Starting phenix.real_space_refine on Fri Jul 3 18:14:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fyi_29579/07_2026/8fyi_29579.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fyi_29579/07_2026/8fyi_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8fyi_29579/07_2026/8fyi_29579.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fyi_29579/07_2026/8fyi_29579.cif" model { file = "/net/cci-nas-00/data/ceres_data/8fyi_29579/07_2026/8fyi_29579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fyi_29579/07_2026/8fyi_29579.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fyi_29579/07_2026/8fyi_29579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fyi_29579/07_2026/8fyi_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-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 10 Time building chain proxies: 3.54, per 1000 atoms: 0.23 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: 1.26 Conformation dependent library (CDL) restraints added in 560.4 milliseconds 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: 0.60 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: 2.71 Time building geometry restraints manager: 1.66 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 - 17.47: 7746 17.47 - 34.94: 961 34.94 - 52.41: 241 52.41 - 69.89: 41 69.89 - 87.36: 18 Dihedral angle restraints: 9007 sinusoidal: 3698 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 9004 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: 5.180 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.510 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 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 : 15.898 87.356 5454 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 are 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/Z covalent geometry : bond 0.00452 / 0.21 (15646) covalent geometry : angle 0.68426 / 0.35 (21201) SS BOND : bond 0.00390 / 0.26 ( 35) SS BOND : angle 1.55679 / 1.07 ( 70) hydrogen bonds : bond 0.20612 / 13.52 ( 483) hydrogen bonds : angle 8.11890 / 5.60 ( 1317) Misc. bond : bond 0.00093 / 0.05 ( 1) link_BETA1-4 : bond 0.00583 / 0.36 ( 11) link_BETA1-4 : angle 2.00881 / 1.41 ( 33) link_NAG-ASN : bond 0.00373 / 0.26 ( 39) link_NAG-ASN : angle 2.72550 / 1.65 ( 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 : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 475 MET cc_start: 0.8570 (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: 0.1123 time to fit residues: 39.0792 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 : 0.644 ------------------------------------------------------------------------------- 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... D 575 GLN D 577 GLN F 575 GLN F 611 ASN Z 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.135294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106047 restraints weight = 22783.878| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.68 r_work: 0.3168 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15732 Z= 0.185 Angle : 0.615 12.396 21421 Z= 0.303 Chirality : 0.047 0.508 2553 Planarity : 0.004 0.064 2619 Dihedral : 4.197 26.163 1949 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.80 % Allowed : 20.33 % Favored : 76.87 % 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 are not related in a simple way. whole: -1.03 (0.20), residues: 1792 helix: 0.79 (0.27), residues: 399 sheet: -1.08 (0.22), residues: 556 loop : -1.04 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 273 TYR 0.012 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/Z covalent geometry : bond 0.00431 / 0.18 (15646) covalent geometry : angle 0.58131 / 0.29 (21201) SS BOND : bond 0.00346 / 0.22 ( 35) SS BOND : angle 1.26795 / 0.88 ( 70) hydrogen bonds : bond 0.04355 / 2.82 ( 483) hydrogen bonds : angle 5.88110 / 4.03 ( 1317) Misc. bond : bond 0.00062 / 0.03 ( 1) link_BETA1-4 : bond 0.00375 / 0.24 ( 11) link_BETA1-4 : angle 1.70359 / 1.16 ( 33) link_NAG-ASN : bond 0.00441 / 0.28 ( 39) link_NAG-ASN : angle 2.47735 / 1.50 ( 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 271 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 225 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 348 GLN cc_start: 0.7834 (tm-30) cc_final: 0.7570 (tm-30) REVERT: Z 40 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8652 (tp-100) REVERT: