Starting phenix.real_space_refine on Fri Jul 3 09:09:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8p8a_17543/07_2026/8p8a_17543.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p8a_17543/07_2026/8p8a_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 { model { file = "/net/cci-nas-00/data/ceres_data/8p8a_17543/07_2026/8p8a_17543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p8a_17543/07_2026/8p8a_17543.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p8a_17543/07_2026/8p8a_17543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p8a_17543/07_2026/8p8a_17543.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8p8a_17543/07_2026/8p8a_17543.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8p8a_17543/07_2026/8p8a_17543.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 chiralities: 2 Time building chain proxies: 2.99, per 1000 atoms: 0.22 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: 0.99 Conformation dependent library (CDL) restraints added in 613.2 milliseconds 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: 0.29 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: 2.15 Time building geometry restraints manager: 1.37 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: 6996 17.95 - 35.89: 658 35.89 - 53.84: 234 53.84 - 71.78: 88 71.78 - 89.73: 17 Dihedral angle restraints: 7993 sinusoidal: 3098 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 7990 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: 4.490 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.710 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 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 : 17.724 89.726 4847 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.005 0.001 ARG B 482 TYR 0.029 0.002 TYR F 51 PHE 0.025 0.002 PHE A 489 TRP 0.011 0.002 TRP B 379 HIS 0.018 0.003 HIS A 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.31 (13629) covalent geometry : angle 1.01334 / 0.56 (18463) SS BOND : bond 0.00642 / 0.33 ( 8) SS BOND : angle 3.03581 / 1.97 ( 16) hydrogen bonds : bond 0.19045 / 13.11 ( 608) hydrogen bonds : angle 7.04865 / 4.74 ( 1719) link_BETA1-4 : bond 0.00449 / 0.22 ( 2) link_BETA1-4 : angle 2.60531 / 1.42 ( 6) link_NAG-ASN : bond 0.00171 / 0.09 ( 2) link_NAG-ASN : angle 3.73755 / 2.20 ( 6) *********************** 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 : 0.486 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: 0.1149 time to fit residues: 71.6430 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 : 0.475 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 37 GLN D 77 ASN E 37 GLN E 38 GLN F 40 GLN Z 60 ASN Z 74 ASN A 68 ASN A 76 ASN A 271 GLN A 425 ASN A 437 GLN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN B 222 ASN B 425 ASN B 437 GLN B 457 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.157114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.126692 restraints weight = 15902.114| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.91 r_work: 0.3090 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1832 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= 0.149 Angle : 0.621 8.794 18491 Z= 0.325 Chirality : 0.042 0.159 2106 Planarity : 0.005 0.064 2311 Dihedral : 9.025 90.557 1904 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.30 % Favored : 93.64 % Rotamer: Outliers : 4.34 % Allowed : 15.52 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.19), residues: 1683 helix: 0.24 (0.21), residues: 604 sheet: -1.46 (0.28), residues: 302 loop : -2.67 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 84 TYR 0.018 0.001 TYR A 276 PHE 0.020 0.001 PHE D 79 TRP 0.011 0.001 TRP A 627 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (13629) covalent geometry : angle 0.61857 / 0.32 (18463) SS BOND : bond 0.00697 / 0.33 ( 8) SS BOND : angle 1.20475 / 0.72 ( 16) hydrogen bonds : bond 0.04932 / 3.30 ( 608) hydrogen bonds : angle 4.71128 / 3.17 ( 1719) link_BETA1-4 : bond 0.00189 / 0.10 ( 2) link_BETA1-4 : angle 1.41577 / 0.88 ( 6) link_NAG-ASN : bond 0.00076 / 0.04 ( 2) link_NAG-ASN : angle 1.84155 / 0.96 ( 6) *********************** 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 320 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 257 time to evaluate : 0.468 Fit side-chains REVERT: E 79 GLN cc_start: 0.6797 (mt0) cc_final: 0.6477 (tt0) REVERT: F 78 GLN cc_start: 0.8999 (mt0) cc_final: 0.8688 (mt0) REVERT: F 89 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7421 (mm-30) REVERT: A 141 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7884 (mt0) REVERT: A 177 LYS cc_start: 0.7330 (mmtp) cc_final: 0.6720 (mtmt) REVERT: A 226 LEU cc_start: 0.8408 (mm) cc_final: 0.8163 (mp) REVERT: A 378 ARG cc_start: 0.7352 (ttp-170) cc_final: 0.6128 (mmt-90) REVERT: A 393 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.6376 (mt0) REVERT: A 417 LYS cc_start: 0.8623 (pttt) cc_final: 0.7812 (mmtm) REVERT: A 616 LYS cc_start: 0.8799 (mttp) cc_final: 0.8290 (mtpp) REVERT: B 162 ASN cc_start: 