Starting phenix.real_space_refine on Sat Aug 23 16:28:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p8a_17543/08_2025/8p8a_17543.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p8a_17543/08_2025/8p8a_17543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p8a_17543/08_2025/8p8a_17543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p8a_17543/08_2025/8p8a_17543.map" model { file = "/net/cci-nas-00/data/ceres_data/8p8a_17543/08_2025/8p8a_17543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p8a_17543/08_2025/8p8a_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-2.0-5787/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.62, per 1000 atoms: 0.27 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: 1.16 Conformation dependent library (CDL) restraints added in 786.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.34 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: 2.48 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3866 1.34 - 1.46: 2722 1.46 - 1.58: 6921 1.58 - 1.69: 6 1.69 - 1.81: 114 Bond restraints: 13629 Sorted by residual: bond pdb=" CA GLN A 181 " pdb=" C GLN A 181 " ideal model delta sigma weight residual 1.523 1.569 -0.046 1.34e-02 5.57e+03 1.17e+01 bond pdb=" CA GLN B 181 " pdb=" C GLN B 181 " ideal model delta sigma weight residual 1.523 1.569 -0.046 1.34e-02 5.57e+03 1.16e+01 bond pdb=" C LYS Z 87 " pdb=" N PRO Z 88 " ideal model delta sigma weight residual 1.337 1.366 -0.030 9.80e-03 1.04e+04 9.21e+00 bond pdb=" N VAL Z 2 " pdb=" CA VAL Z 2 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.74e+00 bond pdb=" N ASP Z 111 " pdb=" CA ASP Z 111 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.15e-02 7.56e+03 7.93e+00 ... (remaining 13624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.95: 18302 3.95 - 7.90: 136 7.90 - 11.84: 20 11.84 - 15.79: 3 15.79 - 19.74: 2 Bond angle restraints: 18463 Sorted by residual: angle pdb=" N ILE B 335 " pdb=" CA ILE B 335 " pdb=" C ILE B 335 " ideal model delta sigma weight residual 113.39 99.49 13.90 1.47e+00 4.63e-01 8.95e+01 angle pdb=" CB LYS B 61 " pdb=" CG LYS B 61 " pdb=" CD LYS B 61 " ideal model delta sigma weight residual 111.30 131.04 -19.74 2.30e+00 1.89e-01 7.37e+01 angle pdb=" CB LYS A 61 " pdb=" CG LYS A 61 " pdb=" CD LYS A 61 " ideal model delta sigma weight residual 111.30 131.00 -19.70 2.30e+00 1.89e-01 7.34e+01 angle pdb=" CA LYS A 61 " pdb=" CB LYS A 61 " pdb=" CG LYS A 61 " ideal model delta sigma weight residual 114.10 125.55 -11.45 2.00e+00 2.50e-01 3.28e+01 angle pdb=" CA LYS B 61 " pdb=" CB LYS B 61 " pdb=" CG LYS B 61 " ideal model delta sigma weight residual 114.10 125.52 -11.42 2.00e+00 2.50e-01 3.26e+01 ... (remaining 18458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7072 17.95 - 35.89: 662 35.89 - 53.84: 238 53.84 - 71.78: 88 71.78 - 89.73: 17 Dihedral angle restraints: 8077 sinusoidal: 3182 harmonic: 4895 Sorted by residual: dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS B 603 " pdb=" CB CYS B 603 " ideal model delta sinusoidal sigma weight residual -86.00 -10.95 -75.05 1 1.00e+01 1.00e-02 7.12e+01 dihedral pdb=" CA GLU A 334 " pdb=" C GLU A 334 " pdb=" N ILE A 335 " pdb=" CA ILE A 335 " ideal model delta harmonic sigma weight residual 180.00 145.44 34.56 0 5.00e+00 4.00e-02 4.78e+01 dihedral pdb=" CA ASN A 604 " pdb=" C ASN A 604 " pdb=" N TYR A 605 " pdb=" CA TYR A 605 " ideal model delta harmonic sigma weight residual 180.00 -151.29 -28.71 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 8074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1823 0.077 - 0.155: 249 0.155 - 0.232: 29 0.232 - 0.309: 2 0.309 - 0.387: 3 Chirality restraints: 2106 Sorted by residual: chirality pdb=" CB THR B 607 " pdb=" CA THR B 607 " pdb=" OG1 THR B 607 " pdb=" CG2 THR B 607 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CB THR A 607 " pdb=" CA THR A 607 " pdb=" OG1 THR A 607 " pdb=" CG2 THR A 607 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CA