Z 136 LYS cc_start: 0.7522 (mptt) cc_final: 0.7303 (pttm) REVERT: Z 165 GLN cc_start: 0.8041 (mt0) cc_final: 0.7742 (tm-30) outliers start: 46 outliers final: 26 residues processed: 256 average time/residue: 0.1100 time to fit residues: 43.3172 Evaluate side-chains 240 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU 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 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: 3.9990 chunk 78 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3661 r_free = 0.3661 target = 0.133213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.103783 restraints weight = 23148.867| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.69 r_work: 0.3138 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15732 Z= 0.246 Angle : 0.649 12.381 21421 Z= 0.318 Chirality : 0.048 0.476 2553 Planarity : 0.004 0.057 2619 Dihedral : 4.307 26.180 1946 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.65 % Allowed : 21.06 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.20), residues: 1792 helix: 0.84 (0.27), residues: 393 sheet: -1.13 (0.22), residues: 556 loop : -1.09 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 617 TYR 0.014 0.002 TYR A 484 PHE 0.019 0.002 PHE F 522 TRP 0.024 0.002 TRP F 610 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.25 (15646) covalent geometry : angle 0.61667 / 0.31 (21201) SS BOND : bond 0.00344 / 0.20 ( 35) SS BOND : angle 1.23390 / 0.85 ( 70) hydrogen bonds : bond 0.04433 / 2.86 ( 483) hydrogen bonds : angle 5.57942 / 3.79 ( 1317) Misc. bond : bond 0.00097 / 0.05 ( 1) link_BETA1-4 : bond 0.00326 / 0.20 ( 11) link_BETA1-4 : angle 1.70084 / 1.15 ( 33) link_NAG-ASN : bond 0.00481 / 0.31 ( 39) link_NAG-ASN : angle 2.52351 / 1.53 ( 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 280 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 220 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8321 (tpt) cc_final: 0.7995 (tpt) REVERT: A 304 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7252 (ttm170) REVERT: B 348 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7583 (tm-30) REVERT: B 475 MET cc_start: 0.8252 (mmm) cc_final: 0.7902 (mmm) REVERT: D 632 ASP cc_start: 0.8939 (t70) cc_final: 0.8606 (t0) REVERT: E 617 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.7551 (mtm-85) REVERT: E 625 ASN cc_start: 0.8263 (m110) cc_final: 0.8008 (m-40) REVERT: Z 136 LYS cc_start: 0.7504 (mptt) cc_final: 0.7281 (pttm) REVERT: Z 162 LEU cc_start: 0.8223 (tt) cc_final: 0.7672 (mt) REVERT: Z 165 GLN cc_start: 0.8134 (mt0) cc_final: 0.7684 (mp10) outliers start: 60 outliers final: 43 residues processed: 262 average time/residue: 0.1143 time to fit residues: 46.3487 Evaluate side-chains 252 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 292 VAL Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 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: 0.1980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 52 optimal weight: 0.0980 chunk 79 optimal weight: 0.0470 chunk 78 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN B 183 GLN C 195 ASN D 607 ASN F 590 GLN ** Z 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 163 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.137088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107886 restraints weight = 22721.087| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.71 r_work: 0.3199 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 15732 Z= 0.108 Angle : 0.556 11.927 21421 Z= 0.270 Chirality : 0.045 0.424 2553 Planarity : 0.003 0.057 2619 Dihedral : 4.026 28.791 1946 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.10 % Allowed : 21.97 % Favored : 74.92 % 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 are not related in a simple way. whole: -0.87 (0.20), residues: 1792 helix: 0.97 (0.27), residues: 417 sheet: -0.98 (0.22), residues: 546 loop : -1.02 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 617 TYR 0.011 0.001 TYR C 39 PHE 0.009 0.001 PHE F 522 TRP 0.012 0.001 TRP C 96 HIS 0.002 0.000 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (15646) covalent geometry : angle 0.52713 / 0.26 (21201) SS BOND : bond 0.00470 / 0.36 ( 35) SS BOND : angle 1.11775 / 0.79 ( 70) hydrogen bonds : bond 0.03549 / 2.30 ( 483) hydrogen bonds : angle 5.10803 / 3.46 ( 