0.6055 (m-40) cc_final: 0.5645 (m-40) REVERT: B 198 MET cc_start: 0.8258 (mtm) cc_final: 0.8045 (mtp) REVERT: B 222 ASN cc_start: 0.8117 (OUTLIER) cc_final: 0.7871 (t0) REVERT: B 263 ARG cc_start: 0.7916 (mmm-85) cc_final: 0.7400 (mmm160) REVERT: B 348 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6542 (mm-30) REVERT: B 375 HIS cc_start: 0.7723 (t70) cc_final: 0.7165 (t-170) REVERT: B 378 ARG cc_start: 0.7683 (ttp-170) cc_final: 0.7068 (ttp-110) REVERT: B 387 ASN cc_start: 0.8408 (t0) cc_final: 0.8160 (t0) REVERT: B 585 GLU cc_start: 0.8594 (tp30) cc_final: 0.8269 (tp30) REVERT: B 616 LYS cc_start: 0.8921 (mttp) cc_final: 0.8720 (mttm) outliers start: 63 outliers final: 36 residues processed: 303 average time/residue: 0.1170 time to fit residues: 51.7000 Evaluate side-chains 283 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 244 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 77 ASN 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 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 297 ILE Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 468 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 68 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 79 GLN A 283 HIS ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN B 629 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.143559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.111308 restraints weight = 16371.054| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.04 r_work: 0.2949 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 13641 Z= 0.282 Angle : 0.727 10.397 18491 Z= 0.374 Chirality : 0.047 0.189 2106 Planarity : 0.005 0.066 2311 Dihedral : 7.238 86.218 1871 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.49 % Favored : 92.45 % Rotamer: Outliers : 4.14 % Allowed : 17.03 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.20), residues: 1683 helix: 0.78 (0.21), residues: 604 sheet: -0.95 (0.29), residues: 304 loop : -2.56 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 426 TYR 0.024 0.002 TYR D 51 PHE 0.021 0.002 PHE F 79 TRP 0.013 0.002 TRP D 109 HIS 0.007 0.002 HIS A 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.28 (13629) covalent geometry : angle 0.72409 / 0.37 (18463) SS BOND : bond 0.00839 / 0.43 ( 8) SS BOND : angle 2.01392 / 1.17 ( 16) hydrogen bonds : bond 0.06209 / 4.17 ( 608) hydrogen bonds : angle 4.71027 / 3.20 ( 1719) link_BETA1-4 : bond 0.00427 / 0.21 ( 2) link_BETA1-4 : angle 0.92634 / 0.49 ( 6) link_NAG-ASN : bond 0.00485 / 0.25 ( 2) link_NAG-ASN : angle 2.01060 / 1.15 ( 6) *********************** 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: 60 poor density : 235 time to evaluate : 0.512 Fit side-chains REVERT: D 82 GLN cc_start: 0.8271 (tp40) cc_final: 0.8006 (tp40) REVERT: E 42 ASN cc_start: 0.8698 (m-40) cc_final: 0.8420 (m-40) REVERT: E 79 GLN cc_start: 0.6770 (mt0) cc_final: 0.6334 (tt0) REVERT: F 89 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7454 (mm-30) REVERT: A 141 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7908 (mt0) REVERT: A 177 LYS cc_start: 0.7462 (mmtp) cc_final: 0.6924 (mtmt) REVERT: A 226 LEU cc_start: 0.8522 (mm) cc_final: 0.8229 (mp) REVERT: A 246 ARG cc_start: 0.8126 (mpt180) cc_final: 0.7325 (mtp85) REVERT: A 285 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7247 (mt-10) REVERT: A 378 ARG cc_start: 0.7502 (ttp-170) cc_final: 0.6125 (mmt-90) REVERT: A 393 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.6492 (mt0) REVERT: A 417 LYS cc_start: 0.8690 (pttt) cc_final: 0.7789 (mmtm) REVERT: A 489 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.8042 (t80) REVERT: A 635 CYS cc_start: 0.8642 (m) cc_final: 0.8217 (m) REVERT: B 225 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6698 (mm) REVERT: B 263 ARG cc_start: 0.7780 (mmm-85) cc_final: 0.7424 (mmm160) REVERT: B 348 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6601 (mm-30) REVERT: B 378 ARG cc_start: 0.7672 (ttp-170) cc_final: 0.7033 (ttp-110) REVERT: B 387 ASN cc_start: 0.8601 (t0) cc_final: 0.8340 (t0) REVERT: B 585 GLU cc_start: 0.8693 (tp30) cc_final: 0.8327 (tp30) outliers start: 60 outliers final: 45 residues processed: 282 average time/residue: 0.1210 time to fit residues: 49.4825 Evaluate side-chains 279 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 230 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 67 SER 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 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 34 MET 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 241 SER 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 468 SER 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 549 MET Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 36 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 303 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 565 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 79 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 159 optimal weight: 0.5980 