Starting phenix.real_space_refine on Thu Jan 18 09:00:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdu_23780/01_2024/7mdu_23780.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdu_23780/01_2024/7mdu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdu_23780/01_2024/7mdu_23780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdu_23780/01_2024/7mdu_23780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdu_23780/01_2024/7mdu_23780.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdu_23780/01_2024/7mdu_23780.pdb" } 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 Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 55": "OE1" <-> "OE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 9 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: 5.07, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 3.72 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.38 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: 3.69 Time building geometry restraints manager: 4.01 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: 91.22 - 99.84: 8 99.84 - 108.46: 935 108.46 - 117.08: 5333 117.08 - 125.70: 5086 125.70 - 134.32: 182 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: 5277 21.27 - 42.53: 120 42.53 - 63.80: 32 63.80 - 85.07: 14 85.07 - 106.33: 6 Dihedral angle restraints: 5449 sinusoidal: 2538 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 5446 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 2.440 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 2.520 nonbonded pdb=" N ASP E 52A" pdb=" OD1 ASP E 52A" model vdw 2.397 2.520 ... (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 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: 4.810 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: 0.000 Extract box with map and model: 10.500 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 28.350 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.930 ------------------------------------------------------------------------------- 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 : 10.830 106.332 3540 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 fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 0.950 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: 0.2568 time to fit residues: 79.8902 Evaluate side-chains 132 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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: 8.9990 chunk 75 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS F 17 GLN B 575 GLN B 577 GLN B 607 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8501 Z= 0.226 Angle : 0.647 9.420 11544 Z= 0.348 Chirality : 0.046 0.214 1385 Planarity : 0.005 0.048 1433 Dihedral : 7.708 82.879 1737 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.27 % Allowed : 8.30 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.73 (0.26), residues: 998 helix: 1.51 (0.46), residues: 134 sheet: 1.07 (0.29), residues: 321 loop : -0.09 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.005 0.001 HIS A 66 PHE 0.014 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 187 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 167 time to evaluate : 0.963 Fit side-chains REVERT: A 373 THR cc_start: 0.8455 (m) cc_final: 0.8117 (p) REVERT: F 45 LYS cc_start: 0.8403 (tttt) cc_final: 0.8200 (ttpp) REVERT: F 81 ASP cc_start: 0.7552 (t0) cc_final: 0.7305 (t0) REVERT: L 45 LYS cc_start: 0.8923 (tttt) cc_final: 0.8543 (tppt) outliers start: 20 outliers final: 17 residues processed: 180 average time/residue: 0.2064 time to fit residues: 50.8676 Evaluate side-chains 135 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 E residue 76 ASN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 85 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 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 49 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 89 optimal weight: 0.0070 chunk 30 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.9804 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 293 GLN A 428 GLN E 3 GLN L 38 GLN L 92 ASN B 575 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3083 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= 0.192 Angle : 0.552 9.693 11544 Z= 0.294 Chirality : 0.044 0.235 1385 Planarity : 0.004 0.036 1433 Dihedral : 6.789 72.655 1737 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.50 % Allowed : 10.57 % Favored : 86.93 % 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: 0.47 (0.26), residues: 998 helix: 1.29 (0.45), residues: 145 sheet: 0.76 (0.29), residues: 327 loop : -0.19 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS B 570 PHE 0.015 0.002 PHE H 78 TYR 0.017 0.001 TYR A 318 ARG 0.005 0.001 ARG F 103 *********************** 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 159 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 0.996 Fit side-chains REVERT: A 111 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8540 (mp) REVERT: A 269 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: F 81 ASP cc_start: 0.7546 (t0) cc_final: 0.7300 (t0) REVERT: L 45 LYS cc_start: 0.8954 (tttt) cc_final: 0.8569 (tppt) REVERT: L 72 THR cc_start: 0.8975 (t) cc_final: 0.8766 (m) outliers start: 22 outliers final: 13 residues processed: 150 average time/residue: 0.2126 time to fit residues: 44.0514 Evaluate side-chains 139 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 111 LEU Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain L residue 11 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 88 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 42 optimal weight: 0.2980 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 428 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8501 Z= 0.340 Angle : 0.625 9.176 11544 Z= 0.323 Chirality : 0.046 0.313 1385 Planarity : 0.004 0.042 1433 Dihedral : 6.627 57.458 1737 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.41 % Allowed : 10.45 % Favored : 86.14 % 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: 0.20 (0.26), residues: 998 helix: 1.11 (0.46), residues: 142 sheet: 0.80 (0.29), residues: 310 loop : -0.51 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 103 HIS 0.004 0.001 HIS A 330 PHE 0.018 0.002 PHE H 78 TYR 0.018 0.002 TYR A 191 ARG 0.006 