Starting phenix.real_space_refine on Thu Jul 31 08:39:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p8a_17543/07_2025/8p8a_17543.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p8a_17543/07_2025/8p8a_17543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p8a_17543/07_2025/8p8a_17543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p8a_17543/07_2025/8p8a_17543.map" model { file = "/net/cci-nas-00/data/ceres_data/8p8a_17543/07_2025/8p8a_17543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p8a_17543/07_2025/8p8a_17543.cif" } resolution = 3.2 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 73 5.16 5 C 8575 2.51 5 N 2212 2.21 5 O 2477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13337 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "Z" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 926 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "A" Number of atoms: 4415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4415 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 19, 'TRANS': 547} Chain breaks: 3 Chain: "B" Number of atoms: 4440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4440 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 19, 'TRANS': 551} Chain breaks: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 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 Time building chain proxies: 9.58, per 1000 atoms: 0.72 Number of scatterers: 13337 At special positions: 0 Unit cell: (141.12, 112.56, 159.6, 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 73 16.00 O 2477 8.00 N 2212 7.00 C 8575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG G 1 " - " ASN A 596 " " NAG H 1 " - " ASN B 596 " Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.8 seconds 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3122 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 14 sheets defined 39.2% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 85 through 94 removed outlier: 3.843A pdb=" N LEU A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 153 through 168 Processing helix chain 'A' and resid 187 through 198 removed outlier: 3.847A pdb=" N LYS A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 removed outlier: 4.004A pdb=" N LYS A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 271 through 278 removed outlier: 4.014A pdb=" N GLU A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 300 removed outlier: 3.813A pdb=" N ASN A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 337 Processing helix chain 'A' and resid 341 through 351 removed outlier: 3.822A pdb=" N THR A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 390 removed outlier: 3.536A pdb=" N GLN A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 413 Processing helix chain 'A' and resid 421 through 441 removed outlier: 3.846A pdb=" N ASN A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N CYS A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.607A pdb=" N VAL A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU A 446 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A 447 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 465 through 478 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 483 through 498 removed outlier: 4.040A pdb=" N ILE A 487 " --> pdb=" O MET A 483 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 529 removed outlier: 3.662A pdb=" N MET A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 549 removed outlier: 3.595A pdb=" N THR A 538 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 553 removed outlier: 4.213A pdb=" N GLY A 553 " --> pdb=" O ILE A 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 550 through 553' Processing helix chain 'A' and resid 565 through 571 removed outlier: 3.620A pdb=" N TYR A 570 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 587 removed outlier: 4.119A pdb=" N LEU A 587 " --> pdb=" O HIS A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 618 removed outlier: 3.574A pdb=" N TYR A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 650 removed outlier: 4.341A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 94 removed outlier: 3.843A pdb=" N LEU B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 148 Processing helix chain 'B' and resid 153 through 168 Processing helix chain 'B' and resid 187 through 198 removed outlier: 3.847A pdb=" N LYS B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 removed outlier: 4.004A pdb=" N LYS B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 271 through 278 removed outlier: 3.961A pdb=" N GLU B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 298 Processing helix chain 'B' and resid 328 through 337 Processing helix chain 'B' and resid 341 through 351 removed outlier: 3.822A pdb=" N THR B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 390 removed outlier: 3.537A pdb=" N GLN B 376 " --> pdb=" O SER B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 413 Processing helix chain 'B' and resid 421 through 441 removed outlier: 3.846A pdb=" N ASN B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N CYS B 438 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 448 removed outlier: 3.607A pdb=" N VAL B 445 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU B 446 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU B 447 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 465 through 478 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 483 through 498 removed outlier: 4.042A pdb=" N ILE B 487 " --> pdb=" O MET B 483 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 529 removed outlier: 3.662A pdb=" N MET B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 549 removed outlier: 3.595A pdb=" N THR B 538 " --> pdb=" O VAL B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 553 removed outlier: 4.212A pdb=" N GLY B 553 " --> pdb=" O ILE B 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 550 through 553' Processing helix chain 'B' and resid 565 through 571 removed outlier: 3.620A pdb=" N TYR B 570 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 587 removed outlier: 