chunk 163 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 79 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.146483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.114093 restraints weight = 16122.548| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.07 r_work: 0.2989 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13641 Z= 0.150 Angle : 0.586 7.944 18491 Z= 0.303 Chirality : 0.042 0.209 2106 Planarity : 0.004 0.064 2311 Dihedral : 6.272 74.875 1862 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.76 % Favored : 94.18 % Rotamer: Outliers : 4.28 % Allowed : 18.48 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.21), residues: 1683 helix: 1.27 (0.22), residues: 604 sheet: -0.67 (0.29), residues: 304 loop : -2.35 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 18 TYR 0.016 0.001 TYR A 276 PHE 0.017 0.001 PHE F 79 TRP 0.011 0.001 TRP B 379 HIS 0.002 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (13629) covalent geometry : angle 0.58401 / 0.30 (18463) SS BOND : bond 0.00593 / 0.29 ( 8) SS BOND : angle 1.22271 / 0.71 ( 16) hydrogen bonds : bond 0.04719 / 3.18 ( 608) hydrogen bonds : angle 4.36212 / 2.96 ( 1719) link_BETA1-4 : bond 0.00316 / 0.16 ( 2) link_BETA1-4 : angle 0.91420 / 0.48 ( 6) link_NAG-ASN : bond 0.00116 / 0.06 ( 2) link_NAG-ASN : angle 1.68881 / 0.95 ( 6) *********************** 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: 62 poor density : 245 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: D 30 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8399 (p) REVERT: D 103 LYS cc_start: 0.9350 (ttpt) cc_final: 0.7864 (mmtt) REVERT: E 79 GLN cc_start: 0.6794 (mt0) cc_final: 0.6299 (tt0) REVERT: F 78 GLN cc_start: 0.9034 (mt0) cc_final: 0.8809 (mt0) REVERT: A 177 LYS cc_start: 0.7464 (mmtp) cc_final: 0.6949 (mtmt) REVERT: A 218 SER cc_start: 0.8061 (OUTLIER) cc_final: 0.7806 (m) REVERT: A 226 LEU cc_start: 0.8493 (mm) cc_final: 0.8204 (mp) REVERT: A 252 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8396 (pp) REVERT: A 378 ARG cc_start: 0.7482 (ttp-170) cc_final: 0.6102 (mmt-90) REVERT: A 393 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.6476 (mt0) REVERT: A 417 LYS cc_start: 0.8653 (pttt) cc_final: 0.7738 (mmtm) REVERT: B 75 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8349 (tt) REVERT: B 165 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7867 (tt) REVERT: B 225 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6549 (mm) REVERT: B 263 ARG cc_start: 0.7801 (mmm-85) cc_final: 0.7442 (mmm160) REVERT: B 348 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6605 (mm-30) REVERT: B 378 ARG cc_start: 0.7645 (ttp-170) cc_final: 0.7015 (ttp-110) REVERT: B 387 ASN cc_start: 0.8525 (t0) cc_final: 0.8247 (t0) REVERT: B 585 GLU cc_start: 0.8669 (tp30) cc_final: 0.8394 (tp30) outliers start: 62 outliers final: 40 residues processed: 291 average time/residue: 0.1041 time to fit residues: 44.4440 Evaluate side-chains 284 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 237 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 30 THR 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 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 53 THR 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 153 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 252 LEU 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 474 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 527 ILE 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 75 LEU Chi-restraints excluded: chain B residue 143 SER 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 297 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 475 LEU 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 44 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.0870 chunk 57 optimal weight: 0.8980 chunk 116 optimal weight: 0.0980 chunk 121 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 79 GLN ** A 68 ASN ** 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 = 0.3600 r_free = 0.3600 target = 0.151233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.121590 restraints weight = 15983.826| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.87 r_work: 0.3017 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2918 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= 0.123 Angle : 0.557 8.357 18491 Z= 0.288 Chirality : 0.041 0.212 2106 Planarity : 0.004 0.058 2311 Dihedral : 5.732 64.479 1857 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.94 % Favored : 94.00 % Rotamer: Outliers : 3.52 % Allowed : 20.34 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.21), residues: 1683 helix: 1.48 (0.22), residues: 614 sheet: -0.49 (0.30), residues: 304 loop : -2.18 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 18 TYR 0.015 0.001 TYR A 276 PHE 0.016 0.001 PHE F 79 TRP 0.011 0.001 TRP A 379 HIS 0.002 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (13629) covalent geometry : angle 0.55573 / 0.29 (18463) SS BOND : bond 0.00443 / 0.23 ( 8) SS BOND : angle 1.07111 / 0.64 ( 16) hydrogen bonds : bond 0.04273 / 2.88 ( 608) hydrogen bonds : angle 4.19760 / 2.85 ( 1719) link_BETA1-4 : bond 0.00205 / 0.10 ( 2) link_BETA1-4 : angle 0.97425 / 0.54 ( 6) link_NAG-ASN : bond 0.00023 / 0.01 ( 2) link_NAG-ASN : angle 1.65769 / 0.96 ( 6) *********************** 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 301 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 250 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: D 30 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8409 (p) REVERT: D 103 LYS cc_start: 0.9310 (ttpt) cc_final: 0.7846 (mmtt) REVERT: E 42 ASN cc_start: 0.8629 (m-40) cc_final: 0.8395 (m-40) REVERT: E 79 GLN cc_start: 0.6789 (mt0) cc_final: 0.6288 (tt0) REVERT: F 78 GLN cc_start: 0.9001 (mt0) cc_final: 0.8727 (mt0) REVERT: A 141 GLN cc_start: 0.8173 (tt0) cc_final: 0.7966 (tt0) REVERT: A 177 LYS cc_start: 0.7426 (mmtp) cc_final: 0.6933 (mtmt) REVERT: A 218 SER cc_start: 0.8017 (OUTLIER) cc_final: 0.7732 (m) REVERT: A 226 LEU cc_start: 0.8407 (mm) cc_final: 0.8101 (mp) REVERT: A 252 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8413 (pp) REVERT: A 378 ARG cc_start: 0.7415 (ttp-170) cc_final: 0.6030 (mmt-90) REVERT: A 393 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6271 (mt0) REVERT: A 417 LYS cc_start: 0.8635 (pttt) cc_final: 0.7737 (mmtm) REVERT: B 45 ARG cc_start: 0.4283 (ttt-90) cc_final: 0.3002 (mtp-110) REVERT: B 75 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8334 (tt) REVERT: B 225 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6635 (mm) REVERT: B 263 ARG cc_start: 0.7755 (mmm-85) cc_final: 0.7406 (mmm160) REVERT: B 348 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6580 (mm-30) REVERT: B 378 ARG cc_start: 0.7610 (ttp-170) cc_final: 0.7000 (ttp-110) REVERT: B 387 ASN cc_start: 0.8466 (t0) cc_final: 0.8163 (t0) REVERT: B 585 GLU cc_start: 0.8657 (tp30) cc_final: 0.8415 (tp30) outliers start: 51 outliers final: 38 residues processed: 285 average time/residue: 0.1099 time to fit residues: 45.9126 Evaluate side-chains 290 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 246 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 30 THR 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 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 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 153 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 252 LEU 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 527 ILE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain B residue 75 LEU 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 393 GLN Chi-restraints excluded: chain B residue 408 VAL 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 73 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 48 optimal weight: 0.0970 chunk 78 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.147672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.116058 restraints weight = 16054.018| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.96 r_work: 0.3024 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13641 Z= 0.131 Angle : 0.556 8.604 18491 Z= 0.287 Chirality : 0.041 0.188 2106 Planarity : 0.004 0.057 2311 Dihedral : 5.400 51.210 1857 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.12 % Favored : 93.82 % Rotamer: Outliers : 4.07 % Allowed : 19.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.21), residues: 1683 helix: 1.66 (0.22), residues: 614 sheet: -0.47 (0.29), residues: 315 loop : -2.04 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 147 TYR 0.015 0.001 TYR B 605 PHE 0.017 0.001 PHE F 79 TRP 0.010 0.001 TRP A 379 HIS 0.003 0.001 HIS A 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (13629) covalent geometry : angle 0.55414 / 0.29 (18463) SS BOND : bond 0.00509 / 0.26 ( 8) SS BOND : angle 1.13648 / 0.66 ( 16) hydrogen bonds : bond 0.04228 / 2.84 ( 608) hydrogen bonds : angle 4.11035 / 2.79 ( 1719) link_BETA1-4 : bond 0.00304 / 0.15 ( 2) link_BETA1-4 : angle 0.98604 / 0.54 ( 6) link_NAG-ASN : bond 0.00027 / 0.01 ( 2) link_NAG-ASN : angle 1.58146 / 0.89 ( 6) *********************** 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 304 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 245 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: D 30 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8364 (p) REVERT: D 103 LYS cc_start: 0.9318 (ttpt) cc_final: 0.7885 (mmtt) REVERT: D 111 GLN cc_start: 0.7802 (pm20) cc_final: 0.7579 (pt0) REVERT: E 79 GLN cc_start: 0.6810 (mt0) cc_final: 0.6337 (tt0) REVERT: F 78 GLN cc_start: 0.9010 (mt0) cc_final: 0.8762 (mt0) REVERT: A 177 LYS cc_start: 0.7439 (mmtp) cc_final: 0.6971 (mtmt) REVERT: A 226 LEU cc_start: 0.8530 (mm) cc_final: 0.8224 (mp) REVERT: A 378 ARG cc_start: 0.7429 (ttp-170) cc_final: 0.6019 (mmt-90) REVERT: A 393 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6878 (tm-30) REVERT: A 417 LYS cc_start: 0.8603 (pttt) cc_final: 0.7738 (mmtm) REVERT: A 635 CYS cc_start: 