: 0.8875 (t70) cc_final: 0.8572 (t0) REVERT: E 625 ASN cc_start: 0.8269 (m110) cc_final: 0.8004 (m-40) REVERT: Z 136 LYS cc_start: 0.7550 (mptt) cc_final: 0.7275 (pttm) REVERT: Z 162 LEU cc_start: 0.8285 (tt) cc_final: 0.7712 (mt) REVERT: Z 165 GLN cc_start: 0.8182 (mt0) cc_final: 0.7729 (mp10) outliers start: 59 outliers final: 41 residues processed: 262 average time/residue: 0.1108 time to fit residues: 44.8436 Evaluate side-chains 257 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 304 ARG 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 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 79 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ** Z 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 163 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.137375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108067 restraints weight = 22708.909| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.71 r_work: 0.3200 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 15732 Z= 0.108 Angle : 0.562 13.031 21421 Z= 0.271 Chirality : 0.045 0.431 2553 Planarity : 0.003 0.057 2619 Dihedral : 6.053 55.289 3116 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.23 % Allowed : 21.67 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.20), residues: 1792 helix: 0.99 (0.27), residues: 417 sheet: -0.95 (0.22), residues: 547 loop : -0.99 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 617 TYR 0.011 0.001 TYR C 39 PHE 0.010 0.001 PHE F 522 TRP 0.013 0.001 TRP C 96 HIS 0.002 0.000 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00245 (15646) covalent geometry : angle 0.53076 (21201) SS BOND : bond 0.00310 ( 35) SS BOND : angle 1.11229 ( 70) hydrogen bonds : bond 0.03522 ( 483) hydrogen bonds : angle 5.08452 ( 1317) Misc. bond : bond 0.00064 ( 1) link_BETA1-4 : bond 0.00415 ( 11) link_BETA1-4 : angle 1.90090 ( 33) link_NAG-ASN : bond 0.00353 ( 39) link_NAG-ASN : angle 2.22833 ( 117) *********************** 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 292 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 239 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8605 (m100) cc_final: 0.8334 (m100) REVERT: A 37 THR cc_start: 0.9426 (m) cc_final: 0.9169 (p) REVERT: A 161 MET cc_start: 0.8322 (tpt) cc_final: 0.8019 (tpt) REVERT: A 304 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.7165 (ttm170) REVERT: A 326 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.6796 (pt) REVERT: B 348 GLN cc_start: 0.7972 (tm-30) cc_final: 0.7543 (tm-30) REVERT: B 392 ASN cc_start: 0.7349 (t0) cc_final: 0.6790 (p0) REVERT: B 475 MET cc_start: 0.8141 (mmm) cc_final: 0.7778 (mmm) REVERT: B 486 TYR cc_start: 0.8469 (m-10) cc_final: 0.8236 (m-10) REVERT: B 492 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8160 (mm-30) REVERT: C 230 ASP cc_start: 0.8300 (t70) cc_final: 0.8047 (t70) REVERT: C 377 ASN cc_start: 0.8896 (p0) cc_final: 0.8534 (p0) REVERT: Z 162 LEU cc_start: 0.8242 (tt) cc_final: 0.7765 (mt) REVERT: Z 165 GLN cc_start: 0.8166 (mt0) cc_final: 0.7704 (tm-30) outliers start: 53 outliers final: 32 residues processed: 275 average time/residue: 0.1136 time to fit residues: 47.5955 Evaluate side-chains 255 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 326 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 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 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 76 ILE Chi-restraints excluded: chain Z residue 175 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 39 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN F 543 ASN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 129 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.135817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106261 restraints weight = 22853.059| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.70 r_work: 0.3174 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15732 Z= 0.158 Angle : 0.583 13.580 21421 Z= 0.280 Chirality : 0.046 0.429 2553 Planarity : 0.003 0.057 2619 Dihedral : 5.641 54.476 3116 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.47 % Allowed : 22.03 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.20), residues: 1792 helix: 1.08 (0.28), residues: 399 sheet: -0.88 (0.23), residues: 535 loop : -0.96 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Z 59 TYR 0.012 0.001 TYR C 39 PHE 0.019 0.001 PHE C 53 TRP 0.012 0.001 TRP C 96 HIS 0.002 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00371 (15646) covalent geometry : angle 0.55487 (21201) SS BOND : bond 0.00249 ( 35) SS BOND : angle 1.06657 ( 70) hydrogen bonds : bond 0.03592 ( 483) hydrogen bonds : angle 4.95716 ( 1317) Misc. bond : bond 0.00083 ( 1) link_BETA1-4 : bond 0.00366 ( 11) link_BETA1-4 : angle 1.79737 ( 33) link_NAG-ASN : bond 0.00366 ( 39) link_NAG-ASN : angle 2.21612 ( 117) *********************** 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 279 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 222 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.8406 (tpt) cc_final: 0.8098 (tpt) REVERT: A 304 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7207 (ttm170) REVERT: A 326 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.6895 (pt) REVERT: A 464 THR cc_start: 0.8006 (p) cc_final: 0.7766 (t) REVERT: B 348 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7558 (tm-30) REVERT: B 475 MET cc_start: 0.8192 (mmm) cc_final: 0.7828 (mmm) REVERT: B 492 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8169 (mm-30) REVERT: C 377 ASN cc_start: 0.8945 (p0) cc_final: 0.8568 (p0) REVERT: D 542 ARG cc_start: 0.8721 (ptm-80) cc_final: 0.8429 (ttp80) REVERT: F 528 SER cc_start: 0.8189 (m) cc_final: 0.7971 (p) REVERT: F 590 GLN cc_start: 0.8226 (tp40) cc_final: 0.7864 (tp40) REVERT: Z 162 LEU cc_start: 0.8266 (tt) cc_final: 0.7650 (mt) REVERT: Z 165 GLN cc_start: 0.8207 (mt0) cc_final: 0.7663 (tm-30) outliers start: 57 outliers final: 42 residues processed: 263 average time/residue: 0.1123 time to fit residues: 45.1825 Evaluate side-chains 262 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 218 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 447 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain 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 76 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 72 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 154 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.136145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.106764 restraints weight = 22684.115| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.69 r_work: 0.3181 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15732 Z= 0.142 Angle : 0.569 14.024 21421 Z= 0.276 Chirality : 0.045 0.426 2553 Planarity : 0.003 0.057 2619 Dihedral : 5.475 54.693 3116 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.65 % Allowed : 22.40 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.20), residues: 1792 helix: 1.13 (0.28), residues: 396 sheet: -0.82 (0.22), residues: 550 loop : -0.93 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 617 TYR 0.014 0.001 TYR B 486 PHE 0.019 0.001 PHE C 53 TRP 0.015 0.001 TRP C 96 HIS 0.002 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00331 (15646) covalent geometry : angle 0.54059 (21201) SS BOND : bond 0.00396 ( 35) SS BOND : angle 1.10694 ( 70) hydrogen bonds : bond 0.03473 ( 483) hydrogen bonds : angle 4.87564 ( 1317) Misc. bond : bond 0.00080 ( 1) link_BETA1-4 : bond 0.00367 ( 11) link_BETA1-4 : angle 1.68439 ( 33) link_NAG-ASN : bond 0.00345 ( 39) link_NAG-ASN : angle 2.17705 ( 117) *********************** 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 289 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 229 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8621 (m100) cc_final: 0.8418 (m100) REVERT: A 122 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8666 (mp) REVERT: A 161 MET cc_start: 0.8412 (tpt) cc_final: 0.8134 (tpt) REVERT: A 304 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7189 (ttm170) REVERT: A 326 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.6915 (pt) REVERT: A 464 THR cc_start: 0.7988 (p) cc_final: 0.7763 (t) REVERT: B 348 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7512 (tm-30) REVERT: B 475 MET cc_start: 0.8147 (mmm) cc_final: 0.7777 (mmm) REVERT: B 492 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8186 (mm-30) REVERT: C 230 ASP cc_start: 0.8356 (t70) cc_final: 0.8063 (t70) REVERT: C 377 ASN cc_start: 0.8890 (p0) cc_final: 0.8530 (p0) REVERT: D 542 ARG cc_start: 0.8684 (ptm-80) cc_final: 0.8431 (ttp80) REVERT: E 631 TRP cc_start: 0.8958 (t-100) cc_final: 0.8713 (t-100) REVERT: F 590 GLN cc_start: 0.8246 (tp40) cc_final: 0.7924 (tp40) REVERT: Z 165 GLN cc_start: 0.8035 (mt0) cc_final: 0.7696 (tm-30) outliers start: 60 outliers final: 45 residues processed: 269 average time/residue: 0.1180 time to fit residues: 49.4229 Evaluate side-chains 263 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 215 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 112 TRP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 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 272 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 115 SER Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 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 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 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 22 