4.119A pdb=" N LEU B 587 " --> pdb=" O HIS B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 618 removed outlier: 3.574A pdb=" N TYR B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 650 removed outlier: 4.341A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.508A pdb=" N THR C 72 " --> pdb=" O THR C 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.534A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N SER C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.568A pdb=" N GLN D 5 " --> pdb=" O THR D 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.764A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR D 51 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TRP D 35 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.508A pdb=" N THR E 72 " --> pdb=" O THR E 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.535A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N SER E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU E 33 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.567A pdb=" N GLN F 5 " --> pdb=" O THR F 23 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.762A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR F 51 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TRP F 35 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Z' and resid 3 through 5 removed outlier: 3.639A pdb=" N LEU Z 81 " --> pdb=" O LEU Z 20 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR Z 78 " --> pdb=" O ASP Z 73 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP Z 73 " --> pdb=" O THR Z 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Z' and resid 58 through 60 removed outlier: 6.825A pdb=" N TRP Z 36 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALA Z 50 " --> pdb=" O MET Z 34 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N MET Z 34 " --> pdb=" O ALA Z 50 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY Z 35 " --> pdb=" O ALA Z 97 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA Z 97 " --> pdb=" O GLY Z 35 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA Z 92 " --> pdb=" O VAL Z 119 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 68 through 71 removed outlier: 3.509A pdb=" N ASP A 105 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 122 through 124 removed outlier: 5.903A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER A 255 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A 266 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 68 through 71 removed outlier: 3.509A pdb=" N ASP B 105 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 122 through 124 removed outlier: 5.904A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER B 255 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE B 266 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) 608 hydrogen bonds defined for protein. 1719 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: 4.07 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3866 1.34 - 1.46: 2722 1.46 - 1.58: 6921 1.58 - 1.69: 6 1.69 - 1.81: 114 Bond restraints: 13629 Sorted by residual: bond pdb=" CA GLN A 181 " pdb=" C GLN A 181 " ideal model delta sigma weight residual 1.523 1.569 -0.046 1.34e-02 5.57e+03 1.17e+01 bond pdb=" CA GLN B 181 " pdb=" C GLN B 181 " ideal model delta sigma weight residual 1.523 1.569 -0.046 1.34e-02 5.57e+03 1.16e+01 bond pdb=" C LYS Z 87 " pdb=" N PRO Z 88 " ideal model delta sigma weight residual 1.337 1.366 -0.030 9.80e-03 1.04e+04 9.21e+00 bond pdb=" N VAL Z 2 " pdb=" CA VAL Z 2 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.74e+00 bond pdb=" N ASP Z 111 " pdb=" CA ASP Z 111 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.15e-02 7.56e+03 7.93e+00 ... (remaining 13624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.95: 18302 3.95 - 7.90: 136 7.90 - 11.84: 20 11.84 - 15.79: 3 15.79 - 19.74: 2 Bond angle restraints: 18463 Sorted by residual: angle pdb=" N ILE B 335 " pdb=" CA ILE B 335 " pdb=" C ILE B 335 " ideal model delta sigma weight residual 113.39 99.49 13.90 1.47e+00 4.63e-01 8.95e+01 angle pdb=" CB LYS B 61 " pdb=" CG LYS B 61 " pdb=" CD LYS B 61 " ideal model delta sigma weight residual 111.30 131.04 -19.74 2.30e+00 1.89e-01 7.37e+01 angle pdb=" CB LYS A 61 " pdb=" CG LYS A 61 " pdb=" CD LYS A 61 " ideal model delta sigma weight residual 111.30 131.00 -19.70 2.30e+00 1.89e-01 7.34e+01 angle pdb=" CA LYS A 61 " pdb=" CB LYS A 61 " pdb=" CG LYS A 61 " ideal model delta sigma weight residual 114.10 125.55 -11.45 2.00e+00 2.50e-01 3.28e+01 angle pdb=" CA LYS B 61 " pdb=" CB LYS B 61 " pdb=" CG LYS B 61 " ideal model delta sigma weight residual 114.10 125.52 -11.42 2.00e+00 2.50e-01 3.26e+01 ... (remaining 18458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7072 17.95 - 35.89: 662 35.89 - 53.84: 238 53.84 - 71.78: 88 71.78 - 89.73: 17 Dihedral angle restraints: 8077 sinusoidal: 3182 harmonic: 4895 Sorted by residual: dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS B 603 " pdb=" CB CYS B 603 " ideal model delta sinusoidal sigma weight residual -86.00 -10.95 -75.05 1 1.00e+01 1.00e-02 7.12e+01 dihedral pdb=" CA GLU A 334 " pdb=" C GLU A 334 " pdb=" N ILE A 335 " pdb=" CA ILE A 335 " ideal model delta harmonic sigma weight residual 180.00 145.44 34.56 0 5.00e+00 4.00e-02 4.78e+01 dihedral pdb=" CA ASN A 604 " pdb=" C ASN A 604 " pdb=" N TYR A 605 " pdb=" CA TYR A 605 " ideal model delta harmonic sigma weight residual 180.00 -151.29 -28.71 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 8074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1823 0.077 - 0.155: 249 0.155 - 0.232: 29 0.232 - 0.309: 2 0.309 - 0.387: 3 Chirality restraints: 2106 Sorted by residual: chirality pdb=" CB THR B 607 " pdb=" CA THR B 607 " pdb=" OG1 THR B 607 " pdb=" CG2 THR B 607 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CB THR A 607 " pdb=" CA THR A 607 " pdb=" OG1 THR A 607 " pdb=" CG2 THR A 607 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CA ILE B 335 " pdb=" N ILE B 335 " pdb=" C ILE B 335 " pdb=" CB ILE B 335 " both_signs ideal model delta sigma weight residual False 