0.8615 (m) cc_final: 0.8133 (m) REVERT: B 45 ARG cc_start: 0.4494 (ttt-90) cc_final: 0.3231 (mtp-110) REVERT: B 160 ARG cc_start: 0.6636 (ttt180) cc_final: 0.6365 (ttt180) REVERT: B 165 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7800 (tt) REVERT: B 225 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.6706 (mm) REVERT: B 263 ARG cc_start: 0.7746 (mmm-85) cc_final: 0.7374 (mmm160) REVERT: B 348 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6585 (mm-30) REVERT: B 378 ARG cc_start: 0.7634 (ttp-170) cc_final: 0.7033 (ttp-110) REVERT: B 387 ASN cc_start: 0.8488 (t0) cc_final: 0.8181 (t0) REVERT: B 515 MET cc_start: 0.8968 (mmm) cc_final: 0.8710 (mtp) REVERT: B 585 GLU cc_start: 0.8635 (tp30) cc_final: 0.8374 (tp30) outliers start: 59 outliers final: 46 residues processed: 290 average time/residue: 0.1083 time to fit residues: 45.7087 Evaluate side-chains 288 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 238 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 30 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 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 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 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 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 259 LEU 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 393 GLN Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 565 LEU 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 67 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3511 r_free = 0.3511 target = 0.144587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.113105 restraints weight = 16082.428| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.94 r_work: 0.2983 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13641 Z= 0.185 Angle : 0.611 9.493 18491 Z= 0.313 Chirality : 0.043 0.220 2106 Planarity : 0.004 0.055 2311 Dihedral : 5.410 49.845 1857 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.77 % Favored : 93.17 % Rotamer: Outliers : 4.62 % Allowed : 19.93 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.21), residues: 1683 helix: 1.58 (0.22), residues: 615 sheet: -0.33 (0.30), residues: 302 loop : -2.08 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 147 TYR 0.018 0.002 TYR D 51 PHE 0.018 0.002 PHE F 79 TRP 0.010 0.002 TRP A 379 HIS 0.005 0.001 HIS A 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 (13629) covalent geometry : angle 0.60924 / 0.31 (18463) SS BOND : bond 0.00642 / 0.32 ( 8) SS BOND : angle 1.48773 / 0.87 ( 16) hydrogen bonds : bond 0.04869 / 3.27 ( 608) hydrogen bonds : angle 4.24323 / 2.89 ( 1719) link_BETA1-4 : bond 0.00229 / 0.11 ( 2) link_BETA1-4 : angle 0.80353 / 0.40 ( 6) link_NAG-ASN : bond 0.00203 / 0.10 ( 2) link_NAG-ASN : angle 1.75039 / 1.00 ( 6) *********************** 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 309 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 242 time to evaluate : 0.524 Fit side-chains REVERT: D 30 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8385 (p) REVERT: D 103 LYS cc_start: 0.9364 (ttpt) cc_final: 0.7926 (mmtt) REVERT: D 111 GLN cc_start: 0.7889 (pm20) cc_final: 0.7646 (pt0) REVERT: E 56 THR cc_start: 0.7665 (OUTLIER) cc_final: 0.7449 (p) REVERT: E 79 GLN cc_start: 0.6843 (mt0) cc_final: 0.6303 (tt0) REVERT: F 3 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7712 (mp10) REVERT: A 168 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7766 (mp) REVERT: A 177 LYS cc_start: 0.7501 (mmtp) cc_final: 0.7019 (mtmt) REVERT: A 226 LEU cc_start: 0.8518 (mm) cc_final: 0.8208 (mp) REVERT: A 252 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8454 (pp) REVERT: A 351 GLN cc_start: 0.6608 (tm-30) cc_final: 0.6256 (tm-30) REVERT: A 378 ARG cc_start: 0.7454 (ttp-170) cc_final: 0.6034 (mmt-90) REVERT: A 393 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6788 (tp-100) REVERT: A 417 LYS cc_start: 0.8641 (pttt) cc_final: 0.7776 (mmtm) REVERT: A 635 CYS cc_start: 0.8629 (m) cc_final: 0.8167 (m) REVERT: B 45 ARG cc_start: 0.4552 (ttt-90) cc_final: 0.3358 (mtp-110) REVERT: B 165 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7824 (tt) REVERT: B 225 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6553 (mm) REVERT: B 226 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7333 (mm) REVERT: B 263 ARG cc_start: 0.7805 (mmm-85) cc_final: 0.7413 (mmm160) REVERT: B 348 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6565 (mm-30) REVERT: B 378 ARG cc_start: 0.7662 (ttp-170) cc_final: 0.7058 (ttp-110) REVERT: B 515 MET cc_start: 0.8996 (mmm) cc_final: 0.8688 (mtp) REVERT: B 585 GLU cc_start: 0.8658 (tp30) cc_final: 0.8366 (tp30) REVERT: B 608 CYS cc_start: 0.8596 (m) cc_final: 0.8298 (m) outliers start: 67 outliers final: 54 residues processed: 294 average time/residue: 0.1095 time to fit residues: 46.8236 Evaluate side-chains 298 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 235 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 D residue 21 