Starting phenix.real_space_refine on Thu Feb 13 01:10:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mdu_23780/02_2025/7mdu_23780.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mdu_23780/02_2025/7mdu_23780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mdu_23780/02_2025/7mdu_23780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mdu_23780/02_2025/7mdu_23780.map" model { file = "/net/cci-nas-00/data/ceres_data/7mdu_23780/02_2025/7mdu_23780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mdu_23780/02_2025/7mdu_23780.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 5206 2.51 5 N 1387 2.21 5 O 1692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8332 Number of models: 1 Model: "" Number of chains: 17 Chain: "H" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 863 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "A" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3501 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "E" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 934 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "F" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "B" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 980 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.02, per 1000 atoms: 0.72 Number of scatterers: 8332 At special positions: 0 Unit cell: (114.33, 69.01, 149.35, 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 47 16.00 O 1692 8.00 N 1387 7.00 C 5206 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.07 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 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=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.07 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 339 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 448 " " NAG A 607 " - " ASN A 137 " " NAG A 608 " - " ASN A 355 " " NAG A 609 " - " ASN A 398 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 618 " " NAG C 1 " - " ASN A 156 " " NAG D 1 " - " ASN A 197 " " NAG G 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 262 " " NAG J 1 " - " ASN A 276 " " NAG K 1 " - " ASN A 295 " " NAG M 1 " - " ASN A 332 " " NAG N 1 " - " ASN A 386 " " NAG O 1 " - " ASN A 88 " Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 969.7 milliseconds 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1864 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 27 sheets defined 15.9% alpha, 77.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.056A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.971A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 571 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.768A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TRP H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.768A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TRP H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.400A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.849A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.945A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA8, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA9, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.603A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.768A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.678A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 315 through 323 removed outlier: 6.549A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.678A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.768A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.957A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.678A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 271 through 274 removed outlier: 7.683A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 393 through 395 removed outlier: 6.261A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.678A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.957A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 315 through 323 removed outlier: 6.549A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.678A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 393 through 395 removed outlier: 6.261A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.678A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 3 through 8 Processing sheet with id=AC2, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.070A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.103A pdb=" N PHE E 102 " --> pdb=" O THR E 94 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 19 through 24 Processing sheet with id=AC5, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.506A pdb=" N TRP F 35 " --> pdb=" O MET F 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.506A pdb=" N TRP F 35 " --> pdb=" O MET F 