2.43 2.79 -0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 2103 not shown) Planarity restraints: 2313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 87 " -0.052 5.00e-02 4.00e+02 7.82e-02 9.78e+00 pdb=" N PRO F 88 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO F 88 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 88 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 87 " 0.052 5.00e-02 4.00e+02 7.82e-02 9.77e+00 pdb=" N PRO D 88 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 159 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" CD GLU A 159 " -0.042 2.00e-02 2.50e+03 pdb=" OE1 GLU A 159 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU A 159 " 0.015 2.00e-02 2.50e+03 ... (remaining 2310 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1637 2.75 - 3.29: 11702 3.29 - 3.83: 21173 3.83 - 4.36: 25009 4.36 - 4.90: 45400 Nonbonded interactions: 104921 Sorted by model distance: nonbonded pdb=" O ASN B 436 " pdb=" OG SER B 440 " model vdw 2.213 3.040 nonbonded pdb=" O ASN A 436 " pdb=" OG SER A 440 " model vdw 2.214 3.040 nonbonded pdb=" O GLY Z 30 " pdb=" OG1 THR Z 53 " model vdw 2.240 3.040 nonbonded pdb=" O MET Z 103 " pdb=" OH TYR Z 110 " model vdw 2.299 3.040 nonbonded pdb=" O PHE B 293 " pdb=" CG2 ILE B 297 " model vdw 2.307 3.460 ... (remaining 104916 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 33 through 301 or resid 327 through 654)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 7.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.850 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 : 0.006 0.076 13641 Z= 0.309 Angle : 1.020 19.740 18491 Z= 0.566 Chirality : 0.057 0.387 2106 Planarity : 0.007 0.078 2311 Dihedral : 17.655 89.726 4931 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.25 % Favored : 92.69 % Rotamer: Outliers : 10.55 % Allowed : 7.66 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.83 (0.16), residues: 1683 helix: -2.07 (0.16), residues: 613 sheet: -2.02 (0.27), residues: 298 loop : -3.13 (0.18), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 379 HIS 0.018 0.003 HIS A 350 PHE 0.025 0.002 PHE A 489 TYR 0.029 0.002 TYR F 51 ARG 0.005 0.001 ARG B 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 2) link_NAG-ASN : angle 3.73755 ( 6) link_BETA1-4 : bond 0.00449 ( 2) link_BETA1-4 : angle 2.60531 ( 6) hydrogen bonds : bond 0.19045 ( 608) hydrogen bonds : angle 7.04865 ( 1719) SS BOND : bond 0.00642 ( 8) SS BOND : angle 3.03581 ( 16) covalent geometry : bond 0.00649 (13629) covalent geometry : angle 1.01334 (18463) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 307 time to evaluate : 1.378 Fit side-chains REVERT: E 79 GLN cc_start: 0.6783 (mt0) cc_final: 0.6508 (tt0) REVERT: F 69 SER cc_start: 0.8885 (t) cc_final: 0.8641 (t) REVERT: F 78 GLN cc_start: 0.8840 (mt0) cc_final: 0.8567 (mt0) REVERT: F 89 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6650 (mm-30) REVERT: Z 19 ARG cc_start: 0.7793 (ttt90) cc_final: 0.7201 (ptm-80) REVERT: Z 111 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7910 (p0) REVERT: A 87 SER cc_start: 0.8947 (OUTLIER) cc_final: 0.8568 (m) REVERT: A 177 LYS cc_start: 0.7386 (mmtp) cc_final: 0.6937 (mtmt) REVERT: A 218 SER cc_start: 0.8201 (OUTLIER) cc_final: 0.7863 (m) REVERT: A 226 LEU cc_start: 0.8427 (mm) cc_final: 0.8218 (mp) REVERT: A 378 ARG cc_start: 0.6923 (ttp-170) cc_final: 0.6165 (mmt-90) REVERT: A 393 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6704 (tm-30) REVERT: A 417 LYS cc_start: 0.8460 (pttt) cc_final: 0.7916 (mmtm) REVERT: A 611 GLU cc_start: 0.8141 (mp0) cc_final: 0.7891 (mp0) REVERT: B 263 ARG cc_start: 0.7575 (mmm-85) cc_final: 0.7367 (mmm160) REVERT: B 285 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6396 (mp0) REVERT: B 375 HIS cc_start: 0.7530 (t70) cc_final: 0.7082 (t-170) REVERT: B 378 ARG cc_start: 0.7082 (ttp-170) cc_final: 0.6866 (ttp-110) REVERT: B 395 SER cc_start: 0.8152 (OUTLIER) cc_final: 0.7827 (p) REVERT: B 585 GLU cc_start: 0.7897 (tp30) cc_final: 0.7673 (tp30) REVERT: B 616 LYS cc_start: 0.8489 (mttp) cc_final: 0.8284 (mttm) outliers start: 153 outliers final: 33 residues processed: 425 average time/residue: 0.2458 time to fit residues: 151.2205 Evaluate side-chains 274 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 111 ASP Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 563 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 0.0770 chunk 97 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 GLN C 38 GLN D 40 GLN D 77 ASN E 37 GLN E 38 GLN F 40 GLN Z 60 ASN Z 74 ASN A 76 ASN A 271 GLN A 283 HIS A 425 ASN A 437 GLN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN B 222 ASN B 387 ASN B 425 ASN B 437 GLN B 457 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.155576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.125359 restraints weight = 15833.914| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.93 r_work: 0.3068 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13641 Z= 0.152 Angle : 0.615 8.677 18491 Z= 0.321 Chirality : 0.042 0.154 2106 Planarity : 0.005 0.065 2311 Dihedral : 9.032 91.508 1988 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.30 % Favored : 93.64 % Rotamer: Outliers : 4.34 % Allowed : 15.45 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.19), residues: 1683 helix: 0.30 (0.21), residues: 604 sheet: -1.45 (0.28), residues: 302 loop : -2.65 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 627 HIS 0.005 0.001 HIS A 283 PHE 0.021 0.001 PHE F 79 TYR 0.018 0.001 TYR A 276 ARG 0.005 0.000 ARG D 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00110 ( 2) link_NAG-ASN : angle 1.95172 ( 6) link_BETA1-4 : bond 0.00343 ( 2) link_BETA1-4 : angle 1.51931 ( 6) hydrogen bonds : bond 0.04858 ( 608) hydrogen bonds : angle 4.67070 ( 1719) SS BOND : bond 0.00497 ( 8) SS BOND : angle 1.29357 ( 16) covalent geometry : bond 0.00345 (13629) covalent geometry : angle 0.61297 (18463) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 258 time to evaluate : 1.649 Fit side-chains REVERT: E 79 GLN cc_start: 0.6746 (mt0) cc_final: 0.6435 (tt0) REVERT: F 78 GLN cc_start: 0.9004 (mt0) cc_final: 0.8685 (mt0) REVERT: F 89 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7445 (mm-30) REVERT: F 111 GLN cc_start: 0.8607 (pm20) cc_final: 0.8380 (pm20) REVERT: A 141 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7934 (mt0) REVERT: A 177 LYS cc_start: 0.7349 (mmtp) cc_final: 0.6728 (mtmt) REVERT: A 226 LEU cc_start: 0.8420 (mm) cc_final: 0.8166 (mp) REVERT: A 378 ARG cc_start: 0.7389 (ttp-170) cc_final: 0.6143 (mmt-90) REVERT: A 393 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.6405 (mt0) REVERT: A 417 LYS cc_start: 0.8622 (pttt) cc_final: 0.7811 (mmtm) REVERT: A 616 LYS cc_start: 0.8834 (mttp) cc_final: 0.8325 (mtpp) REVERT: B 160 ARG cc_start: 0.6808 (ttt180) cc_final: 0.6500 (ttt180) REVERT: B 162 ASN cc_start: 0.6090 (m-40) cc_final: 0.5672 (m-40) REVERT: B 198 MET cc_start: 0.8283 (mtm) cc_final: 0.8074 (mtp) REVERT: B 222 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.7850 (t0) REVERT: B 263 ARG cc_start: 0.7916 (mmm-85) cc_final: 0.7398 (mmm160) REVERT: B 348 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6516 (mm-30) REVERT: B 375 HIS cc_start: 0.7735 (t70) cc_final: 0.7167 (t-170) REVERT: B 378 ARG cc_start: 0.7707 (ttp-170) cc_final: 0.7074 (ttp-110) REVERT: B 387 ASN cc_start: 0.8421 (t0) cc_final: 0.8124 (t0) REVERT: B 473 LYS cc_start: 0.8171 (tptp) cc_final: 0.7956 (mmmt) REVERT: B 585 GLU cc_start: 0.8622 (tp30) cc_final: 0.8307 (tp30) outliers start: 63 outliers final: 37 residues processed: 302 average time/residue: 0.2938 time to fit residues: 129.6281 Evaluate side-chains 282 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 242 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 3 GLN Chi-restraints excluded: chain Z residue 53 THR Chi-restraints excluded: chain Z residue 111 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 563 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 52 optimal weight: 0.0980 chunk 124 optimal weight: 1.9990 chunk 140 optimal weight: 0.0870 chunk 25 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.2364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN D 77 ASN A 629 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.149823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.118759 restraints weight = 15972.839| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.94 r_work: 0.3002 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 13641 Z= 0.208 Angle : 0.651 9.592 18491 Z= 0.336 Chirality : 0.044 0.159 2106 Planarity : 0.004 0.064 2311 Dihedral : 7.451 89.903 1954 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.07 % Favored : 92.87 % Rotamer: Outliers : 3.93 % Allowed : 16.97 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.20), residues: 1683 helix: 0.99 (0.21), residues: 605 sheet: -0.93 (0.29), residues: 308 loop : -2.44 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 109 HIS 0.005 0.001 HIS A 630 PHE 0.021 0.002 PHE F 79 TYR 0.022 0.002 TYR B 605 ARG 0.004 0.000 ARG Z 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 2) link_NAG-ASN : angle 2.05659 ( 6) link_BETA1-4 : bond 0.00126 ( 2) link_BETA1-4 : angle 1.47595 ( 6) hydrogen bonds : bond 0.05507 ( 608) hydrogen bonds : angle 4.52802 ( 1719) SS BOND : bond 0.00767 ( 8) SS BOND : angle 1.66546 ( 16) covalent geometry : bond 0.00500 (13629) covalent geometry : angle 0.64784 (18463) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 238 time to evaluate : 2.190 Fit side-chains REVERT: E 79 GLN cc_start: 0.6639 (mt0) cc_final: 0.6254 (tt0) REVERT: F 89 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7432 (mm-30) REVERT: A 177 LYS cc_start: 0.7472 (mmtp) cc_final: 0.6884 (mtmt) REVERT: A 226 LEU cc_start: 0.8488 (mm) cc_final: 0.8206 (mp) REVERT: A 378 ARG cc_start: 0.7458 (ttp-170) cc_final: 0.6115 (mmt-90) REVERT: A 393 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.6455 (mt0) REVERT: A 417 LYS cc_start: 0.8685 (pttt) cc_final: 0.7792 (mmtm) REVERT: A 489 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7961 (t80) REVERT: B 198 MET cc_start: 0.8407 (mtm) cc_final: 0.8166 (mtp) REVERT: B 225 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6602 (mm) REVERT: B 263 ARG cc_start: 0.7763 (mmm-85) cc_final: 0.7367 (mmm160) REVERT: B 348 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6571 (mm-30) REVERT: B 378 ARG cc_start: 0.7671 (ttp-170) cc_final: 0.7052 (ttp-110) REVERT: B 387 ASN cc_start: 0.8489 (t0) cc_final: 0.8171 (t0) REVERT: B 585 GLU cc_start: 0.8650 (tp30) cc_final: 0.8373 (tp30) outliers start: 57 outliers final: 41 residues processed: 282 average time/residue: 0.3319 time to fit residues: 136.4871 Evaluate side-chains 274 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 229 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 53 THR Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 111 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 42 optimal weight: 0.5980 chunk 2 optimal weight: 0.0980 chunk 135 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 57 optimal weight: 0.0970 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 25 optimal weight: 0.0870 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.155306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.124997 restraints weight = 15678.701| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.87 r_work: 0.3078 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13641 Z= 0.103 Angle : 0.538 7.030 18491 Z= 0.280 Chirality : 0.040 0.144 2106 Planarity : 0.004 0.059 2311 Dihedral : 6.708 84.569 1948 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.88 % Favored : 94.06 % Rotamer: Outliers : 3.45 % Allowed : 18.90 % Favored : 77.66 % 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: -0.80 (0.21), residues: 1683 helix: 1.55 (0.22), residues: 598 sheet: -0.70 (0.29), residues: 309 loop : -2.23 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 627 HIS 0.002 0.001 HIS B 375 PHE 0.017 0.001 PHE D 79 TYR 0.016 0.001 TYR A 276 ARG 0.003 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00105 ( 2) link_NAG-ASN : angle 1.76277 ( 