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 36 ASN 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 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 5 GLN 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 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 168 LEU Chi-restraints excluded: chain A residue 252 LEU 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 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 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 259 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 370 THR 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 565 LEU 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 122 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 25 optimal weight: 0.0170 chunk 60 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 161 optimal weight: 0.3980 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 ASN ** 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 = 0.3529 r_free = 0.3529 target = 0.146138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.114425 restraints weight = 15903.358| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.99 r_work: 0.3000 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13641 Z= 0.142 Angle : 0.573 9.047 18491 Z= 0.295 Chirality : 0.041 0.201 2106 Planarity : 0.004 0.055 2311 Dihedral : 5.261 50.273 1856 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.06 % Favored : 93.88 % Rotamer: Outliers : 4.62 % Allowed : 20.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.22), residues: 1683 helix: 1.68 (0.22), residues: 615 sheet: -0.26 (0.30), residues: 301 loop : -1.99 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 147 TYR 0.016 0.001 TYR A 276 PHE 0.017 0.001 PHE F 79 TRP 0.010 0.001 TRP A 379 HIS 0.003 0.001 HIS A 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (13629) covalent geometry : angle 0.57169 / 0.29 (18463) SS BOND : bond 0.00488 / 0.25 ( 8) SS BOND : angle 1.14259 / 0.66 ( 16) hydrogen bonds : bond 0.04393 / 2.95 ( 608) hydrogen bonds : angle 4.13083 / 2.81 ( 1719) link_BETA1-4 : bond 0.00237 / 0.12 ( 2) link_BETA1-4 : angle 0.88295 / 0.44 ( 6) link_NAG-ASN : bond 0.00051 / 0.03 ( 2) link_NAG-ASN : angle 1.62683 / 0.92 ( 6) *********************** 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 306 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 239 time to evaluate : 0.369 Fit side-chains REVERT: C 18 ARG cc_start: 0.7155 (ttp80) cc_final: 0.6670 (ttp-170) REVERT: D 5 GLN cc_start: 0.8266 (mm-40) cc_final: 0.8024 (tp40) REVERT: D 30 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8360 (p) REVERT: D 103 LYS cc_start: 0.9348 (ttpt) cc_final: 0.7876 (mmtt) REVERT: E 56 THR cc_start: 0.7691 (OUTLIER) cc_final: 0.7491 (p) REVERT: E 79 GLN cc_start: 0.6798 (mt0) cc_final: 0.6313 (tt0) REVERT: F 3 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7676 (mp10) REVERT: A 177 LYS cc_start: 0.7488 (mmtp) cc_final: 0.7012 (mtmt) REVERT: A 226 LEU cc_start: 0.8487 (mm) cc_final: 0.8184 (mp) REVERT: A 252 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8413 (pp) REVERT: A 351 GLN cc_start: 0.6491 (tm-30) cc_final: 0.6139 (tm-30) REVERT: A 378 ARG cc_start: 0.7412 (ttp-170) cc_final: 0.5978 (mmt-90) REVERT: A 393 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6856 (tp-100) REVERT: A 417 LYS cc_start: 0.8608 (pttt) cc_final: 0.7714 (mmtm) REVERT: A 635 CYS cc_start: 0.8621 (m) cc_final: 0.8169 (m) REVERT: B 45 ARG cc_start: 0.4549 (ttt-90) cc_final: 0.3344 (mtp-110) REVERT: B 160 ARG cc_start: 0.6637 (ttt180) cc_final: 0.6336 (ttt180) REVERT: B 165 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7746 (tt) REVERT: B 222 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.8002 (m-40) REVERT: B 225 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6661 (mm) REVERT: B 263 ARG cc_start: 0.7807 (mmm-85) cc_final: 0.7414 (mmm160) REVERT: B 348 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6561 (mm-30) REVERT: B 378 ARG cc_start: 0.7655 (ttp-170) cc_final: 0.7034 (ttp-110) REVERT: B 515 MET cc_start: 0.9010 (mmm) cc_final: 0.8697 (mtp) REVERT: B 585 GLU cc_start: 0.8648 (tp30) cc_final: 0.8378 (tp30) REVERT: B 608 CYS cc_start: 0.8611 (m) cc_final: 0.8318 (m) outliers start: 67 outliers final: 53 residues processed: 292 average time/residue: 0.1095 time to fit residues: 46.6356 Evaluate side-chains 298 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 237 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 D residue 21 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 36 ASN 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 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 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 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 252 LEU 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 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 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 222 ASN 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 