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.579A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.689A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.280A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.314A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AC9, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.692A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1131 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: 3.33 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 1706 1.32 - 1.46: 3056 1.46 - 1.60: 3665 1.60 - 1.75: 20 1.75 - 1.89: 54 Bond restraints: 8501 Sorted by residual: bond pdb=" CG GLN L 89 " pdb=" CD GLN L 89 " ideal model delta sigma weight residual 1.516 1.377 0.139 2.50e-02 1.60e+03 3.08e+01 bond pdb=" NE1 TRP B 623 " pdb=" CE2 TRP B 623 " ideal model delta sigma weight residual 1.370 1.311 0.059 1.10e-02 8.26e+03 2.93e+01 bond pdb=" CB TYR L 49 " pdb=" CG TYR L 49 " ideal model delta sigma weight residual 1.512 1.400 0.112 2.20e-02 2.07e+03 2.58e+01 bond pdb=" CG GLU E 6 " pdb=" CD GLU E 6 " ideal model delta sigma weight residual 1.516 1.394 0.122 2.50e-02 1.60e+03 2.38e+01 bond pdb=" CB LEU A 125 " pdb=" CG LEU A 125 " ideal model delta sigma weight residual 1.530 1.433 0.097 2.00e-02 2.50e+03 2.34e+01 ... (remaining 8496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.25: 11170 4.25 - 8.50: 364 8.50 - 12.75: 8 12.75 - 17.00: 1 17.00 - 21.25: 1 Bond angle restraints: 11544 Sorted by residual: angle pdb=" N PRO L 95 " pdb=" CA PRO L 95 " pdb=" C PRO L 95 " ideal model delta sigma weight residual 112.47 91.22 21.25 2.06e+00 2.36e-01 1.06e+02 angle pdb=" N LEU B 544 " pdb=" CA LEU B 544 " pdb=" C LEU B 544 " ideal model delta sigma weight residual 110.48 97.30 13.18 1.48e+00 4.57e-01 7.93e+01 angle pdb=" C GLY H 8 " pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 120.31 128.55 -8.24 9.80e-01 1.04e+00 7.07e+01 angle pdb=" N TYR L 94 " pdb=" CA TYR L 94 " pdb=" C TYR L 94 " ideal model delta sigma weight residual 112.35 123.39 -11.04 1.34e+00 5.57e-01 6.78e+01 angle pdb=" C CYS A 205 " pdb=" N PRO A 206 " pdb=" CA PRO A 206 " ideal model delta sigma weight residual 119.56 127.17 -7.61 1.02e+00 9.61e-01 5.57e+01 ... (remaining 11539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.27: 5313 21.27 - 42.53: 122 42.53 - 63.80: 32 63.80 - 85.07: 14 85.07 - 106.33: 6 Dihedral angle restraints: 5487 sinusoidal: 2576 harmonic: 2911 Sorted by residual: dihedral pdb=" C TYR L 94 " pdb=" N TYR L 94 " pdb=" CA TYR L 94 " pdb=" CB TYR L 94 " ideal model delta harmonic sigma weight residual -122.60 -152.97 30.37 0 2.50e+00 1.60e-01 1.48e+02 dihedral pdb=" N TYR L 94 " pdb=" C TYR L 94 " pdb=" CA TYR L 94 " pdb=" CB TYR L 94 " ideal model delta harmonic sigma weight residual 122.80 150.96 -28.16 0 2.50e+00 1.60e-01 1.27e+02 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.34 -65.34 1 1.00e+01 1.00e-02 5.59e+01 ... (remaining 5484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.262: 1270 0.262 - 0.523: 114 0.523 - 0.785: 0 0.785 - 1.046: 0 1.046 - 1.307: 1 Chirality restraints: 1385 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.46e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.40e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.25e+02 ... (remaining 1382 not shown) Planarity restraints: 1454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " -0.251 2.00e-02 2.50e+03 2.10e-01 5.50e+02 pdb=" C7 NAG C 2 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " -0.171 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " 0.351 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 611 " -0.058 2.00e-02 2.50e+03 6.23e-02 4.85e+01 pdb=" CG ASN B 611 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN B 611 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN B 611 " 0.099 2.00e-02 2.50e+03 pdb=" C1 NAG B 701 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 448 " -0.057 2.00e-02 2.50e+03 5.83e-02 4.25e+01 pdb=" CG ASN A 448 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 448 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 448 " 0.090 2.00e-02 2.50e+03 pdb=" C1 NAG A 606 " -0.070 2.00e-02 2.50e+03 ... (remaining 1451 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2284 2.82 - 3.34: 7324 3.34 - 3.86: 13595 3.86 - 4.38: 16457 4.38 - 4.90: 26559 Nonbonded interactions: 66219 Sorted by model distance: nonbonded pdb=" N LEU B 544 " pdb=" O LEU B 544 " model vdw 2.302 2.496 nonbonded pdb=" O ILE L 2 " pdb=" OG1 THR L 97 " model vdw 2.354 3.040 nonbonded pdb=" N TYR L 50 " pdb=" O TYR L 50 " model vdw 2.375 2.496 nonbonded pdb=" N ASP E 84 " pdb=" OD1 ASP E 84 " model vdw 2.379 3.120 nonbonded pdb=" N ASP E 52A" pdb=" OD1 ASP E 52A" model vdw 2.397 3.120 ... (remaining 66214 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 'C' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.790 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 31.