ILE B 335 " pdb=" N ILE B 335 " pdb=" C ILE B 335 " pdb=" CB ILE B 335 " both_signs ideal model delta sigma weight residual False 2.43 2.79 -0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 2103 not shown) Planarity restraints: 2313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 87 " -0.052 5.00e-02 4.00e+02 7.82e-02 9.78e+00 pdb=" N PRO F 88 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO F 88 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 88 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 87 " 0.052 5.00e-02 4.00e+02 7.82e-02 9.77e+00 pdb=" N PRO D 88 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 159 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" CD GLU A 159 " -0.042 2.00e-02 2.50e+03 pdb=" OE1 GLU A 159 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU A 159 " 0.015 2.00e-02 2.50e+03 ... (remaining 2310 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1637 2.75 - 3.29: 11702 3.29 - 3.83: 21173 3.83 - 4.36: 25009 4.36 - 4.90: 45400 Nonbonded interactions: 104921 Sorted by model distance: nonbonded pdb=" O ASN B 436 " pdb=" OG SER B 440 " model vdw 2.213 3.040 nonbonded pdb=" O ASN A 436 " pdb=" OG SER A 440 " model vdw 2.214 3.040 nonbonded pdb=" O GLY Z 30 " pdb=" OG1 THR Z 53 " model vdw 2.240 3.040 nonbonded pdb=" O MET Z 103 " pdb=" OH TYR Z 110 " model vdw 2.299 3.040 nonbonded pdb=" O PHE B 293 " pdb=" CG2 ILE B 297 " model vdw 2.307 3.460 ... (remaining 104916 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 33 through 301 or resid 327 through 654)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.070 Find NCS groups from input model: 0.200 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 13641 Z= 0.309 Angle : 1.020 19.740 18491 Z= 0.566 Chirality : 0.057 0.387 2106 Planarity : 0.007 0.078 2311 Dihedral : 17.655 89.726 4931 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.25 % Favored : 92.69 % Rotamer: Outliers : 10.55 % Allowed : 7.66 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00649 (13629) covalent geometry : angle 1.01334 (18463) SS BOND : bond 0.00642 ( 8) SS BOND : angle 3.03581 ( 16) hydrogen bonds : bond 0.19045 ( 608) hydrogen bonds : angle 7.04865 ( 1719) link_BETA1-4 : bond 0.00449 ( 2) link_BETA1-4 : angle 2.60531 ( 6) link_NAG-ASN : bond 0.00171 ( 2) link_NAG-ASN : angle 3.73755 ( 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 : 0.482 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: 0.1155 time to fit residues: 71.5690 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 : 0.440 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 387 ASN B 425 ASN B 437 GLN B 457 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.157000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.126486 restraints weight = 15923.576| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.91 r_work: 0.3087 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1905 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= 0.151 Angle : 0.617 8.593 18491 Z= 0.323 Chirality : 0.042 0.166 2106 Planarity : 0.005 0.064 2311 Dihedral : 9.029 90.555 1988 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.24 % Favored : 93.70 % Rotamer: Outliers : 4.34 % Allowed : 15.59 % Favored : 80.07 % 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 aren not related in a simple way. whole: -2.02 (0.19), residues: 1683 helix: 0.26 (0.20), residues: 604 sheet: -1.47 (0.28), residues: 302 loop : -2.65 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 84 TYR 0.017 0.001 TYR A 605 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 covalent geometry : bond 0.00341 (13629) covalent geometry : angle 0.61465 (18463) SS BOND : bond 0.00615 ( 8) SS BOND : angle 1.26298 ( 16) hydrogen bonds : bond 0.04927 ( 608) hydrogen bonds : angle 4.68180 ( 1719) link_BETA1-4 : bond 0.00251 ( 2) link_BETA1-4 : angle 1.52744 ( 6) link_NAG-ASN : bond 0.00128 ( 2) link_NAG-ASN : angle 2.00941 ( 