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 174 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 D 607 ASN F 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.135566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106009 restraints weight = 22564.783| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.68 r_work: 0.3174 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1706 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= 0.164 Angle : 0.579 14.340 21421 Z= 0.279 Chirality : 0.046 0.427 2553 Planarity : 0.003 0.057 2619 Dihedral : 5.404 54.536 3116 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.59 % Allowed : 23.13 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.20), residues: 1792 helix: 1.09 (0.28), residues: 396 sheet: -0.85 (0.22), residues: 552 loop : -0.92 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 617 TYR 0.010 0.001 TYR C 39 PHE 0.019 0.001 PHE C 53 TRP 0.014 0.001 TRP C 96 HIS 0.002 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00386 (15646) covalent geometry : angle 0.55063 (21201) SS BOND : bond 0.00307 ( 35) SS BOND : angle 1.11245 ( 70) hydrogen bonds : bond 0.03511 ( 483) hydrogen bonds : angle 4.85011 ( 1317) Misc. bond : bond 0.00087 ( 1) link_BETA1-4 : bond 0.00363 ( 11) link_BETA1-4 : angle 1.67225 ( 33) link_NAG-ASN : bond 0.00358 ( 39) link_NAG-ASN : angle 2.22311 ( 117) *********************** 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 277 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 218 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8666 (m100) cc_final: 0.8426 (m100) REVERT: A 161 MET cc_start: 0.8626 (tpt) cc_final: 0.8327 (tpt) REVERT: A 304 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.7314 (ttm170) REVERT: A 326 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.6978 (pt) REVERT: A 464 THR cc_start: 0.8104 (p) cc_final: 0.7848 (t) REVERT: B 348 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7655 (tm-30) REVERT: B 475 MET cc_start: 0.8463 (mmm) cc_final: 0.8005 (mmm) REVERT: B 492 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8372 (mm-30) REVERT: D 542 ARG cc_start: 0.8890 (ptm-80) cc_final: 0.8579 (ttp80) REVERT: D 639 THR cc_start: 0.8470 (p) cc_final: 0.8234 (p) REVERT: F 590 GLN cc_start: 0.8466 (tp40) cc_final: 0.8101 (tp40) REVERT: F 610 TRP cc_start: 0.6917 (t-100) cc_final: 0.6651 (t-100) REVERT: Z 165 GLN cc_start: 0.8256 (mt0) cc_final: 0.7918 (mp10) outliers start: 59 outliers final: 49 residues processed: 257 average time/residue: 0.1044 time to fit residues: 41.2179 Evaluate side-chains 271 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 220 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 112 TRP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 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 182 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 569 THR 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 535 MET Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 172 ILE Chi-restraints excluded: chain Z residue 175 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 80 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 105 optimal weight: 0.0020 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 117 optimal weight: 0.0000 chunk 177 optimal weight: 0.0170 chunk 82 optimal weight: 4.9990 overall best weight: 0.7832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN F 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.137655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.108174 restraints weight = 22661.788| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.68 r_work: 0.3198 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15732 Z= 0.115 Angle : 0.548 13.600 21421 Z= 0.264 Chirality : 0.045 0.414 2553 Planarity : 0.003 0.056 2619 Dihedral : 5.171 54.925 3116 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.47 % Allowed : 23.43 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.20), residues: 1792 helix: 1.23 (0.28), residues: 396 sheet: -0.77 (0.22), residues: 542 loop : -0.89 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 617 TYR 0.012 0.001 TYR A 484 PHE 0.017 0.001 PHE C 53 TRP 0.016 0.001 TRP C 96 HIS 0.002 0.000 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00265 (15646) covalent geometry : angle 0.51960 (21201) SS BOND : bond 0.00231 ( 35) SS BOND : angle 0.98552 ( 70) hydrogen bonds : bond 0.03261 ( 483) hydrogen bonds : angle 4.70330 ( 1317) Misc. bond : bond 0.00078 ( 1) link_BETA1-4 : bond 0.00410 ( 11) link_BETA1-4 : angle 1.56357 ( 33) link_NAG-ASN : bond 0.00317 ( 39) link_NAG-ASN : angle 2.16939 ( 117) *********************** 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 289 