1317) Misc. bond : bond 0.00074 / 0.04 ( 1) link_BETA1-4 : bond 0.00357 / 0.21 ( 11) link_BETA1-4 : angle 1.46742 / 0.99 ( 33) link_NAG-ASN : bond 0.00338 / 0.25 ( 39) link_NAG-ASN : angle 2.23182 / 1.34 ( 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 282 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 231 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8608 (m100) cc_final: 0.8355 (m100) REVERT: A 37 THR cc_start: 0.9439 (m) cc_final: 0.9170 (p) REVERT: A 161 MET cc_start: 0.8341 (tpt) cc_final: 0.8047 (tpt) REVERT: A 304 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.7084 (ttm170) REVERT: B 348 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7512 (tm-30) REVERT: B 475 MET cc_start: 0.8136 (mmm) cc_final: 0.7800 (mmm) REVERT: B 486 TYR cc_start: 0.8485 (m-10) cc_final: 0.8237 (m-10) REVERT: B 492 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8165 (mm-30) REVERT: C 377 ASN cc_start: 0.8917 (p0) cc_final: 0.8541 (p0) REVERT: D 632 ASP cc_start: 0.8896 (t70) cc_final: 0.8527 (t0) REVERT: E 617 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7593 (mtm-85) REVERT: Z 162 LEU cc_start: 0.8232 (tt) cc_final: 0.7779 (mt) REVERT: Z 165 GLN cc_start: 0.8182 (mt0) cc_final: 0.7708 (tm-30) outliers start: 51 outliers final: 31 residues processed: 265 average time/residue: 0.1160 time to fit residues: 47.2427 Evaluate side-chains 249 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain Z residue 76 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 39 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 64 GLN Z 129 GLN Z 163 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.132797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.103374 restraints weight = 23007.221| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.68 r_work: 0.3131 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 15732 Z= 0.242 Angle : 0.647 13.452 21421 Z= 0.312 Chirality : 0.048 0.449 2553 Planarity : 0.004 0.057 2619 Dihedral : 4.251 26.868 1946 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.63 % Allowed : 21.73 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.20), residues: 1792 helix: 0.88 (0.27), residues: 399 sheet: -0.98 (0.22), residues: 535 loop : -1.06 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 59 TYR 0.014 0.002 TYR A 484 PHE 0.012 0.002 PHE C 317 TRP 0.014 0.001 TRP B 316 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.24 (15646) covalent geometry : angle 0.61767 / 0.31 (21201) SS BOND : bond 0.00344 / 0.20 ( 35) SS BOND : angle 1.20839 / 0.84 ( 70) hydrogen bonds : bond 0.04000 / 2.60 ( 483) hydrogen bonds : angle 5.16210 / 3.51 ( 1317) Misc. bond : bond 0.00091 / 0.05 ( 1) link_BETA1-4 : bond 0.00316 / 0.21 ( 11) link_BETA1-4 : angle 1.67919 / 1.12 ( 33) link_NAG-ASN : bond 0.00478 / 0.31 ( 39) link_NAG-ASN : angle 2.41459 / 1.47 ( 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 294 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 218 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8445 (tpt) cc_final: 0.8153 (tpt) REVERT: A 304 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.7190 (ttm170) REVERT: B 348 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7712 (tm-30) REVERT: B 475 MET cc_start: 0.8231 (mmm) cc_final: 0.7959 (mmm) REVERT: B 492 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8177 (mm-30) REVERT: D 632 ASP cc_start: 0.8899 (t70) cc_final: 0.8559 (t0) REVERT: E 619 LEU cc_start: 0.8606 (mt) cc_final: 0.8393 (mt) REVERT: E 625 ASN cc_start: 0.8285 (m110) cc_final: 0.8024 (m-40) REVERT: F 528 SER cc_start: 0.8212 (m) cc_final: 0.7993 (p) REVERT: Z 64 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7964 (pt0) REVERT: Z 165 GLN cc_start: 0.8183 (mt0) cc_final: 0.7688 (tm-30) outliers start: 76 outliers final: 56 residues processed: 272 average time/residue: 0.1146 time to fit residues: 48.4981 Evaluate side-chains 271 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 213 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 116 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 D residue 627 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 64 GLN Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 172 ILE Chi-restraints excluded: chain Z residue 175 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 72 