6) link_BETA1-4 : bond 0.00231 ( 2) link_BETA1-4 : angle 1.62106 ( 6) hydrogen bonds : bond 0.04038 ( 608) hydrogen bonds : angle 4.16953 ( 1719) SS BOND : bond 0.00472 ( 8) SS BOND : angle 0.96766 ( 16) covalent geometry : bond 0.00221 (13629) covalent geometry : angle 0.53566 (18463) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 257 time to evaluate : 2.339 Fit side-chains REVERT: D 103 LYS cc_start: 0.9230 (ttpt) cc_final: 0.7880 (mmtt) REVERT: E 79 GLN cc_start: 0.6791 (mt0) cc_final: 0.6305 (tt0) REVERT: F 78 GLN cc_start: 0.9013 (mt0) cc_final: 0.8615 (mt0) REVERT: Z 11 LEU cc_start: 0.5907 (OUTLIER) cc_final: 0.5678 (pp) REVERT: A 177 LYS cc_start: 0.7482 (mmtp) cc_final: 0.6889 (mtmt) REVERT: A 226 LEU cc_start: 0.8458 (mm) cc_final: 0.8155 (mp) REVERT: A 378 ARG cc_start: 0.7331 (ttp-170) cc_final: 0.5911 (mmt-90) REVERT: A 393 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6417 (mt0) REVERT: A 417 LYS cc_start: 0.8619 (pttt) cc_final: 0.7738 (mmtm) REVERT: B 162 ASN cc_start: 0.6139 (m-40) cc_final: 0.5601 (m-40) REVERT: B 225 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6581 (mm) REVERT: B 263 ARG cc_start: 0.7708 (mmm-85) cc_final: 0.7340 (mmm160) REVERT: B 348 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6574 (mm-30) REVERT: B 378 ARG cc_start: 0.7618 (ttp-170) cc_final: 0.7021 (ttp-110) REVERT: B 387 ASN cc_start: 0.8388 (t0) cc_final: 0.8111 (t0) REVERT: B 585 GLU cc_start: 0.8565 (tp30) cc_final: 0.8312 (tp30) outliers start: 50 outliers final: 34 residues processed: 295 average time/residue: 0.2724 time to fit residues: 117.4853 Evaluate side-chains 281 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 244 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 53 THR Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 111 ASP Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 165 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.147844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.115917 restraints weight = 16101.152| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.01 r_work: 0.3005 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13641 Z= 0.161 Angle : 0.586 9.001 18491 Z= 0.302 Chirality : 0.042 0.150 2106 Planarity : 0.004 0.058 2311 Dihedral : 6.221 68.671 1942 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.30 % Favored : 93.64 % Rotamer: Outliers : 4.21 % Allowed : 19.10 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.63 (0.21), residues: 1683 helix: 1.62 (0.22), residues: 607 sheet: -0.53 (0.30), residues: 310 loop : -2.14 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 379 HIS 0.004 0.001 HIS A 630 PHE 0.019 0.001 PHE F 79 TYR 0.019 0.002 TYR B 605 ARG 0.008 0.000 ARG B 147 Details of bonding type rmsd link_NAG-ASN : bond 0.00148 ( 2) link_NAG-ASN : angle 1.91535 ( 6) link_BETA1-4 : bond 0.00174 ( 2) link_BETA1-4 : angle 1.45293 ( 6) hydrogen bonds : bond 0.04675 ( 608) hydrogen bonds : angle 4.20700 ( 1719) SS BOND : bond 0.00636 ( 8) SS BOND : angle 1.40202 ( 16) covalent geometry : bond 0.00380 (13629) covalent geometry : angle 0.58310 (18463) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 247 time to evaluate : 1.514 Fit side-chains REVERT: D 103 LYS cc_start: 0.9273 (ttpt) cc_final: 0.7961 (mmtt) REVERT: E 79 GLN cc_start: 0.6784 (mt0) cc_final: 0.6304 (tt0) REVERT: F 78 GLN cc_start: 0.9048 (mt0) cc_final: 0.8824 (mt0) REVERT: Z 11 LEU cc_start: 0.6056 (OUTLIER) cc_final: 0.5832 (pp) REVERT: A 108 ILE cc_start: 0.8498 (mm) cc_final: 0.8260 (tt) REVERT: A 177 LYS cc_start: 0.7494 (mmtp) cc_final: 0.6927 (mtmt) REVERT: A 226 LEU cc_start: 0.8514 (mm) cc_final: 0.8200 (mp) REVERT: A 378 ARG cc_start: 0.7447 (ttp-170) cc_final: 0.6056 (mmt-90) REVERT: A 393 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: A 417 LYS cc_start: 0.8666 (pttt) cc_final: 0.7764 (mmtm) REVERT: A 635 CYS cc_start: 0.8641 (m) cc_final: 0.8160 (m) REVERT: B 45 ARG cc_start: 0.4313 (ttt-90) cc_final: 0.3087 (mtp-110) REVERT: B 160 ARG cc_start: 0.6577 (ttt180) cc_final: 0.6248 (ttt180) REVERT: B 165 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7876 (tt) REVERT: B 222 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7907 (m-40) REVERT: B 225 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6648 (mm) REVERT: B 263 ARG cc_start: 0.7750 (mmm-85) cc_final: 0.7387 (mmm160) REVERT: B 348 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6606 (mm-30) REVERT: B 378 ARG cc_start: 0.7674 (ttp-170) cc_final: 0.7058 (ttp-110) REVERT: B 387 ASN cc_start: 0.8435 (t0) cc_final: 0.8117 (t0) REVERT: B 515 MET cc_start: 0.9010 (mmm) cc_final: 0.8764 (mtp) REVERT: B 585 GLU cc_start: 0.8654 (tp30) cc_final: 0.8387 (tp30) outliers start: 61 outliers final: 47 residues processed: 295 average time/residue: 0.2681 time to fit residues: 114.2083 Evaluate side-chains 293 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 241 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 111 ASP Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 276 TYR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 125 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 156 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.150066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.120275 restraints weight = 16111.392| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.88 r_work: 0.2993 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13641 Z= 0.206 Angle : 0.619 8.859 18491 Z= 0.320 Chirality : 0.043 0.152 2106 Planarity : 0.004 0.057 2311 Dihedral : 6.230 55.390 1942 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.65 % Favored : 93.29 % Rotamer: Outliers : 4.83 % Allowed : 19.17 % Favored : 76.00 % 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: -0.65 (0.21), residues: 1683 helix: 1.54 (0.22), residues: 607 sheet: -0.44 (0.30), residues: 305 loop : -2.13 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 109 HIS 0.005 0.001 HIS A 630 PHE 0.019 0.002 PHE F 79 TYR 0.020 0.002 TYR F 51 ARG 0.013 0.000 ARG B 96 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 2) link_NAG-ASN : angle 1.91623 ( 6) link_BETA1-4 : bond 0.00079 ( 2) link_BETA1-4 : angle 1.35374 ( 6) hydrogen bonds : bond 0.05069 ( 608) hydrogen bonds : angle 4.32010 ( 1719) SS BOND : bond 0.00647 ( 8) SS BOND : angle 1.55052 ( 16) covalent geometry : bond 0.00496 (13629) covalent geometry : angle 0.61683 (18463) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 242 time to evaluate : 1.332 Fit side-chains REVERT: D 103 LYS cc_start: 0.9277 (ttpt) cc_final: 0.7909 (mmtt) REVERT: E 79 GLN cc_start: 0.6847 (mt0) cc_final: 0.6328 (tt0) REVERT: A 108 ILE cc_start: 0.8543 (mm) cc_final: 0.8304 (tt) REVERT: A 177 LYS cc_start: 0.7478 (mmtp) cc_final: 0.6973 (mtmt) REVERT: A 226 LEU cc_start: 0.8529 (mm) cc_final: 0.8201 (mp) REVERT: A 246 ARG cc_start: 0.8121 (mpt180) cc_final: 0.7365 (mtp85) REVERT: A 378 ARG cc_start: 0.7493 (ttp-170) cc_final: 0.6057 (mmt-90) REVERT: A 393 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.7012 (tm-30) REVERT: A 417 LYS cc_start: 0.8638 (pttt) cc_final: 0.7726 (mmtm) REVERT: A 635 CYS cc_start: 0.8624 (m) cc_final: 0.8169 (m) REVERT: B 45 ARG cc_start: 0.4410 (ttt-90) cc_final: 0.3204 (mtp-110) REVERT: B 165 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7874 (tt) REVERT: B 225 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6550 (mm) REVERT: B 251 LYS cc_start: 0.8779 (pttm) cc_final: 0.8544 (pttm) REVERT: B 263 ARG cc_start: 0.7775 (mmm-85) cc_final: 0.7391 (mmm160) REVERT: B 348 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6598 (mm-30) REVERT: B 378 ARG cc_start: 0.7645 (ttp-170) cc_final: 0.7017 (ttp-110) REVERT: B 387 ASN cc_start: 0.8441 (t0) cc_final: 0.8112 (t0) REVERT: B 585 GLU cc_start: 0.8645 (tp30) cc_final: 0.8340 (tp30) outliers start: 70 outliers final: 56 residues processed: 297 average time/residue: 0.2614 time to fit residues: 112.9069 Evaluate side-chains 299 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 240 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 111 ASP Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 276 TYR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 109 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 0.0870 chunk 138 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN A 68 ASN A 350 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.147226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.115671 restraints weight = 15997.800| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.96 r_work: 0.3016 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13641 Z= 0.136 Angle : 0.559 7.494 18491 Z= 0.289 Chirality : 0.041 0.147 2106 Planarity : 0.004 0.054 2311 Dihedral : 5.917 51.143 1942 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.82 % Favored : 94.12 % Rotamer: Outliers : 3.93 % Allowed : 20.69 % Favored : 75.38 % 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: -0.43 (0.21), residues: 1683 helix: 1.76 (0.22), residues: 608 sheet: -0.36 (0.30), residues: 304 loop : -2.03 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 379 HIS 0.003 0.001 HIS A 267 PHE 0.016 0.001 PHE F 79 TYR 0.016 0.001 TYR A 276 ARG 0.005 0.000 ARG B 96 Details of bonding type rmsd link_NAG-ASN : bond 0.00071 ( 2) link_NAG-ASN : angle 1.86168 ( 6) link_BETA1-4 : bond 0.00164 ( 2) link_BETA1-4 : angle 1.56798 ( 6) hydrogen bonds : bond 0.04292 ( 608) hydrogen bonds : angle 4.12895 ( 1719) SS BOND : bond 0.00480 ( 8) SS BOND : angle 1.06442 ( 16) covalent geometry : bond 0.00317 (13629) covalent geometry : angle 0.55646 (18463) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 246 time to evaluate : 1.482 Fit side-chains REVERT: D 103 LYS cc_start: 0.9256 (ttpt) cc_final: 0.7908 (mmtt) REVERT: D 111 GLN cc_start: 0.7806 (pm20) cc_final: 0.7595 (pt0) REVERT: E 56 THR cc_start: 0.7659 (OUTLIER) cc_final: 0.7448 (p) REVERT: E 79 GLN cc_start: 0.6822 (mt0) cc_final: 0.6297 (tt0) REVERT: F 3 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7713 (mp10) REVERT: F 78 GLN cc_start: 0.9006 (mt0) cc_final: 0.8756 (mt0) REVERT: A 108 ILE cc_start: 0.8535 (mm) cc_final: 0.8298 (tt) REVERT: A 126 GLN cc_start: 0.8143 (tt0) cc_final: 0.7882 (tt0) REVERT: A 177 LYS cc_start: 0.7462 (mmtp) cc_final: 0.6991 (mtmt) REVERT: A 226 LEU cc_start: 0.8525 (mm) cc_final: 0.8201 (mp) REVERT: A 378 ARG cc_start: 0.7421 (ttp-170) cc_final: 0.5996 (mmt-90) REVERT: A 393 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6205 (mt0) REVERT: A 417 LYS cc_start: 0.8617 (pttt) cc_final: 0.7708 (mmtm) REVERT: A 635 CYS cc_start: 0.8615 (m) cc_final: 0.8143 (m) REVERT: B 45 ARG cc_start: 0.4607 (ttt-90) cc_final: 0.3382 (mtp-110) REVERT: B 126 GLN cc_start: 0.8007 (tm-30) cc_final: 0.7731 (tm-30) REVERT: B 160 ARG cc_start: 0.6697 (ttt180) cc_final: 0.6373 (ttt180) REVERT: B 225 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6637 (mm) REVERT: B 251 LYS cc_start: 0.8780 (pttm) cc_final: 0.8559 (pttm) REVERT: B 263 ARG cc_start: 0.7799 (mmm-85) cc_final: 0.7413 (mmm160) REVERT: B 276 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.8075 (t80) REVERT: B 348 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6550 (mm-30) REVERT: B 378 ARG cc_start: 0.7657 (ttp-170) cc_final: 0.7043 (ttp-110) REVERT: B 515 MET cc_start: 0.8978 (mmm) cc_final: 0.8694 (mtp) REVERT: B 585 GLU cc_start: 0.8640 (tp30) cc_final: 0.8375 (tp30) REVERT: B 608 CYS cc_start: 0.8571 (m) cc_final: 0.8284 (m) outliers start: 57 outliers final: 48 residues processed: 292 average time/residue: 0.2891 time to fit residues: 121.7084 Evaluate side-chains 295 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 242 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 111 ASP Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 276 TYR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 147 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 0.0070 chunk 65 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN A 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.147875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.116191 restraints weight = 16053.069| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.99 r_work: 0.3019 