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 0.627 Fit side-chains REVERT: A 35 TRP cc_start: 0.8627 (m100) cc_final: 0.8418 (m100) REVERT: A 122 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8542 (mp) REVERT: A 304 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.7212 (ttm170) REVERT: A 326 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.6867 (pt) REVERT: A 464 THR cc_start: 0.8138 (p) cc_final: 0.7868 (t) REVERT: B 84 ILE cc_start: 0.8713 (mt) cc_final: 0.8451 (mt) REVERT: B 161 MET cc_start: 0.8735 (tpp) cc_final: 0.8394 (ttm) REVERT: B 348 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7536 (tm-30) REVERT: B 392 ASN cc_start: 0.7656 (t0) cc_final: 0.7027 (p0) REVERT: B 475 MET cc_start: 0.8431 (mmm) cc_final: 0.7908 (mmm) REVERT: B 486 TYR cc_start: 0.8601 (m-10) cc_final: 0.8300 (m-10) REVERT: B 492 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8353 (mm-30) REVERT: C 230 ASP cc_start: 0.8498 (t70) cc_final: 0.8160 (t70) REVERT: C 377 ASN cc_start: 0.9012 (p0) cc_final: 0.8626 (p0) REVERT: D 542 ARG cc_start: 0.8857 (ptm-80) cc_final: 0.8571 (ttp80) REVERT: D 639 THR cc_start: 0.8463 (p) cc_final: 0.8210 (p) REVERT: F 590 GLN cc_start: 0.8383 (tp40) cc_final: 0.7938 (tp40) REVERT: Z 165 GLN cc_start: 0.8271 (mt0) cc_final: 0.7952 (mp10) outliers start: 57 outliers final: 45 residues processed: 267 average time/residue: 0.1015 time to fit residues: 41.6465 Evaluate side-chains 264 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 112 TRP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 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 182 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 569 THR 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 660 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 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 128 VAL 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 62 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 166 optimal weight: 0.6980 chunk 153 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN D 607 ASN F 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.137790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108330 restraints weight = 22478.659| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.70 r_work: 0.3202 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1913 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 : 0.561 14.974 21421 Z= 0.270 Chirality : 0.045 0.405 2553 Planarity : 0.003 0.056 2619 Dihedral : 5.042 54.934 3116 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.16 % Allowed : 23.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.20), residues: 1792 helix: 1.23 (0.28), residues: 396 sheet: -0.68 (0.23), residues: 540 loop : -0.90 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Z 59 TYR 0.012 0.001 TYR A 484 PHE 0.019 0.001 PHE C 53 TRP 0.018 0.001 TRP C 96 HIS 0.002 0.000 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00274 (15646) covalent geometry : angle 0.53362 (21201) SS BOND : bond 0.00349 ( 35) SS BOND : angle 1.12589 ( 70) hydrogen bonds : bond 0.03205 ( 483) hydrogen bonds : angle 4.66773 ( 1317) Misc. bond : bond 0.00081 ( 1) link_BETA1-4 : bond 0.00393 ( 11) link_BETA1-4 : angle 1.54027 ( 33) link_NAG-ASN : bond 0.00321 ( 39) link_NAG-ASN : angle 2.16283 ( 117) *********************** 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 279 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 227 time to evaluate : 0.600 Fit side-chains REVERT: A 95 MET cc_start: 0.9044 (ttp) cc_final: 0.8811 (ttp) REVERT: A 122 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8452 (mp) REVERT: A 304 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7117 (ttm170) REVERT: A 326 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.6857 (pt) REVERT: A 464 THR cc_start: 0.8031 (p) cc_final: 0.7817 (t) REVERT: B 84 ILE cc_start: 0.8671 (mt) cc_final: 0.8433 (mt) REVERT: B 161 MET cc_start: 0.8492 (tpp) cc_final: 0.8132 (ttm) REVERT: B 348 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7433 (tm-30) REVERT: B 392 ASN cc_start: 0.7472 (t0) cc_final: 0.6948 (p0) REVERT: B 475 MET cc_start: 0.8199 (mmm) cc_final: 0.7764 (mmm) REVERT: C 377 ASN cc_start: 0.8857 (p0) cc_final: 0.8475 (p0) REVERT: D 542 ARG cc_start: 0.8653 (ptm-80) cc_final: 0.8421 (ttp80) REVERT: D 639 THR cc_start: 0.8350 (p) cc_final: 0.8111 (p) REVERT: F 590 GLN cc_start: 0.8216 (tp40) cc_final: 0.7745 (tp40) REVERT: Z 165 GLN cc_start: 0.8149 (mt0) cc_final: 0.7861 (mp10) outliers start: 52 outliers final: 42 residues processed: 264 average time/residue: 0.1057 time to fit residues: 42.8070 Evaluate side-chains 267 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 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 