332 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 408 VAL 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 565 LEU 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 12 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 70 optimal weight: 0.0570 chunk 93 optimal weight: 0.4980 chunk 142 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 ASN ** 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 = 0.3550 r_free = 0.3550 target = 0.148158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.116183 restraints weight = 16086.259| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.14 r_work: 0.3029 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13641 Z= 0.108 Angle : 0.546 8.268 18491 Z= 0.282 Chirality : 0.040 0.192 2106 Planarity : 0.003 0.051 2311 Dihedral : 4.985 50.918 1853 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.12 % Favored : 93.82 % Rotamer: Outliers : 3.79 % Allowed : 21.38 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.22), residues: 1683 helix: 1.74 (0.22), residues: 617 sheet: -0.18 (0.30), residues: 299 loop : -1.90 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 482 TYR 0.015 0.001 TYR A 276 PHE 0.014 0.001 PHE F 79 TRP 0.012 0.001 TRP B 627 HIS 0.002 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (13629) covalent geometry : angle 0.54461 / 0.28 (18463) SS BOND : bond 0.00383 / 0.20 ( 8) SS BOND : angle 0.91165 / 0.53 ( 16) hydrogen bonds : bond 0.03921 / 2.63 ( 608) hydrogen bonds : angle 4.00449 / 2.72 ( 1719) link_BETA1-4 : bond 0.00306 / 0.15 ( 2) link_BETA1-4 : angle 0.99632 / 0.54 ( 6) link_NAG-ASN : bond 0.00084 / 0.04 ( 2) link_NAG-ASN : angle 1.57157 / 0.92 ( 6) *********************** 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 302 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 247 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: C 18 ARG cc_start: 0.7148 (ttp80) cc_final: 0.6714 (ttp-170) REVERT: D 5 GLN cc_start: 0.8348 (mm-40) cc_final: 0.8120 (tp40) REVERT: D 103 LYS cc_start: 0.9336 (ttpt) cc_final: 0.7877 (mmtt) REVERT: E 79 GLN cc_start: 0.6770 (mt0) cc_final: 0.6303 (tt0) REVERT: F 78 GLN cc_start: 0.8986 (mt0) cc_final: 0.8709 (mt0) REVERT: A 177 LYS cc_start: 0.7420 (mmtp) cc_final: 0.6955 (mtmt) REVERT: A 226 LEU cc_start: 0.8467 (mm) cc_final: 0.8160 (mp) REVERT: A 252 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8431 (pp) REVERT: A 378 ARG cc_start: 0.7371 (ttp-170) cc_final: 0.5931 (mmt-90) REVERT: A 417 LYS cc_start: 0.8593 (pttt) cc_final: 0.7717 (mmtm) REVERT: A 458 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8581 (mt-10) REVERT: A 481 MET cc_start: 0.7935 (mmt) cc_final: 0.6690 (ttp) REVERT: B 45 ARG cc_start: 0.4486 (ttt-90) cc_final: 0.3296 (mtp-110) REVERT: B 165 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7672 (tt) REVERT: B 225 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.6677 (mm) REVERT: B 263 ARG cc_start: 0.7797 (mmm-85) cc_final: 0.7412 (mmm160) REVERT: B 348 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6524 (mm-30) REVERT: B 378 ARG cc_start: 0.7630 (ttp-170) cc_final: 0.7038 (ttp-110) REVERT: B 481 MET cc_start: 0.7274 (mmt) cc_final: 0.7020 (tpt) REVERT: B 515 MET cc_start: 0.8982 (mmm) cc_final: 0.8708 (mtp) REVERT: B 531 GLN cc_start: 0.6894 (mm110) cc_final: 0.6502 (mm-40) REVERT: B 585 GLU cc_start: 0.8638 (tp30) cc_final: 0.8379 (tp30) REVERT: B 608 CYS cc_start: 0.8611 (m) cc_final: 0.8324 (m) outliers start: 55 outliers final: 44 residues processed: 289 average time/residue: 0.1097 time to fit residues: 45.9416 Evaluate side-chains 287 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 240 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 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 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 102 LEU 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 165 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 446 GLU 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 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 370 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 565 LEU 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 22 optimal weight: 0.2980 chunk 110 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 0.0040 chunk 107 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 157 optimal weight: 2.