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 321 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 258 time to evaluate : 0.561 Fit side-chains REVERT: E 79 GLN cc_start: 0.6775 (mt0) cc_final: 0.6464 (tt0) REVERT: F 78 GLN cc_start: 0.8996 (mt0) cc_final: 0.8611 (mt0) REVERT: F 89 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7418 (mm-30) REVERT: F 111 GLN cc_start: 0.8575 (pm20) cc_final: 0.8343 (pm20) REVERT: A 141 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7918 (mt0) REVERT: A 177 LYS cc_start: 0.7345 (mmtp) cc_final: 0.6726 (mtmt) REVERT: A 226 LEU cc_start: 0.8407 (mm) cc_final: 0.8157 (mp) REVERT: A 285 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6889 (mt-10) REVERT: A 378 ARG cc_start: 0.7354 (ttp-170) cc_final: 0.6120 (mmt-90) REVERT: A 393 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6394 (mt0) REVERT: A 417 LYS cc_start: 0.8612 (pttt) cc_final: 0.7803 (mmtm) REVERT: A 616 LYS cc_start: 0.8815 (mttp) cc_final: 0.8302 (mtpp) REVERT: B 160 ARG cc_start: 0.6771 (ttt180) cc_final: 0.6494 (ttt180) REVERT: B 162 ASN cc_start: 0.6069 (m-40) cc_final: 0.5651 (m-40) REVERT: B 198 MET cc_start: 0.8250 (mtm) cc_final: 0.8038 (mtp) REVERT: B 222 ASN cc_start: 0.8149 (OUTLIER) cc_final: 0.7871 (t0) REVERT: B 263 ARG cc_start: 0.7897 (mmm-85) cc_final: 0.7381 (mmm160) REVERT: B 348 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6511 (mm-30) REVERT: B 375 HIS cc_start: 0.7715 (t70) cc_final: 0.7151 (t-170) REVERT: B 378 ARG cc_start: 0.7674 (ttp-170) cc_final: 0.7051 (ttp-110) REVERT: B 387 ASN cc_start: 0.8397 (t0) cc_final: 0.8104 (t0) REVERT: B 585 GLU cc_start: 0.8590 (tp30) cc_final: 0.8274 (tp30) outliers start: 63 outliers final: 36 residues processed: 304 average time/residue: 0.1270 time to fit residues: 55.7444 Evaluate side-chains 284 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 248 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 563 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 68 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN A 283 HIS 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 = 0.3494 r_free = 0.3494 target = 0.142634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.110449 restraints weight = 16396.169| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.04 r_work: 0.2938 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 13641 Z= 0.315 Angle : 0.751 10.795 18491 Z= 0.387 Chirality : 0.048 0.211 2106 Planarity : 0.005 0.066 2311 Dihedral : 7.761 85.164 1954 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.55 % Favored : 92.39 % Rotamer: Outliers : 4.62 % Allowed : 17.10 % Favored : 78.28 % 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 aren not related in a simple way. whole: -1.54 (0.20), residues: 1683 helix: 0.75 (0.21), residues: 604 sheet: -0.96 (0.29), residues: 304 loop : -2.57 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 107 TYR 0.025 0.002 TYR D 51 PHE 0.022 0.002 PHE F 79 TRP 0.014 0.003 TRP D 109 HIS 0.008 0.002 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00766 (13629) covalent geometry : angle 0.74769 (18463) SS BOND : bond 0.00902 ( 8) SS BOND : angle 2.15796 ( 16) hydrogen bonds : bond 0.06479 ( 608) hydrogen bonds : angle 4.76957 ( 1719) link_BETA1-4 : bond 0.00130 ( 2) link_BETA1-4 : angle 1.33132 ( 6) link_NAG-ASN : bond 0.00681 ( 2) link_NAG-ASN : angle 2.26737 ( 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 305 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 238 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: D 82 GLN cc_start: 0.8272 (tp40) cc_final: 0.8006 (tp40) REVERT: E 79 GLN cc_start: 0.6651 (mt0) cc_final: 0.6271 (tt0) REVERT: F 89 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7433 (mm-30) REVERT: A 141 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7836 (mt0) REVERT: A 177 LYS cc_start: 0.7474 (mmtp) cc_final: 0.6925 (mtmt) REVERT: A 205 SER cc_start: 0.8398 (p) cc_final: 0.8193 (t) REVERT: A 226 LEU cc_start: 0.8521 (mm) cc_final: 0.8222 (mp) REVERT: A 246 ARG cc_start: 0.8130 (mpt180) cc_final: 0.7338 (mtp85) REVERT: A 285 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7267 (mt-10) REVERT: A 378 ARG cc_start: 0.7515 (ttp-170) cc_final: 0.6119 (mmt-90) REVERT: A 393 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.6462 (mt0) REVERT: A 417 LYS cc_start: 0.8688 (pttt) cc_final: 0.7762 (mmtm) REVERT: A 489 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.8013 (t80) REVERT: A 635 CYS cc_start: 0.8645 (m) cc_final: 0.8221 (m) REVERT: B 75 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8420 (tt) REVERT: B 225 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6629 (mm) REVERT: B 263 ARG cc_start: 0.7786 (mmm-85) cc_final: 0.7425 (mmm160) REVERT: B 348 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6588 (mm-30) REVERT: B 378 ARG cc_start: 0.7665 (ttp-170) cc_final: 0.7027 (ttp-110) REVERT: B 387 ASN cc_start: 0.8605 (t0) cc_final: 0.8290 (t0) REVERT: B 585 GLU cc_start: 0.8696 (tp30) cc_final: 0.8328 (tp30) REVERT: B 608 CYS cc_start: 0.8585 (m) cc_final: 0.8297 (m) outliers start: 67 outliers final: 49 residues processed: 290 average time/residue: 0.1254 time to fit residues: 52.0284 Evaluate side-chains 288 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 234 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 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 75 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 202 THR 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 532 SER 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: 0.7980 chunk 50 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.145881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.113407 restraints weight = 16137.002| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.08 r_work: 0.2992 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13641 Z= 0.148 Angle : 0.589 7.966 18491 Z= 0.306 Chirality : 0.042 0.212 2106 Planarity : 0.004 0.062 2311 Dihedral : 6.752 73.534 1946 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.82 % Favored : 94.12 % Rotamer: Outliers : 4.07 % Allowed : 19.38 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.21), residues: 1683 helix: 1.24 (0.22), residues: 604 sheet: -0.67 (0.29), residues: 303 loop : -2.37 (0.21), residues: 776 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 0.003 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00346 (13629) covalent geometry : angle 0.58683 (18463) SS BOND : bond 0.00527 ( 8) SS BOND : angle 1.19605 ( 16) hydrogen bonds : bond 0.04785 ( 608) hydrogen bonds : angle 4.39503 ( 1719) link_BETA1-4 : bond 0.00360 ( 2) link_BETA1-4 : angle 1.54006 ( 6) link_NAG-ASN : bond 0.00170 ( 2) link_NAG-ASN : angle 1.88858 ( 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 302 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 243 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: D 30 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8379 (p) REVERT: D 103 LYS cc_start: 0.9322 (ttpt) cc_final: 0.7980 (mmtt) REVERT: E 79 GLN cc_start: 0.6844 (mt0) cc_final: 0.6353 (tt0) REVERT: F 78 GLN cc_start: 0.9038 (mt0) cc_final: 0.8811 (mt0) REVERT: A 177 LYS cc_start: 0.7482 (mmtp) cc_final: 0.6980 (mtmt) REVERT: A 205 SER cc_start: 0.8388 (p) cc_final: 0.8180 (t) REVERT: A 226 LEU cc_start: 0.8533 (mm) cc_final: 0.8238 (mp) REVERT: A 252 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8415 (pp) REVERT: A 285 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7419 (mt-10) REVERT: A 378 ARG cc_start: 0.7524 (ttp-170) cc_final: 0.6158 (mmt-90) REVERT: A 393 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.6455 (mt0) REVERT: A 417 LYS cc_start: 0.8661 (pttt) cc_final: 0.7749 (mmtm) REVERT: B 160 ARG cc_start: 0.6787 (ttt180) cc_final: 0.6493 (ttt180) REVERT: B 165 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7906 (tt) REVERT: B 225 