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 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 : 0.023 0.150 8501 Z= 1.496 Angle : 1.758 21.247 11544 Z= 1.159 Chirality : 0.141 1.307 1385 Planarity : 0.010 0.210 1433 Dihedral : 10.793 106.332 3578 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 998 helix: -0.48 (0.39), residues: 146 sheet: 1.14 (0.27), residues: 345 loop : 0.34 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.008 TRP H 47 HIS 0.017 0.002 HIS A 374 PHE 0.034 0.006 PHE L 98 TYR 0.043 0.008 TYR F 36 ARG 0.009 0.001 ARG E 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: H 12 VAL cc_start: 0.6656 (t) cc_final: 0.6436 (t) REVERT: A 142 MET cc_start: 0.8235 (mmm) cc_final: 0.7944 (mmm) REVERT: L 45 LYS cc_start: 0.8840 (tttt) cc_final: 0.8538 (tppt) REVERT: L 72 THR cc_start: 0.8769 (t) cc_final: 0.8537 (m) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2588 time to fit residues: 80.9300 Evaluate side-chains 132 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN A 374 HIS F 17 GLN B 575 GLN B 577 GLN B 607 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.090249 restraints weight = 13742.710| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.44 r_work: 0.2850 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8501 Z= 0.236 Angle : 0.667 9.665 11544 Z= 0.362 Chirality : 0.046 0.236 1385 Planarity : 0.005 0.040 1433 Dihedral : 7.641 83.839 1775 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.82 % Allowed : 8.64 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 998 helix: 1.53 (0.46), residues: 134 sheet: 1.06 (0.28), residues: 323 loop : -0.03 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 47 HIS 0.009 0.001 HIS A 66 PHE 0.016 0.002 PHE H 78 TYR 0.024 0.001 TYR L 94 ARG 0.006 0.001 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 1.008 Fit side-chains REVERT: H 72 ASP cc_start: 0.7559 (t0) cc_final: 0.7351 (t0) REVERT: A 142 MET cc_start: 0.8160 (mmm) cc_final: 0.7846 (mmm) REVERT: A 373 THR cc_start: 0.8732 (m) cc_final: 0.8168 (p) REVERT: F 45 LYS cc_start: 0.8454 (tttt) cc_final: 0.8106 (ttpp) REVERT: L 42 LYS cc_start: 0.8217 (mmmt) cc_final: 0.7962 (mmmt) REVERT: L 45 LYS cc_start: 0.8852 (tttt) cc_final: 0.8230 (tppt) REVERT: L 92 ASN cc_start: 0.8644 (t0) cc_final: 0.8431 (t0) outliers start: 16 outliers final: 13 residues processed: 179 average time/residue: 0.2077 time to fit residues: 51.3945 Evaluate side-chains 136 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 95 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN A 428 GLN E 3 GLN E 73 ASN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.084482 restraints weight = 14194.154| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.49 r_work: 0.2741 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8501 Z= 0.391 Angle : 0.680 8.438 11544 Z= 0.359 Chirality : 0.048 0.268 1385 Planarity : 0.005 0.038 1433 Dihedral : 7.354 73.115 1775 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.52 % Allowed : 10.00 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 998 helix: 1.07 (0.45), residues: 145 sheet: 0.72 (0.29), residues: 312 loop : -0.38 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 103 HIS 0.006 0.002 HIS B 570 PHE 0.019 0.002 PHE H 78 TYR 0.022 0.002 TYR A 318 ARG 0.007 0.001 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.886 Fit side-chains REVERT: H 72 ASP cc_start: 0.7696 (t0) cc_final: 0.7433 (t0) REVERT: H 102 PHE cc_start: 0.8830 (m-80) cc_final: 0.8416 (m-10) REVERT: A 269 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7636 (mt-10) REVERT: F 45 LYS cc_start: 0.8541 (tttt) cc_final: 0.8270 (ttpm) REVERT: F 81 ASP cc_start: 0.7440 (t0) cc_final: 0.7216 (t0) REVERT: L 72 THR cc_start: 0.8936 (t) cc_final: 0.8708 (m) outliers start: 31 outliers final: 24 residues processed: 157 average time/residue: 0.2169 time to fit residues: 46.5945 Evaluate side-chains 146 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 30 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 57 optimal weight: 0.0470 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 66 HIS A 103 GLN A 428 GLN E 81 GLN L 92 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.089349 restraints weight = 13966.228| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.33 r_work: 0.2838 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8501 Z= 0.200 Angle : 0.557 10.252 11544 Z= 0.293 Chirality : 0.044 0.247 1385 Planarity : 0.004 0.040 1433 Dihedral : 6.594 60.407 1775 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.16 % Allowed : 12.16 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 998 helix: 1.29 (0.46), residues: 142 sheet: 0.62 (0.29), residues: 329 loop : -0.56 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 103 HIS 0.003 0.001 HIS B 570 PHE 0.013 0.001 PHE H 78 TYR 0.010 0.001 TYR F 49 ARG 0.003 0.000 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.945 Fit side-chains REVERT: H 72 ASP cc_start: 0.7696 (t0) cc_final: 0.7440 (t0) REVERT: H 102 PHE cc_start: 0.8783 (m-80) cc_final: 0.8533 (m-10) REVERT: A 211 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7960 (mm-30) REVERT: A 318 TYR cc_start: 0.8901 (m-80) cc_final: 0.8699 (m-80) REVERT: F 33 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8326 (m) REVERT: F 45 LYS cc_start: 0.8541 (tttt) cc_final: 0.8085 (ttpp) outliers start: 19 outliers final: 12 residues processed: 147 average time/residue: 0.2180 time to fit residues: 43.3946 Evaluate side-chains 136 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 69 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 0.0040 chunk 65 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.090189 restraints weight = 13967.145| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.36 r_work: 0.2872 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8501 Z= 0.177 Angle : 0.547 11.555 11544 Z= 0.284 Chirality : 0.043 0.219 1385 Planarity : 0.004 0.040 1433 Dihedral : 6.110 58.772 1775 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.39 % Allowed : 12.27 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 998 helix: 1.40 (0.46), residues: 142 sheet: 0.64 (0.30), residues: 304 loop : -0.53 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 34 HIS 0.005 0.001 HIS B 570 PHE 0.013 0.001 PHE H 78 TYR 0.022 0.001 TYR A 484 ARG 0.003 0.000 ARG F 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: H 45 LEU cc_start: 0.8519 (mt) cc_final: 0.8197 (mt) REVERT: H 102 PHE cc_start: 0.8781 (m-80) cc_final: 0.8535 (m-10) REVERT: A 211 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7997 (mm-30) REVERT: A 318 TYR cc_start: 0.8891 (m-80) cc_final: 0.8658 (m-80) REVERT: F 33 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8303 (m) REVERT: F 45 LYS cc_start: 0.8535 (tttt) cc_final: 0.8284 (ptmt) outliers start: 21 outliers final: 16 residues processed: 143 average time/residue: 0.2175 time to fit residues: 42.2696 Evaluate side-chains 142 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 40 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.086585 restraints weight = 14120.891| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.31 r_work: 0.2810 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8501 Z= 0.354 Angle : 0.630 11.542 11544 Z= 0.324 Chirality : 0.045 0.151 1385 Planarity : 0.004 0.042 1433 Dihedral : 5.633 33.979 1775 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.84 % Allowed : 12.61 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.26), residues: 998 helix: 1.51 (0.46), residues: 139 sheet: 0.60 (0.30), residues: 313 loop : -0.76 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 103 HIS 0.005 0.001 HIS A 330 PHE 0.019 0.002 PHE H 78 TYR 0.016 0.002 TYR A 191 ARG 0.005 0.001 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: H 102 PHE cc_start: 0.8883 (m-80) cc_final: 0.8638 (m-10) REVERT: A 318 TYR cc_start: 0.8950 (m-80) cc_final: 0.8749 (m-80) REVERT: L 105 GLU cc_start: 0.1766 (OUTLIER) cc_final: 0.0681 (tp30) outliers start: 25 outliers final: 22 residues processed: 145 average time/residue: 0.2230 time to fit residues: 44.0732 Evaluate side-chains 144 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 94 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 23 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 103 GLN A 425 ASN B 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.089918 restraints weight = 14009.186| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.34 r_work: 0.2868 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8501 Z= 0.159 Angle : 0.534 11.106 11544 Z= 0.278 Chirality : 0.042 0.149 1385 Planarity : 0.004 0.038 1433 Dihedral : 5.109 33.577 1775 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.95 % Allowed : 13.75 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.27), residues: 998 helix: 1.79 (0.47), residues: 139 sheet: 0.59 (0.30), residues: 313 loop : -0.65 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 34 HIS 0.004 0.001 HIS A 72 PHE 0.012 0.001 PHE H 78 TYR 0.021 0.001 TYR A 484 ARG 0.002 0.000 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: H 102 PHE cc_start: 0.8764 (m-80) cc_final: 0.8483 (m-10) REVERT: A 411 ASN cc_start: 0.7906 (m-40) cc_final: 0.6947 (p0) REVERT: F 33 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8311 (m) REVERT: B 624 ASP cc_start: 0.8960 (m-30) cc_final: 0.8751 (m-30) outliers start: 26 outliers final: 16 residues processed: 153 average time/residue: 0.2148 time to fit residues: 44.8706 Evaluate side-chains 145 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 46 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.087941 restraints weight = 14143.279| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.38 r_work: 0.2835 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8501 Z= 0.267 Angle : 0.573 10.866 11544 Z= 0.297 Chirality : 0.044 0.149 1385 Planarity : 0.004 0.040 1433 Dihedral : 5.278 34.213 1775 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.73 % Allowed : 13.64 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.27), residues: 998 helix: 1.75 (0.46), residues: 139 sheet: 0.47 (0.29), residues: 319 loop : -0.67 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 34 HIS 0.003 0.001 HIS B 570 PHE 0.016 0.002 PHE H 78 TYR 0.017 0.001 TYR A 318 ARG 0.004 0.000 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 1.086 Fit side-chains REVERT: H 102 PHE cc_start: 0.8785 (m-80) cc_final: 0.8446 (m-10) REVERT: A 373 THR cc_start: 0.8916 (m) cc_final: 0.8369 (p) REVERT: A 411 ASN cc_start: 0.7820 (m-40) cc_final: 0.6905 (p0) REVERT: F 33 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8299 (m) outliers start: 24 outliers final: 20 residues processed: 142 average time/residue: 0.2226 time to fit residues: 43.6880 Evaluate side-chains 145 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 72 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.089126 restraints weight = 14233.091| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.38 r_work: 0.2861 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8501 Z= 0.199 Angle : 0.539 10.473 11544 Z= 0.280 Chirality : 0.043 0.147 1385 Planarity : 0.004 0.039 1433 Dihedral : 5.108 36.413 1775 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.84 % Allowed : 13.86 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.27), residues: 998 helix: 1.86 (0.46), residues: 139 sheet: 0.46 (0.29), residues: 319 loop : -0.65 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 34 HIS 0.002 0.001 HIS B 570 PHE 0.013 0.001 PHE H 78 TYR 0.021 0.001 TYR A 484 ARG 0.003 0.000 ARG F 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.915 Fit side-chains REVERT: H 102 PHE cc_start: 0.8754 (m-80) cc_final: 0.8407 (m-10) REVERT: A 411 ASN cc_start: 0.7914 (m-40) cc_final: 0.6998 (p0) REVERT: F 33 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8311 (m) REVERT: L 4 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7295 (ptm) REVERT: L 105 GLU cc_start: 0.2063 (OUTLIER) cc_final: 0.1095 (tp30) outliers start: 25 outliers final: 20 residues processed: 147 average time/residue: 0.2204 time to fit residues: 44.1035 Evaluate side-chains 151 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 19 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 56 optimal weight: 0.0470 chunk 34 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN F 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.115512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.090741 restraints weight = 14223.879| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.34 r_work: 0.2885 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8501 Z= 0.157 Angle : 0.516 10.268 11544 Z= 0.269 Chirality : 0.042 0.145 1385 Planarity : 0.004 0.037 1433 Dihedral : 4.800 36.026 1775 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.50 % Allowed : 14.09 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.27), residues: 998 helix: 2.01 (0.47), residues: 139 sheet: 0.43 (0.30), residues: 310 loop : -0.56 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 36 HIS 0.003 0.001 HIS B 570 PHE 0.010 0.001 PHE H 78 TYR 0.012 0.001 TYR A 191 ARG 0.003 0.000 ARG F 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.817 Fit side-chains REVERT: H 76 ASN cc_start: 0.8390 (m-40) cc_final: 0.8189 (m110) REVERT: H 102 PHE cc_start: 0.8699 (m-80) cc_final: 0.8364 (m-10) REVERT: A 111 LEU cc_start: 0.8870 (tp) cc_final: 0.8531 (mt) REVERT: A 211 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7943 (mm-30) REVERT: A 411 ASN cc_start: 0.7871 (m-40) cc_final: 0.6964 (p0) REVERT: F 33 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8279 (m) REVERT: L 4 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7211 (ptm) REVERT: B 624 ASP cc_start: 0.8855 (m-30) cc_final: 0.8649 (m-30) outliers start: 22 outliers final: 18 residues processed: 153 average time/residue: 0.2133 time to fit residues: 44.6338 Evaluate side-chains 152 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 38 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 4 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN E 3 GLN F 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.113226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.088079 restraints weight = 14321.436| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.40 r_work: 0.2831 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8501 Z= 0.306 Angle : 0.592 10.515 11544 Z= 0.302 Chirality : 0.044 0.182 1385 Planarity : 0.004 0.036 1433 Dihedral : 5.081 36.196 1775 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.73 % Allowed : 14.32 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.27), residues: 998 helix: 1.71 (0.46), residues: 140 sheet: 0.41 (0.29), residues: 324 loop : -0.70 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 34 HIS 0.003 0.001 HIS A 330 PHE 0.015 0.002 PHE H 78 TYR 0.022 0.002 TYR A 484 ARG 0.005 0.000 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4427.65 seconds wall clock time: 79 minutes 31.81 seconds (4771.81 seconds total)