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3547 r_free = 0.3547 target = 0.147868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.115903 restraints weight = 15954.605| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.03 r_work: 0.3017 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3399 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= 0.117 Angle : 0.552 10.581 18491 Z= 0.284 Chirality : 0.040 0.191 2106 Planarity : 0.003 0.050 2311 Dihedral : 4.700 51.038 1850 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.24 % Favored : 93.70 % Rotamer: Outliers : 3.38 % Allowed : 21.59 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.22), residues: 1683 helix: 1.81 (0.22), residues: 618 sheet: -0.22 (0.30), residues: 305 loop : -1.82 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 147 TYR 0.015 0.001 TYR A 276 PHE 0.015 0.001 PHE F 79 TRP 0.011 0.001 TRP B 627 HIS 0.002 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (13629) covalent geometry : angle 0.55115 / 0.28 (18463) SS BOND : bond 0.00421 / 0.22 ( 8) SS BOND : angle 0.99444 / 0.59 ( 16) hydrogen bonds : bond 0.03976 / 2.67 ( 608) hydrogen bonds : angle 3.97954 / 2.71 ( 1719) link_BETA1-4 : bond 0.00251 / 0.12 ( 2) link_BETA1-4 : angle 0.97136 / 0.52 ( 6) link_NAG-ASN : bond 0.00074 / 0.04 ( 2) link_NAG-ASN : angle 1.54132 / 0.87 ( 6) ********************** 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 297 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 248 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: C 18 ARG cc_start: 0.7131 (ttp80) cc_final: 0.6657 (ttp-170) REVERT: D 5 GLN cc_start: 0.8358 (mm-40) cc_final: 0.8132 (tp40) REVERT: D 103 LYS cc_start: 0.9327 (ttpt) cc_final: 0.7891 (mmtt) REVERT: E 79 GLN cc_start: 0.6773 (mt0) cc_final: 0.6320 (tt0) REVERT: F 3 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7628 (mp10) REVERT: F 78 GLN cc_start: 0.9001 (mt0) cc_final: 0.8755 (mt0) REVERT: A 177 LYS cc_start: 0.7433 (mmtp) cc_final: 0.6984 (mtmt) REVERT: A 226 LEU cc_start: 0.8468 (mm) cc_final: 0.8160 (mp) REVERT: A 252 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8441 (pp) REVERT: A 378 ARG cc_start: 0.7361 (ttp-170) cc_final: 0.5930 (mmt-90) REVERT: A 417 LYS cc_start: 0.8587 (pttt) cc_final: 0.7712 (mmtm) REVERT: A 481 MET cc_start: 0.7937 (mmt) cc_final: 0.6724 (ttp) REVERT: A 635 CYS cc_start: 0.8629 (m) cc_final: 0.8173 (m) REVERT: B 45 ARG cc_start: 0.4495 (ttt-90) cc_final: 0.3316 (mtp-110) REVERT: B 160 ARG cc_start: 0.6751 (ttm-80) cc_final: 0.6412 (ttt180) REVERT: B 165 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7686 (tt) REVERT: B 225 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6672 (mm) REVERT: B 263 ARG cc_start: 0.7819 (mmm-85) cc_final: 0.7429 (mmm160) REVERT: B 348 GLU cc_start: 0.6804 (mt-10) cc_final: 0.6517 (mm-30) REVERT: B 378 ARG cc_start: 0.7653 (ttp-170) cc_final: 0.7053 (ttp-110) REVERT: B 481 MET cc_start: 0.7384 (mmt) cc_final: 0.7031 (tpt) REVERT: B 515 MET cc_start: 0.8966 (mmm) cc_final: 0.8690 (mtp) REVERT: B 531 GLN cc_start: 0.6866 (mm110) cc_final: 0.6467 (mm-40) REVERT: B 585 GLU cc_start: 0.8647 (tp30) cc_final: 0.8387 (tp30) REVERT: B 608 CYS cc_start: 0.8623 (m) cc_final: 0.8338 (m) outliers start: 49 outliers final: 45 residues processed: 283 average time/residue: 0.1059 time to fit residues: 43.6498 Evaluate side-chains 290 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 241 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 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 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 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 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 153 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 370 THR 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 536 VAL Chi-restraints excluded: chain A residue 556 VAL 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 370 THR 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 565 LEU 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 114 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 chunk 166 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 HIS ** 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 = 0.3532 r_free = 0.3532 target = 0.146664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.114607 restraints weight = 15960.135| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.03 r_work: 0.3003 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13641 Z= 0.137 Angle : 0.568 10.738 18491 Z= 0.292 Chirality : 0.041 0.203 2106 Planarity : 0.003 0.048 2311 Dihedral : 4.704 50.519 1848 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.77 % Favored : 93.17 % Rotamer: Outliers : 3.86 % Allowed : 21.31 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.22), residues: 1683 helix: 1.81 (0.22), residues: 618 sheet: -0.16 (0.30), residues: 301 loop : -1.84 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 147 TYR 0.015 0.001 TYR A 276 PHE 0.016 0.001 PHE F 79 TRP 0.010 0.001 TRP A 379 HIS 0.003 0.001 HIS A 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (13629) covalent geometry : angle 0.56652 / 0.29 (18463) SS BOND : bond 0.00484 / 0.25 ( 8) SS BOND : angle 1.17652 / 0.70 ( 16) hydrogen bonds : bond 0.04205 / 2.82 ( 608) hydrogen bonds : angle 4.00987 / 2.73 ( 1719) link_BETA1-4 : bond 0.00275 / 0.14 ( 2) link_BETA1-4 : angle 0.91098 / 0.48 ( 6) link_NAG-ASN : bond 0.00008 / 0.00 ( 2) link_NAG-ASN : angle 1.72450 / 0.97 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3882.63 seconds wall clock time: 67 minutes 2.33 seconds (4022.33 seconds total)