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6660 (mm) REVERT: B 263 ARG cc_start: 0.7832 (mmm-85) cc_final: 0.7471 (mmm160) REVERT: B 348 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6625 (mm-30) REVERT: B 378 ARG cc_start: 0.7703 (ttp-170) cc_final: 0.7071 (ttp-110) REVERT: B 387 ASN cc_start: 0.8539 (t0) cc_final: 0.8235 (t0) REVERT: B 585 GLU cc_start: 0.8689 (tp30) cc_final: 0.8417 (tp30) REVERT: B 608 CYS cc_start: 0.8617 (m) cc_final: 0.8339 (m) outliers start: 59 outliers final: 41 residues processed: 287 average time/residue: 0.1148 time to fit residues: 47.7248 Evaluate side-chains 288 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 242 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 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 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 135 THR Chi-restraints excluded: chain A residue 153 THR 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 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 332 LEU 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 489 PHE 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: 0.7980 chunk 57 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 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 = 0.3490 r_free = 0.3490 target = 0.142493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.110436 restraints weight = 16342.193| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.04 r_work: 0.2939 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13641 Z= 0.247 Angle : 0.667 9.265 18491 Z= 0.343 Chirality : 0.045 0.228 2106 Planarity : 0.004 0.062 2311 Dihedral : 6.548 54.662 1941 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.13 % Favored : 92.81 % Rotamer: Outliers : 5.17 % Allowed : 19.03 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.21), residues: 1683 helix: 1.13 (0.21), residues: 616 sheet: -0.57 (0.30), residues: 300 loop : -2.38 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 18 TYR 0.021 0.002 TYR D 51 PHE 0.020 0.002 PHE F 79 TRP 0.012 0.002 TRP D 109 HIS 0.006 0.001 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00598 (13629) covalent geometry : angle 0.66366 (18463) SS BOND : bond 0.00755 ( 8) SS BOND : angle 1.79974 ( 16) hydrogen bonds : bond 0.05575 ( 608) hydrogen bonds : angle 4.53633 ( 1719) link_BETA1-4 : bond 0.00139 ( 2) link_BETA1-4 : angle 1.36867 ( 6) link_NAG-ASN : bond 0.00434 ( 2) link_NAG-ASN : angle 2.10521 ( 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 312 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 237 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: D 30 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8419 (p) REVERT: D 82 GLN cc_start: 0.8280 (tp40) cc_final: 0.7965 (tp40) REVERT: D 103 LYS cc_start: 0.9315 (ttpt) cc_final: 0.7958 (mmtt) REVERT: E 42 ASN cc_start: 0.8702 (m-40) cc_final: 0.8423 (m110) REVERT: E 79 GLN cc_start: 0.6827 (mt0) cc_final: 0.6314 (tt0) REVERT: A 168 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7867 (mp) REVERT: A 205 SER cc_start: 0.8407 (p) cc_final: 0.8195 (t) REVERT: A 226 LEU cc_start: 0.8592 (mm) cc_final: 0.8280 (mp) REVERT: A 246 ARG cc_start: 0.8131 (mpt180) cc_final: 0.7387 (mtp85) REVERT: A 252 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8490 (pp) REVERT: A 378 ARG cc_start: 0.7509 (ttp-170) cc_final: 0.6115 (mmt-90) REVERT: A 393 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6246 (mt0) REVERT: A 417 LYS cc_start: 0.8656 (pttt) cc_final: 0.7718 (mmtm) REVERT: A 635 CYS cc_start: 0.8652 (m) cc_final: 0.8207 (m) REVERT: B 75 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8394 (tt) REVERT: B 160 ARG cc_start: 0.6653 (ttt180) cc_final: 0.6406 (ttt180) REVERT: B 225 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6599 (mm) REVERT: B 263 ARG cc_start: 0.7828 (mmm-85) cc_final: 0.7441 (mmm160) REVERT: B 348 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6573 (mm-30) REVERT: B 378 ARG cc_start: 