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13641 Z= 0.127 Angle : 0.551 7.410 18491 Z= 0.286 Chirality : 0.041 0.148 2106 Planarity : 0.003 0.052 2311 Dihedral : 5.707 51.360 1941 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.12 % Favored : 93.82 % Rotamer: Outliers : 4.41 % Allowed : 20.34 % Favored : 75.24 % 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: -0.34 (0.22), residues: 1683 helix: 1.80 (0.22), residues: 608 sheet: -0.30 (0.30), residues: 304 loop : -1.96 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 627 HIS 0.002 0.001 HIS B 375 PHE 0.016 0.001 PHE F 79 TYR 0.015 0.001 TYR A 276 ARG 0.007 0.000 ARG B 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00029 ( 2) link_NAG-ASN : angle 1.76939 ( 6) link_BETA1-4 : bond 0.00212 ( 2) link_BETA1-4 : angle 1.55549 ( 6) hydrogen bonds : bond 0.04163 ( 608) hydrogen bonds : angle 4.05463 ( 1719) SS BOND : bond 0.00448 ( 8) SS BOND : angle 1.08907 ( 16) covalent geometry : bond 0.00294 (13629) covalent geometry : angle 0.54901 (18463) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 244 time to evaluate : 1.402 Fit side-chains REVERT: C 18 ARG cc_start: 0.7107 (ttp80) cc_final: 0.6653 (ttp-170) REVERT: D 103 LYS cc_start: 0.9213 (ttpt) cc_final: 0.7830 (mmtt) REVERT: E 79 GLN cc_start: 0.6787 (mt0) cc_final: 0.6255 (tt0) REVERT: F 3 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7673 (mp10) REVERT: F 78 GLN cc_start: 0.8997 (mt0) cc_final: 0.8745 (mt0) REVERT: A 108 ILE cc_start: 0.8529 (mm) cc_final: 0.8295 (tt) REVERT: A 126 GLN cc_start: 0.8093 (tt0) cc_final: 0.7828 (tt0) REVERT: A 177 LYS cc_start: 0.7462 (mmtp) cc_final: 0.6989 (mtmt) REVERT: A 226 LEU cc_start: 0.8450 (mm) cc_final: 0.8140 (mp) REVERT: A 378 ARG cc_start: 0.7351 (ttp-170) cc_final: 0.5909 (mmt-90) REVERT: A 393 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6145 (mt0) REVERT: A 417 LYS cc_start: 0.8582 (pttt) cc_final: 0.7669 (mmtm) REVERT: A 635 CYS cc_start: 0.8594 (m) cc_final: 0.8142 (m) REVERT: B 45 ARG cc_start: 0.4533 (ttt-90) cc_final: 0.3347 (mtp-110) REVERT: B 126 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7703 (tm-30) REVERT: B 160 ARG cc_start: 0.6566 (ttt180) cc_final: 0.6267 (ttt180) REVERT: B 165 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7701 (tt) REVERT: B 225 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6683 (mm) REVERT: B 251 LYS cc_start: 0.8741 (pttm) cc_final: 0.8506 (pttm) REVERT: B 263 ARG cc_start: 0.7765 (mmm-85) cc_final: 0.7354 (mmm160) REVERT: B 276 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.7982 (t80) REVERT: B 348 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6507 (mm-30) REVERT: B 378 ARG cc_start: 0.7627 (ttp-170) cc_final: 0.7001 (ttp-110) REVERT: B 481 MET cc_start: 0.7233 (mmt) cc_final: 0.6986 (tpt) REVERT: B 515 MET cc_start: 0.8968 (mmm) cc_final: 0.8693 (mtp) REVERT: B 585 GLU cc_start: 0.8623 (tp30) cc_final: 0.8357 (tp30) REVERT: B 608 CYS cc_start: 0.8602 (m) cc_final: 0.8327 (m) outliers start: 64 outliers final: 53 residues processed: 297 average time/residue: 0.3271 time to fit residues: 140.2289 Evaluate side-chains 295 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 237 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 111 ASP Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 276 TYR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 161 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 120 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.146147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.114135 restraints weight = 15968.277| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.08 r_work: 0.3000 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13641 Z= 0.153 Angle : 0.572 7.972 18491 Z= 0.296 Chirality : 0.041 0.151 2106 Planarity : 0.004 0.048 2311 Dihedral : 5.734 51.403 1941 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.65 % Favored : 93.29 % Rotamer: Outliers : 4.34 % Allowed : 20.41 % Favored : 75.24 % 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: -0.37 (0.21), residues: 1683 helix: 1.75 (0.22), residues: 608 sheet: -0.28 (0.30), residues: 304 loop : -1.96 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 379 HIS 0.003 0.001 HIS A 630 PHE 0.018 0.001 PHE F 79 TYR 0.016 0.001 TYR B 605 ARG 0.004 0.000 ARG B 147 Details of bonding type rmsd link_NAG-ASN : bond 0.00089 ( 2) link_NAG-ASN : angle 1.87206 ( 6) link_BETA1-4 : bond 0.00224 ( 2) link_BETA1-4 : angle 1.48571 ( 6) hydrogen bonds : bond 0.04426 ( 608) hydrogen bonds : angle 4.10242 ( 1719) SS BOND : bond 0.00525 ( 8) SS BOND : angle 1.25501 ( 16) covalent geometry : bond 0.00363 (13629) covalent geometry : angle 0.56950 (18463) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 234 time to evaluate : 1.458 Fit side-chains revert: symmetry clash REVERT: C 18 ARG cc_start: 0.7166 (ttp80) cc_final: 0.6679 (ttp-170) REVERT: D 103 LYS cc_start: 0.9257 (ttpt) cc_final: 0.7886 (mmtt) REVERT: E 79 GLN cc_start: 0.6856 (mt0) cc_final: 0.6376 (tt0) REVERT: F 3 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7744 (mp10) REVERT: A 108 ILE cc_start: 0.8571 (mm) cc_final: 0.8347 (tt) REVERT: A 126 GLN cc_start: 0.8135 (tt0) cc_final: 0.7868 (tt0) REVERT: A 177 LYS cc_start: 0.7538 (mmtp) cc_final: 0.7067 (mtmt) REVERT: A 226 LEU cc_start: 0.8505 (mm) cc_final: 0.8192 (mp) REVERT: A 378 ARG cc_start: 0.7454 (ttp-170) cc_final: 0.6017 (mmt-90) REVERT: A 393 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.6598 (tm-30) REVERT: A 417 LYS cc_start: 0.8630 (pttt) cc_final: 0.7745 (mmtm) REVERT: A 635 CYS cc_start: 0.8660 (m) cc_final: 0.8221 (m) REVERT: B 45 ARG cc_start: 0.4519 (ttt-90) cc_final: 0.3352 (mtp-110) REVERT: B 126 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7754 (tm-30) REVERT: B 160 ARG cc_start: 0.6651 (ttt180) cc_final: 0.6333 (ttt180) REVERT: B 165 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7751 (tt) REVERT: B 225 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6682 (mm) REVERT: B 263 ARG cc_start: 0.7827 (mmm-85) cc_final: 0.7435 (mmm160) REVERT: B 348 