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 A residue 499 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 29 optimal weight: 0.0970 chunk 147 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 115 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 73 optimal weight: 0.3980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN D 607 ASN F 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.138527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.109384 restraints weight = 22515.171| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.69 r_work: 0.3222 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 15732 Z= 0.104 Angle : 0.552 14.723 21421 Z= 0.265 Chirality : 0.045 0.400 2553 Planarity : 0.003 0.056 2619 Dihedral : 4.934 55.099 3116 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.80 % Allowed : 24.77 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.20), residues: 1792 helix: 1.22 (0.27), residues: 414 sheet: -0.63 (0.23), residues: 542 loop : -0.91 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 58 TYR 0.011 0.001 TYR C 39 PHE 0.019 0.001 PHE C 53 TRP 0.020 0.001 TRP C 96 HIS 0.003 0.000 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00238 (15646) covalent geometry : angle 0.52437 (21201) SS BOND : bond 0.00261 ( 35) SS BOND : angle 1.04911 ( 70) hydrogen bonds : bond 0.03112 ( 483) hydrogen bonds : angle 4.58485 ( 1317) Misc. bond : bond 0.00079 ( 1) link_BETA1-4 : bond 0.00447 ( 11) link_BETA1-4 : angle 1.48715 ( 33) link_NAG-ASN : bond 0.00310 ( 39) link_NAG-ASN : angle 2.16983 ( 117) ********************** 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 275 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 229 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8481 (m100) cc_final: 0.8052 (m100) REVERT: A 95 MET cc_start: 0.9070 (ttp) cc_final: 0.8847 (ttp) REVERT: A 304 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7108 (ttm170) REVERT: A 326 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.6826 (pt) REVERT: A 464 THR cc_start: 0.8018 (p) cc_final: 0.7805 (t) REVERT: B 84 ILE cc_start: 0.8659 (mt) cc_final: 0.8406 (mt) REVERT: B 161 MET cc_start: 0.8448 (tpp) cc_final: 0.8119 (ttm) REVERT: B 348 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7465 (tm-30) REVERT: B 392 ASN cc_start: 0.7418 (OUTLIER) cc_final: 0.6927 (p0) REVERT: B 475 MET cc_start: 0.8207 (mmm) cc_final: 0.7763 (mmm) REVERT: D 542 ARG cc_start: 0.8637 (ptm-80) cc_final: 0.8423 (ttp80) REVERT: D 639 THR cc_start: 0.8306 (p) cc_final: 0.8088 (p) REVERT: F 590 GLN cc_start: 0.8226 (tp40) cc_final: 0.7765 (tp40) REVERT: Z 165 GLN cc_start: 0.8163 (mt0) cc_final: 0.7874 (mp10) outliers start: 46 outliers final: 40 residues processed: 258 average time/residue: 0.1099 time to fit residues: 43.3386 Evaluate side-chains 262 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 388 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 392 ASN 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 182 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 660 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 Z residue 23 SER Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 172 ILE Chi-restraints excluded: chain Z residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 38 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 41 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN D 607 ASN F 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.137220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107978 restraints weight = 22410.843| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.67 r_work: 0.3199 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15732 Z= 0.136 Angle : 0.567 15.046 21421 Z= 0.273 Chirality : 0.045 0.406 2553 Planarity : 0.003 0.056 2619 Dihedral : 4.954 54.783 3115 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.16 % Allowed : 24.35 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.20), residues: 1792 helix: 1.19 (0.27), residues: 414 sheet: -0.61 (0.22), residues: 552 loop : -0.87 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 500 TYR 0.011 0.001 TYR B 486 PHE 0.018 0.001 PHE C 53 TRP 0.021 0.001 TRP C 96 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00320 (15646) covalent geometry : angle 0.54068 (21201) SS BOND : bond 0.00266 ( 35) SS BOND : angle 1.03727 ( 70) hydrogen bonds : bond 0.03255 ( 483) hydrogen bonds : angle 4.61391 ( 1317) Misc. bond : bond 0.00087 ( 1) link_BETA1-4 : bond 0.00369 ( 11) link_BETA1-4 : angle 1.52416 ( 33) link_NAG-ASN : bond 0.00318 ( 39) link_NAG-ASN : angle 2.12643 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3355.33 seconds wall clock time: 58 minutes 31.60 seconds (3511.60 seconds total)