0.7676 (ttp-170) cc_final: 0.7020 (ttp-110) REVERT: B 387 ASN cc_start: 0.8589 (t0) cc_final: 0.8278 (t0) REVERT: B 585 GLU cc_start: 0.8710 (tp30) cc_final: 0.8403 (tp30) REVERT: B 608 CYS cc_start: 0.8638 (m) cc_final: 0.8361 (m) outliers start: 75 outliers final: 57 residues processed: 294 average time/residue: 0.1228 time to fit residues: 51.9105 Evaluate side-chains 295 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 232 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 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 489 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 48 optimal weight: 0.2980 chunk 78 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.146342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.114330 restraints weight = 16155.993| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.03 r_work: 0.2999 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13641 Z= 0.126 Angle : 0.556 7.571 18491 Z= 0.290 Chirality : 0.041 0.211 2106 Planarity : 0.004 0.058 2311 Dihedral : 6.077 50.647 1941 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.76 % Favored : 94.18 % Rotamer: Outliers : 4.07 % Allowed : 21.03 % Favored : 74.90 % 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 aren not related in a simple way. whole: -0.65 (0.21), residues: 1683 helix: 1.58 (0.22), residues: 606 sheet: -0.57 (0.29), residues: 314 loop : -2.12 (0.22), residues: 763 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 0.015 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 covalent geometry : bond 0.00288 (13629) covalent geometry : angle 0.55433 (18463) SS BOND : bond 0.00442 ( 8) SS BOND : angle 0.99896 ( 16) hydrogen bonds : bond 0.04315 ( 608) hydrogen bonds : angle 4.23613 ( 1719) link_BETA1-4 : bond 0.00248 ( 2) link_BETA1-4 : angle 1.61421 ( 6) link_NAG-ASN : bond 0.00042 ( 2) link_NAG-ASN : angle 1.81977 ( 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 305 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 246 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: D 30 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8389 (p) REVERT: D 103 LYS cc_start: 0.9266 (ttpt) cc_final: 0.7948 (mmtt) REVERT: E 42 ASN cc_start: 0.8674 (m-40) cc_final: 0.8385 (m-40) REVERT: E 56 THR cc_start: 0.7643 (OUTLIER) cc_final: 0.7437 (p) REVERT: E 79 GLN cc_start: 0.6822 (mt0) cc_final: 0.6280 (tt0) REVERT: F 78 GLN cc_start: 0.9015 (mt0) cc_final: 0.8780 (mt0) REVERT: A 177 LYS cc_start: 0.7481 (mmtp) cc_final: 0.7016 (mtmt) REVERT: A 226 LEU cc_start: 0.8553 (mm) cc_final: 0.8238 (mp) REVERT: A 252 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8389 (pp) REVERT: A 378 ARG cc_start: 0.7444 (ttp-170) cc_final: 0.6043 (mmt-90) REVERT: A 393 GLN cc_start: 0.7232 (OUTLIER) cc_final: 0.6080 (mt0) REVERT: A 417 LYS cc_start: 0.8619 (pttt) cc_final: 0.7700 (mmtm) REVERT: B 45 ARG cc_start: 0.4494 (ttt-90) cc_final: 0.3292 (mtp-110) REVERT: B 75 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8337 (tt) REVERT: B 160 ARG cc_start: 0.6718 (ttt180) cc_final: 0.6462 (ttt180) REVERT: B 165 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7840 (tt) REVERT: B 225 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6700 (mm) REVERT: B 230 ARG cc_start: 0.6729 (mtm110) cc_final: 0.6484 (mtm-85) REVERT: B 263 ARG cc_start: 0.7796 (mmm-85) cc_final: 0.7400 (mmm160) REVERT: B 348 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6578 (mm-30) REVERT: B 378 ARG cc_start: 0.7630 (ttp-170) cc_final: 0.7016 (ttp-110) REVERT: B 387 ASN cc_start: 0.8486 (t0) cc_final: 0.8151 (t0) REVERT: B 585 GLU cc_start: 0.8652 (tp30) cc_final: 0.8390 (tp30) REVERT: B 608 CYS cc_start: 0.8637 (m) cc_final: 0.8380 (m) outliers start: 59 outliers final: 46 residues processed: 290 average time/residue: 0.1312 time to fit residues: 54.4413 Evaluate side-chains 289 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 236 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain D residue 21 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 60 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 111 ASP Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 252 LEU 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 A residue 587 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 276 TYR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 67 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 162 optimal weight: 0.1980 chunk 135 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.146612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.116009 restraints weight = 16026.050| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.90 r_work: 0.3014 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13641 Z= 0.130 Angle : 0.561 8.642 18491 Z= 0.289 Chirality : 0.041 0.196 2106 Planarity : 0.004 0.057 2311 Dihedral : 5.857 50.235 1941 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.36 % Favored : 93.58 % Rotamer: Outliers : 4.41 % Allowed : 21.31 % Favored : 74.28 % 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 aren not related in a simple way. whole: -0.49 (0.21), residues: 1683 helix: 1.71 (0.22), residues: 607 sheet: -0.49 (0.29), residues: 314 loop : -2.02 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 147 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 0.003 0.001 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00301 (13629) covalent geometry : angle 0.55869 (18463) SS BOND : bond 0.00471 ( 8) SS BOND : angle 1.08087 ( 16) hydrogen bonds : bond 0.04251 ( 608) hydrogen bonds : angle 4.15873 ( 1719) link_BETA1-4 : bond 0.00236 ( 2) link_BETA1-4 : angle 1.59393 ( 6) link_NAG-ASN : bond 0.00011 ( 2) link_NAG-ASN : angle 1.89525 ( 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 304 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 240 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: D 30 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8392 (p) REVERT: D 103 LYS cc_start: 0.9284 (ttpt) cc_final: 0.7964 (mmtt) REVERT: D 111 GLN cc_start: 0.7797 (pm20) cc_final: 0.7578 (pt0) REVERT: E 56 THR cc_start: 0.7665 (OUTLIER) cc_final: 0.7456 (p) REVERT: E 79 GLN cc_start: 0.6799 (mt0) cc_final: 0.6297 (tt0) REVERT: F 3 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7660 (mp10) REVERT: F 78 GLN cc_start: 0.8995 (mt0) cc_final: 0.8760 (mt0) REVERT: Z 99 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7393 (ttt90) REVERT: A 177 LYS cc_start: 0.7473 (mmtp) cc_final: 0.7013 (mtmt) REVERT: A 226 LEU cc_start: 0.8545 (mm) cc_final: 0.8241 (mp) REVERT: A 252 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8406 (pp) REVERT: A 378 ARG cc_start: 0.7418 (ttp-170) cc_final: 0.6001 (mmt-90) REVERT: A 393 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6744 (tp-100) REVERT: A 417 LYS cc_start: 0.8615 (pttt) cc_final: 0.7714 (mmtm) REVERT: B 45 ARG cc_start: 0.4549 (ttt-90) cc_final: 0.3351 (mtp-110) REVERT: B 160 ARG cc_start: 0.6723 (ttt180) cc_final: 0.6442 (ttt180) REVERT: B 165 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7790 (tt) REVERT: B 225 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6678 (mm) REVERT: B 263 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.7412 (mmm160) REVERT: B 348 GLU cc_start: 0.6871 (mt-10) cc_final: 0.6558 (mm-30) REVERT: B 378 ARG cc_start: 0.7645 (ttp-170) cc_final: 0.7028 (ttp-110) REVERT: B 387 ASN cc_start: 0.8499 (t0) cc_final: 0.8153 (t0) REVERT: B 515 MET cc_start: 0.8968 (mmm) cc_final: 0.8700 (mtp) REVERT: B 585 GLU cc_start: 0.8664 (tp30) cc_final: 0.8401 (tp30) REVERT: B 608 CYS cc_start: 0.8590 (m) cc_final: 0.8332 (m) REVERT: B 620 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7998 (t70) outliers start: 64 outliers final: 50 residues processed: 289 average time/residue: 0.1334 time to fit residues: 55.5636 Evaluate side-chains 294 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 235 