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6582 (mm-30) REVERT: B 378 ARG cc_start: 0.7690 (ttp-170) cc_final: 0.7065 (ttp-110) REVERT: B 481 MET cc_start: 0.7450 (mmt) cc_final: 0.7081 (tpt) REVERT: B 515 MET cc_start: 0.9007 (mmm) cc_final: 0.8734 (mtp) REVERT: B 585 GLU cc_start: 0.8672 (tp30) cc_final: 0.8419 (tp30) REVERT: B 608 CYS cc_start: 0.8652 (m) cc_final: 0.8387 (m) REVERT: B 620 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8065 (t70) outliers start: 63 outliers final: 55 residues processed: 284 average time/residue: 0.2694 time to fit residues: 110.7635 Evaluate side-chains 296 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 236 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 111 ASP Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 276 TYR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 620 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 27 optimal weight: 4.9990 chunk 128 optimal weight: 0.0170 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 153 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 61 optimal weight: 0.0060 chunk 38 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 157 optimal weight: 1.9990 overall best weight: 0.3034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.149940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.118605 restraints weight = 15831.246| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.98 r_work: 0.3054 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13641 Z= 0.099 Angle : 0.522 6.343 18491 Z= 0.272 Chirality : 0.040 0.164 2106 Planarity : 0.003 0.045 2311 Dihedral : 5.367 51.474 1938 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.64 % Favored : 94.30 % Rotamer: Outliers : 3.17 % Allowed : 21.45 % Favored : 75.38 % 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 (0.22), residues: 1683 helix: 1.93 (0.22), residues: 609 sheet: -0.23 (0.30), residues: 306 loop : -1.82 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 627 HIS 0.002 0.001 HIS B 375 PHE 0.016 0.001 PHE F 79 TYR 0.015 0.001 TYR A 276 ARG 0.005 0.000 ARG B 147 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 2) link_NAG-ASN : angle 1.70910 ( 6) link_BETA1-4 : bond 0.00219 ( 2) link_BETA1-4 : angle 1.63411 ( 6) hydrogen bonds : bond 0.03622 ( 608) hydrogen bonds : angle 3.94383 ( 1719) SS BOND : bond 0.00335 ( 8) SS BOND : angle 0.81439 ( 16) covalent geometry : bond 0.00219 (13629) covalent geometry : angle 0.51976 (18463) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 247 time to evaluate : 1.288 Fit side-chains REVERT: C 18 ARG cc_start: 0.7119 (ttp80) cc_final: 0.6648 (ttp-170) REVERT: D 5 GLN cc_start: 0.8340 (mm-40) cc_final: 0.8109 (tp40) REVERT: D 103 LYS cc_start: 0.9206 (ttpt) cc_final: 0.7812 (mmtt) REVERT: E 79 GLN cc_start: 0.6732 (mt0) cc_final: 0.6294 (tt0) REVERT: F 78 GLN cc_start: 0.8963 (mt0) cc_final: 0.8605 (mt0) REVERT: A 108 ILE cc_start: 0.8547 (mm) cc_final: 0.8334 (tt) REVERT: A 126 GLN cc_start: 0.8065 (tt0) cc_final: 0.7794 (tt0) REVERT: A 177 LYS cc_start: 0.7451 (mmtp) cc_final: 0.6979 (mtmt) REVERT: A 226 LEU cc_start: 0.8439 (mm) cc_final: 0.8111 (mp) REVERT: A 378 ARG cc_start: 0.7229 (ttp-170) cc_final: 0.5839 (mmt-90) REVERT: A 417 LYS cc_start: 0.8571 (pttt) cc_final: 0.7646 (mmtm) REVERT: A 481 MET cc_start: 0.7888 (mmt) cc_final: 0.6704 (ttp) REVERT: B 45 ARG cc_start: 0.4523 (ttt-90) cc_final: 0.3368 (mtp-110) REVERT: B 126 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7664 (tm-30) REVERT: B 160 ARG cc_start: 0.6567 (ttt180) cc_final: 0.6258 (ttt180) REVERT: B 165 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7639 (tt) REVERT: B 225 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.6742 (mm) REVERT: B 251 LYS cc_start: 0.8767 (pttm) cc_final: 0.8500 (pttm) REVERT: B 263 ARG cc_start: 0.7748 (mmm-85) cc_final: 0.7349 (mmm160) REVERT: B 348 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6524 (mm-30) REVERT: B 378 ARG cc_start: 0.7618 (ttp-170) cc_final: 0.7002 (ttp-110) REVERT: B 481 MET cc_start: 0.7328 (mmt) cc_final: 0.7045 (tpt) REVERT: B 515 MET cc_start: 0.8931 (mmm) cc_final: 0.8662 (mtp) REVERT: B 531 GLN cc_start: 0.6784 (mm110) cc_final: 0.6391 (mm-40) REVERT: B 585 GLU cc_start: 0.8615 (tp30) cc_final: 0.8373 (tp30) REVERT: B 608 CYS cc_start: 0.8614 (m) cc_final: 0.8351 (m) outliers start: 46 outliers final: 41 residues processed: 283 average time/residue: 0.2613 time to fit residues: 106.7507 Evaluate side-chains 283 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 240 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 276 TYR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 76 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 86 optimal weight: 0.0020 chunk 27 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.144136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.112460 restraints weight = 15989.985| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.01 r_work: 0.2972 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13641 Z= 0.212 Angle : 0.633 9.965 18491 Z= 0.325 Chirality : 0.044 0.152 2106 Planarity : 0.004 0.042 2311 Dihedral : 5.590 51.519 1933 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.95 % Favored : 92.99 % Rotamer: Outliers : 3.79 % Allowed : 20.90 % Favored : 75.31 % 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: -0.34 (0.21), residues: 1683 helix: 1.73 (0.22), residues: 610 sheet: -0.31 (0.30), residues: 307 loop : -1.89 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 35 HIS 0.004 0.001 HIS A 630 PHE 0.020 0.002 PHE A 39 TYR 0.021 0.002 TYR B 605 ARG 0.003 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 2) link_NAG-ASN : angle 1.99383 ( 6) link_BETA1-4 : bond 0.00163 ( 2) link_BETA1-4 : angle 1.30584 ( 6) hydrogen bonds : bond 0.05048 ( 608) hydrogen bonds : angle 4.19986 ( 1719) SS BOND : bond 0.00738 ( 8) SS BOND : angle 1.69924 ( 16) covalent geometry : bond 0.00513 (13629) covalent geometry : angle 0.62990 (18463) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8628.80 seconds wall clock time: 154 minutes 35.69 seconds (9275.69 seconds total)