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 135 optimal weight: 0.0000 chunk 139 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.132411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.102990 restraints weight = 22912.835| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.67 r_work: 0.3131 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 15732 Z= 0.243 Angle : 0.648 13.981 21421 Z= 0.311 Chirality : 0.048 0.457 2553 Planarity : 0.004 0.057 2619 Dihedral : 4.290 26.514 1946 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.38 % Allowed : 23.13 % 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 are not related in a simple way. whole: -1.06 (0.20), residues: 1792 helix: 0.78 (0.27), residues: 399 sheet: -1.10 (0.22), residues: 543 loop : -1.07 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 59 TYR 0.016 0.002 TYR B 486 PHE 0.011 0.002 PHE C 159 TRP 0.029 0.002 TRP F 610 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.24 (15646) covalent geometry : angle 0.61831 / 0.30 (21201) SS BOND : bond 0.00378 / 0.24 ( 35) SS BOND : angle 1.27388 / 0.92 ( 70) hydrogen bonds : bond 0.03923 / 2.54 ( 483) hydrogen bonds : angle 5.11597 / 3.47 ( 1317) Misc. bond : bond 0.00090 / 0.05 ( 1) link_BETA1-4 : bond 0.00294 / 0.20 ( 11) link_BETA1-4 : angle 1.64292 / 1.09 ( 33) link_NAG-ASN : bond 0.00460 / 0.30 ( 39) link_NAG-ASN : angle 2.44324 / 1.48 ( 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 291 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 219 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8662 (m100) cc_final: 0.8407 (m100) REVERT: A 304 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.7301 (ttm170) REVERT: B 348 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7629 (tm-30) REVERT: B 416 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8271 (mt) REVERT: B 475 MET cc_start: 0.8262 (mmm) cc_final: 0.7912 (mmm) REVERT: B 492 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8163 (mm-30) REVERT: D 542 ARG cc_start: 0.8793 (ptm-80) cc_final: 0.8468 (ttp80) REVERT: D 632 ASP cc_start: 0.8897 (t70) cc_final: 0.8551 (t0) REVERT: D 639 THR cc_start: 0.8431 (p) cc_final: 0.8182 (p) REVERT: E 625 ASN cc_start: 0.8274 (m110) cc_final: 0.8001 (m-40) REVERT: Z 73 ASN cc_start: 0.8830 (t0) cc_final: 0.8614 (t0) REVERT: Z 165 GLN cc_start: 0.8149 (mt0) cc_final: 0.7777 (mp10) outliers start: 72 outliers final: 58 residues processed: 268 average time/residue: 0.1141 time to fit residues: 47.4589 Evaluate side-chains 273 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 213 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 420 ILE 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 D residue 658 GLN Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain F residue 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: 3.9990 chunk 12 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 88 optimal weight: 0.0370 chunk 174 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS C 195 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 = 0.3703 r_free = 0.3703 target = 0.136626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107392 restraints weight = 22447.156| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.68 r_work: 0.3190 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15732 Z= 0.109 Angle : 0.561 14.297 21421 Z= 0.270 Chirality : 0.045 0.416 2553 Planarity : 0.003 0.057 2619 Dihedral : 4.007 29.165 1946 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.59 % Allowed : 23.62 % Favored : 72.79 % 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 are not related in a simple way. whole: -0.86 (0.20), residues: 1792 helix: 1.00 (0.27), residues: 417 sheet: -0.96 (0.22), residues: 544 loop : -1.04 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 59 TYR 0.011 0.001 TYR C 39 PHE 0.016 0.001 PHE F 522 TRP 0.028 0.001 TRP A 69 HIS 0.002 0.000 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (15646) covalent geometry : angle 0.53380 / 0.26 (21201) SS BOND : bond 0.00236 / 0.16 ( 35) SS BOND : angle 1.04287 / 0.75 ( 70) hydrogen bonds : bond 0.03351 / 2.16 ( 483) hydrogen bonds : angle 4.82191 / 3.27 ( 1317) Misc. bond : bond 0.00060 / 0.03 ( 1) link_BETA1-4 : bond 0.00375 / 0.23 ( 11) link_BETA1-4 : angle 1.42912 / 0.96 ( 33) link_NAG-ASN : bond 0.00322 / 0.24 ( 39) link_NAG-ASN : angle 2.20401 / 1.32 ( 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 286 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 227 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8587 (m100) cc_final: 0.8358 (m100) REVERT: A 37 THR cc_start: 0.9406 (m) cc_final: 0.9191 (p) REVERT: A 69 TRP cc_start: 0.7808 (m-90) cc_final: 0.7603 (m-90) REVERT: A 304 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7208 (ttm170) REVERT: A 464 THR cc_start: 0.8004 (p) cc_final: 0.7761 (t) REVERT: B 161 MET cc_start: 0.8488 (tpp) cc_final: 0.8097 (ttm) REVERT: B 348 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7402 (tm-30) REVERT: B 475 MET cc_start: 0.8129 (mmm) cc_final: 0.7708 (mmm) REVERT: B 492 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8144 (mm-30) REVERT: C 377 ASN cc_start: 0.8902 (p0) cc_final: 0.8535 (p0) REVERT: D 542 ARG cc_start: 0.8656 (ptm-80) cc_final: 0.8422 (ttp80) REVERT: D 632 ASP cc_start: 0.8817 (t70) cc_final: 0.8491 (t0) REVERT: D 639 THR cc_start: 0.8406 (p) cc_final: 0.8118 (p) REVERT: F 590 GLN cc_start: 0.8340 (tp-100) cc_final: 0.8071 (tp40) REVERT: Z 73 ASN cc_start: 0.8825 (t0) cc_final: 0.8611 (t0) REVERT: Z 165 GLN cc_start: 0.8108 (mt0) cc_final: 0.7804 (mp10) outliers start: 59 outliers final: 44 residues processed: 269 average time/residue: 0.1177 time to fit residues: 48.5560 Evaluate side-chains 261 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 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 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 357 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 87 GLU Chi-restraints excluded: chain Z residue 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: 2.9990 chunk 96 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.0070 chunk 169 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 249 HIS D 607 ASN F 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.135094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105630 restraints weight = 22754.782| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.70 r_work: 0.3159 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15732 Z= 0.162 Angle : 0.592 13.857 21421 Z= 0.284 Chirality : 0.046 0.418 2553 Planarity : 0.003 0.057 2619 Dihedral : 4.043 28.727 1946 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.41 % Allowed : 24.35 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.20), residues: 1792 helix: 1.07 (0.28), residues: 399 sheet: -0.87 (0.22), residues: 544 loop : -0.98 (0.21), residues: 849 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 0.020 0.001 PHE F 522 TRP 0.016 0.001 TRP C 96 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (15646) covalent geometry : angle 0.56191 / 0.28 (21201) SS BOND : bond 0.00320 / 0.22 ( 35) SS BOND : angle 1.24293 / 0.92 ( 70) hydrogen bonds : bond 0.03446 / 2.23 ( 483) hydrogen bonds : angle 4.81855 / 3.27 ( 1317) Misc. bond : bond 0.00078 / 0.04 ( 1) link_BETA1-4 : bond 0.00309 / 0.20 ( 11) link_BETA1-4 : angle 1.50467 / 1.00 ( 33) link_NAG-ASN : bond 0.00350 / 0.25 ( 39) link_NAG-ASN : angle 2.30936 / 1.39 ( 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 279 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 223 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8636 (m100) cc_final: 0.8403 (m100) REVERT: A 69 TRP cc_start: 0.7839 (m-90) cc_final: 0.7611 (m-90) REVERT: A 304 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7195 (ttm170) REVERT: B 348 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7474 (tm-30) REVERT: B 475 MET cc_start: 0.8283 (mmm) cc_final: 0.7801 (mmm) REVERT: B 492 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8175 (mm-30) REVERT: C 377 ASN cc_start: 0.8924 (p0) cc_final: 0.8566 (p0) REVERT: D 542 ARG cc_start: 0.8705 (ptm-80) cc_final: 0.8460 (ttp80) REVERT: D 632 ASP cc_start: 0.8858 (t70) cc_final: 0.8516 (t0) REVERT: D 639 THR cc_start: 0.8411 (p) cc_final: 0.8168 (p) REVERT: Z 73 ASN cc_start: 0.8827 (t0) cc_final: 0.8606 (t0) REVERT: Z 165 GLN cc_start: 0.8099 (mt0) cc_final: 0.7797 (mp10) outliers start: 56 outliers final: 51 residues processed: 262 average time/residue: 0.1154 time to fit residues: 46.7442 Evaluate side-chains 270 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 218 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 