0.001 ARG B 617 *********************** 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 160 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 0.950 Fit side-chains REVERT: A 269 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: A 373 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8300 (p) REVERT: F 33 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.8064 (m) REVERT: F 81 ASP cc_start: 0.7571 (t0) cc_final: 0.7293 (t0) REVERT: L 72 THR cc_start: 0.9012 (t) cc_final: 0.8809 (m) outliers start: 30 outliers final: 21 residues processed: 151 average time/residue: 0.2197 time to fit residues: 44.9731 Evaluate side-chains 149 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 136 ASN Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain B residue 636 SER 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 79 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN A 188 ASN A 428 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 8501 Z= 0.448 Angle : 0.681 9.180 11544 Z= 0.350 Chirality : 0.048 0.185 1385 Planarity : 0.005 0.044 1433 Dihedral : 6.500 45.763 1737 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.98 % Allowed : 10.68 % 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: -0.17 (0.26), residues: 998 helix: 1.12 (0.46), residues: 136 sheet: 0.53 (0.30), residues: 305 loop : -0.79 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 103 HIS 0.006 0.002 HIS A 330 PHE 0.023 0.002 PHE H 102 TYR 0.019 0.002 TYR A 318 ARG 0.006 0.001 ARG B 617 *********************** 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 160 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 125 time to evaluate : 1.044 Fit side-chains REVERT: A 141 ASP cc_start: 0.7227 (p0) cc_final: 0.7007 (p0) REVERT: A 269 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: A 373 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8367 (p) REVERT: F 81 ASP cc_start: 0.7707 (t0) cc_final: 0.7324 (t0) outliers start: 35 outliers final: 28 residues processed: 150 average time/residue: 0.2155 time to fit residues: 43.8640 Evaluate side-chains 148 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 118 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 80 LEU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 111 VAL 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 323 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 MET 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 E residue 77 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 31 ASN 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 32 optimal weight: 0.3980 chunk 86 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 0.0770 chunk 23 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN A 188 ASN A 348 GLN L 92 ASN B 575 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8501 Z= 0.151 Angle : 0.543 9.188 11544 Z= 0.283 Chirality : 0.042 0.152 1385 Planarity : 0.004 0.041 1433 Dihedral : 5.690 36.484 1737 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.30 % Allowed : 11.70 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.05 (0.27), residues: 998 helix: 1.62 (0.47), residues: 136 sheet: 0.60 (0.30), residues: 312 loop : -0.71 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 96 HIS 0.003 0.001 HIS B 570 PHE 0.011 0.001 PHE H 78 TYR 0.018 0.001 TYR A 191 ARG 0.002 0.000 ARG A 419 *********************** 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 160 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 0.947 Fit side-chains REVERT: H 1 GLN cc_start: 0.6888 (pm20) cc_final: 0.6682 (pm20) REVERT: H 101 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7248 (m-30) REVERT: A 269 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: A 318 TYR cc_start: 0.8658 (m-80) cc_final: 0.8457 (m-80) REVERT: A 373 THR cc_start: 0.8478 (m) cc_final: 0.8134 (p) REVERT: A 411 ASN cc_start: 0.7787 (m-40) cc_final: 0.6957 (p0) REVERT: F 33 VAL cc_start: 0.8324 (OUTLIER) cc_final: 0.8103 (m) REVERT: F 81 ASP cc_start: 0.7623 (t0) cc_final: 0.7266 (t0) outliers start: 29 outliers final: 19 residues processed: 149 average time/residue: 0.2148 time to fit residues: 43.8059 Evaluate side-chains 145 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL 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 101 ASP Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 125 LEU 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 A residue 426 MET Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain B residue 595 ILE 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 92 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 428 GLN L 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8501 Z= 0.326 Angle : 0.608 8.363 11544 Z= 0.313 Chirality : 0.045 0.149 1385 Planarity : 0.004 0.041 1433 Dihedral : 5.967 37.770 1737 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.41 % Allowed : 12.73 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 998 helix: 1.56 (0.46), residues: 139 sheet: 0.58 (0.30), residues: 307 loop : -0.79 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 34 HIS 0.004 0.001 HIS A 66 PHE 0.018 0.002 PHE H 78 TYR 0.014 0.001 TYR A 191 ARG 0.004 0.001 ARG B 617 *********************** 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 155 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 0.884 Fit side-chains REVERT: H 1 GLN cc_start: 0.6909 (pm20) cc_final: 0.6648 (pm20) REVERT: A 269 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7674 (mt-10) REVERT: A 373 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8232 (p) REVERT: F 81 ASP cc_start: 0.7601 (t0) cc_final: 0.7210 (t0) outliers start: 30 outliers final: 21 residues processed: 143 average time/residue: 0.2095 time to fit residues: 40.8212 Evaluate side-chains 144 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL 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 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 A residue 373 THR Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 31 ASN 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 56 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 188 ASN A 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8501 Z= 0.156 Angle : 0.518 8.048 11544 Z= 0.270 Chirality : 0.042 0.146 1385 Planarity : 0.004 0.039 1433 Dihedral : 5.306 40.804 1737 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.07 % Allowed : 12.84 % Favored : 84.09 % 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 (0.27), residues: 998 helix: 1.96 (0.47), residues: 133 sheet: 0.60 (0.31), residues: 300 loop : -0.65 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 479 HIS 0.003 0.001 HIS A 66 PHE 0.012 0.001 PHE H 78 TYR 0.015 0.001 TYR A 318 ARG 0.003 0.000 ARG A 419 *********************** 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 159 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 132 time to evaluate : 0.888 Fit side-chains REVERT: H 101 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7177 (m-30) REVERT: A 246 GLN cc_start: 0.7026 (pm20) cc_final: 0.6227 (mm-40) REVERT: A 373 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8063 (p) REVERT: A 411 ASN cc_start: 0.7889 (m-40) cc_final: 0.7068 (p0) REVERT: F 81 ASP cc_start: 0.7539 (t0) cc_final: 0.7204 (t0) REVERT: L 38 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: B 535 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.7978 (mmm) outliers start: 27 outliers final: 18 residues processed: 147 average time/residue: 0.2086 time to fit residues: 41.8897 Evaluate side-chains 151 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL 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 101 ASP Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain B residue 535 MET 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 88 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 27 optimal weight: 0.0070 chunk 80 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- 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 188 ASN F 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.4198 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= 0.183 Angle : 0.527 7.603 11544 Z= 0.273 Chirality : 0.042 0.145 1385 Planarity : 0.004 0.038 1433 Dihedral : 5.117 40.589 1737 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.73 % Allowed : 13.75 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.27), residues: 998 helix: 2.13 (0.47), residues: 133 sheet: 0.57 (0.31), residues: 302 loop : -0.65 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.003 0.001 HIS A 66 PHE 0.011 0.001 PHE H 78 TYR 0.014 0.001 TYR E 91 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 153 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.049 Fit side-chains REVERT: H 101 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7257 (m-30) REVERT: A 246 GLN cc_start: 0.7012 (pm20) cc_final: 0.6193 (mm-40) REVERT: A 268 GLU cc_start: 0.8012 (pm20) cc_final: 0.7741 (tt0) REVERT: A 318 TYR cc_start: 0.8657 (m-80) cc_final: 0.8456 (m-80) REVERT: A 373 THR cc_start: 0.8379 (m) cc_final: 0.8044 (p) REVERT: A 411 ASN cc_start: 0.7909 (m-40) cc_final: 0.7083 (p0) REVERT: F 81 ASP cc_start: 0.7561 (t0) cc_final: 0.7138 (t0) REVERT: L 38 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7130 (tt0) REVERT: B 535 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.7960 (mmm) outliers start: 24 outliers final: 17 residues processed: 141 average time/residue: 0.2349 time to fit residues: 45.0196 Evaluate side-chains 149 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 101 ASP Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain B residue 535 MET 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 44 optimal weight: 0.8980 chunk 65 optimal weight: 0.2980 chunk 98 optimal weight: 0.7980 chunk 90 optimal weight: 0.2980 chunk 78 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 0.0040 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 188 ASN F 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8501 Z= 0.135 Angle : 0.488 7.432 11544 Z= 0.254 Chirality : 0.041 0.144 1385 Planarity : 0.004 0.037 1433 Dihedral : 4.569 40.594 1737 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.73 % Allowed : 13.52 % Favored : 83.75 % 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: 0.39 (0.27), residues: 998 helix: 2.47 (0.48), residues: 127 sheet: 0.73 (0.31), residues: 299 loop : -0.50 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 479 HIS 0.003 0.001 HIS A 66 PHE 0.007 0.001 PHE E 29 TYR 0.012 0.001 TYR E 91 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 167 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 143 time to evaluate : 0.945 Fit side-chains REVERT: A 246 GLN cc_start: 0.6959 (pm20) cc_final: 0.6150 (mm-40) REVERT: A 411 ASN cc_start: 0.7845 (m-40) cc_final: 0.7037 (p0) REVERT: B 535 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.7888 (mmm) outliers start: 24 outliers final: 20 residues processed: 155 average time/residue: 0.2145 time to fit residues: 45.3840 Evaluate side-chains 151 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 101 ASP Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain B residue 535 MET 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 72 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 21 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 32 optimal weight: 0.0970 chunk 80 optimal weight: 0.1980 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 4 optimal weight: 0.0870 chunk 56 optimal weight: 0.3980 overall best weight: 0.2156 ------------------------------------------------------------------------------- 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 188 ASN F 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.093698 restraints weight = 13918.596| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.36 r_work: 0.2919 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8501 Z= 0.132 Angle : 0.492 7.197 11544 Z= 0.256 Chirality : 0.041 0.146 1385 Planarity : 0.004 0.032 1433 Dihedral : 4.343 38.793 1737 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.05 % Allowed : 14.43 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.27), residues: 998 helix: 2.50 (0.48), residues: 127 sheet: 0.83 (0.31), residues: 311 loop : -0.51 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 103 HIS 0.003 0.000 HIS B 570 PHE 0.010 0.001 PHE H 102 TYR 0.014 0.001 TYR E 91 ARG 0.006 0.000 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2181.28 seconds wall clock time: 40 minutes 15.31 seconds (2415.31 seconds total)