208 VAL Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 SER 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 371 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 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 F residue 660 LEU Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 87 GLU Chi-restraints excluded: chain Z residue 95 LEU Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 172 ILE Chi-restraints excluded: chain Z residue 175 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 62 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.135851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.106558 restraints weight = 22549.766| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.69 r_work: 0.3178 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15732 Z= 0.129 Angle : 0.574 14.817 21421 Z= 0.275 Chirality : 0.045 0.412 2553 Planarity : 0.003 0.056 2619 Dihedral : 3.957 29.245 1946 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.29 % Allowed : 24.77 % Favored : 71.94 % 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 are not related in a simple way. whole: -0.74 (0.20), residues: 1792 helix: 1.12 (0.28), residues: 399 sheet: -0.85 (0.22), residues: 552 loop : -0.94 (0.21), residues: 841 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 0.016 0.001 PHE F 522 TRP 0.018 0.001 TRP C 96 HIS 0.002 0.000 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (15646) covalent geometry : angle 0.54454 / 0.27 (21201) SS BOND : bond 0.00290 / 0.20 ( 35) SS BOND : angle 1.11337 / 0.82 ( 70) hydrogen bonds : bond 0.03334 / 2.14 ( 483) hydrogen bonds : angle 4.75547 / 3.23 ( 1317) Misc. bond : bond 0.00073 / 0.04 ( 1) link_BETA1-4 : bond 0.00347 / 0.22 ( 11) link_BETA1-4 : angle 1.43660 / 0.96 ( 33) link_NAG-ASN : bond 0.00320 / 0.24 ( 39) link_NAG-ASN : angle 2.27258 / 1.36 ( 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 280 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 226 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8591 (m100) cc_final: 0.8378 (m100) REVERT: A 304 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.7170 (ttm170) REVERT: A 464 THR cc_start: 0.8011 (p) cc_final: 0.7780 (t) REVERT: B 84 ILE cc_start: 0.8674 (mt) cc_final: 0.8440 (mt) REVERT: B 348 GLN cc_start: 0.7917 (tm-30) cc_final: 0.7421 (tm-30) REVERT: B 475 MET cc_start: 0.8221 (mmm) cc_final: 0.7760 (mmm) REVERT: B 492 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8136 (mm-30) REVERT: D 542 ARG cc_start: 0.8692 (ptm-80) cc_final: 0.8466 (ttp80) REVERT: D 632 ASP cc_start: 0.8842 (t70) cc_final: 0.8515 (t0) REVERT: D 639 THR cc_start: 0.8384 (p) cc_final: 0.8129 (p) REVERT: Z 73 ASN cc_start: 0.8860 (t0) cc_final: 0.8646 (t0) REVERT: Z 165 GLN cc_start: 0.8115 (mt0) cc_final: 0.7824 (mp10) outliers start: 54 outliers final: 45 residues processed: 267 average time/residue: 0.1158 time to fit residues: 47.9635 Evaluate side-chains 272 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 208 VAL Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 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 371 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 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 23 SER Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 95 LEU Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 172 ILE Chi-restraints excluded: chain Z residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 29 optimal weight: 0.0470 chunk 147 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 115 optimal weight: 0.0370 chunk 30 optimal weight: 2.9990 chunk 176 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106774 restraints weight = 22641.904| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.68 r_work: 0.3176 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15732 Z= 0.136 Angle : 0.580 15.163 21421 Z= 0.278 Chirality : 0.045 0.407 2553 Planarity : 0.003 0.056 2619 Dihedral : 3.993 29.259 1946 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.98 % Allowed : 25.02 % Favored : 72.00 % 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 are not related in a simple way. whole: -0.69 (0.20), residues: 1792 helix: 1.15 (0.28), residues: 399 sheet: -0.78 (0.22), residues: 552 loop : -0.94 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 617 TYR 0.014 0.001 TYR B 486 PHE 0.018 0.001 PHE F 522 TRP 0.019 0.001 TRP C 96 HIS 0.002 0.000 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (15646) covalent geometry : angle 0.55096 / 0.27 (21201) SS BOND : bond 0.00278 / 0.19 ( 35) SS BOND : angle 1.09935 / 0.80 ( 70) hydrogen bonds : bond 0.03318 / 2.14 ( 483) hydrogen bonds : angle 4.73736 / 3.22 ( 1317) Misc. bond : bond 0.00076 / 0.04 ( 1) link_BETA1-4 : bond 0.00333 / 0.20 ( 11) link_BETA1-4 : angle 1.44287 / 0.97 ( 33) link_NAG-ASN : bond 0.00323 / 0.24 ( 39) link_NAG-ASN : angle 2.28197 / 1.36 ( 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 283 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 234 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8643 (m100) cc_final: 0.8426 (m100) REVERT: A 69 TRP cc_start: 0.7876 (m-90) cc_final: 0.7638 (m-90) REVERT: A 304 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.7168 (ttm170) REVERT: A 464 THR cc_start: 0.8029 (p) cc_final: 0.7797 (t) REVERT: B 84 ILE cc_start: 0.8686 (mt) cc_final: 0.8460 (mt) REVERT: B 161 MET cc_start: 0.8529 (tpp) cc_final: 0.8128 (ttm) REVERT: B 348 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7440 (tm-30) REVERT: B 475 MET cc_start: 0.8248 (mmm) cc_final: 0.7784 (mmm) REVERT: B 492 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8142 (mm-30) REVERT: C 230 ASP cc_start: 0.8355 (t70) cc_final: 0.8062 (t70) REVERT: D 542 ARG cc_start: 0.8685 (ptm-80) cc_final: 0.8457 (ttp80) REVERT: D 632 ASP cc_start: 0.8852 (t70) cc_final: 0.8551 (t0) REVERT: D 634 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7610 (tm-30) REVERT: D 639 THR cc_start: 0.8384 (p) cc_final: 0.8133 (p) REVERT: D 652 GLN cc_start: 0.7896 (pt0) cc_final: 0.7559 (mt0) REVERT: Z 73 ASN cc_start: 0.8854 (t0) cc_final: 0.8642 (t0) REVERT: Z 165 GLN cc_start: 0.8124 (mt0) cc_final: 0.7833 (mp10) outliers start: 49 outliers final: 43 residues processed: 268 average time/residue: 0.1144 time to fit residues: 47.3367 Evaluate side-chains 264 residues out of total 1643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 220 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 208 VAL Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 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 371 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 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 Z residue 23 SER Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 95 LEU Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 172 ILE Chi-restraints excluded: chain Z residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 38 optimal weight: 0.0370 chunk 144 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 136 optimal weight: 0.0670 chunk 41 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 118 optimal weight: 0.0020 chunk 19 optimal weight: 0.9980 overall best weight: 0.2404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.139089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110438 restraints weight = 22377.283| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.60 r_work: 0.3235 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15732 Z= 0.093 Angle : 0.558 14.876 21421 Z= 0.268 Chirality : 0.044 0.388 2553 Planarity : 0.003 0.056 2619 Dihedral : 3.858 31.315 1946 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.25 % Allowed : 25.93 % Favored : 71.82 % 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 are not related in a simple way. whole: -0.64 (0.20), residues: 1792 helix: 1.17 (0.27), residues: 417 sheet: -0.69 (0.23), residues: 539 loop : -1.00 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 58 TYR 0.012 0.001 TYR A 484 PHE 0.027 0.001 PHE F 522 TRP 0.020 0.001 TRP C 96 HIS 0.003 0.000 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 (15646) covalent geometry : angle 0.53255 / 0.26 (21201) SS BOND : bond 0.00243 / 0.18 ( 35) SS BOND : angle 0.96293 / 0.70 ( 70) hydrogen bonds : bond 0.03070 / 1.97 ( 483) hydrogen bonds : angle 4.59014 / 3.13 ( 1317) Misc. bond : bond 0.00067 / 0.04 ( 1) link_BETA1-4 : bond 0.00384 / 0.22 ( 11) link_BETA1-4 : angle 1.32666 / 0.90 ( 33) link_NAG-ASN : bond 0.00315 / 0.24 ( 39) link_NAG-ASN : angle 2.13356 / 1.27 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3649.15 seconds wall clock time: 63 minutes 37.60 seconds (3817.60 seconds total)