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 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 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 81 GLU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 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 99 ARG 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 165 ILE Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 252 LEU 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 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 303 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 370 THR 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 609 THR Chi-restraints excluded: chain B residue 620 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 122 optimal weight: 0.0040 chunk 63 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.143961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.113025 restraints weight = 15987.654| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.94 r_work: 0.2971 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13641 Z= 0.197 Angle : 0.618 9.669 18491 Z= 0.318 Chirality : 0.043 0.216 2106 Planarity : 0.004 0.053 2311 Dihedral : 5.938 50.564 1940 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.95 % Favored : 92.99 % Rotamer: Outliers : 5.17 % Allowed : 20.62 % Favored : 74.21 % 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 aren not related in a simple way. whole: -0.57 (0.21), residues: 1683 helix: 1.59 (0.22), residues: 608 sheet: -0.39 (0.29), residues: 302 loop : -2.08 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 147 TYR 0.018 0.002 TYR D 51 PHE 0.019 0.002 PHE F 79 TRP 0.010 0.002 TRP A 379 HIS 0.004 0.001 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00474 (13629) covalent geometry : angle 0.61575 (18463) SS BOND : bond 0.00633 ( 8) SS BOND : angle 1.51388 ( 16) hydrogen bonds : bond 0.04913 ( 608) hydrogen bonds : angle 4.28792 ( 1719) link_BETA1-4 : bond 0.00205 ( 2) link_BETA1-4 : angle 1.44543 ( 6) link_NAG-ASN : bond 0.00175 ( 2) link_NAG-ASN : angle 1.96798 ( 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 309 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 234 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: D 30 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8385 (p) REVERT: D 103 LYS cc_start: 0.9274 (ttpt) cc_final: 0.7898 (mmtt) REVERT: D 111 GLN cc_start: 0.7839 (pm20) cc_final: 0.7616 (pt0) REVERT: E 56 THR cc_start: 0.7676 (OUTLIER) cc_final: 0.7461 (p) REVERT: E 79 GLN cc_start: 0.6791 (mt0) cc_final: 0.6282 (tt0) REVERT: F 3 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7688 (mp10) REVERT: Z 99 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7333 (ttt90) REVERT: A 177 LYS cc_start: 0.7483 (mmtp) cc_final: 0.7002 (mtmt) REVERT: A 226 LEU cc_start: 0.8556 (mm) cc_final: 0.8252 (mp) REVERT: A 252 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8440 (pp) REVERT: A 351 GLN cc_start: 0.6414 (tm-30) cc_final: 0.6137 (tm-30) REVERT: A 378 ARG cc_start: 0.7442 (ttp-170) cc_final: 0.5996 (mmt-90) REVERT: A 417 LYS cc_start: 0.8642 (pttt) cc_final: 0.7726 (mmtm) REVERT: A 635 CYS cc_start: 0.8619 (m) cc_final: 0.8165 (m) REVERT: B 45 ARG cc_start: 0.4617 (ttt-90) cc_final: 0.3432 (mtp-110) REVERT: B 160 ARG cc_start: 0.6706 (ttt180) cc_final: 0.6405 (ttt180) REVERT: B 165 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7752 (tt) REVERT: B 225 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6587 (mm) REVERT: B 263 ARG cc_start: 0.7786 (mmm-85) cc_final: 0.7380 (mmm160) REVERT: B 348 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6568 (mm-30) REVERT: B 378 ARG cc_start: 0.7651 (ttp-170) cc_final: 0.7030 (ttp-110) REVERT: B 515 MET cc_start: 0.8992 (mmm) cc_final: 0.8707 (mtp) REVERT: B 585 GLU cc_start: 0.8672 (tp30) cc_final: 0.8382 (tp30) REVERT: B 608 CYS cc_start: 0.8626 (m) cc_final: 0.8370 (m) REVERT: B 620 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8019 (t70) outliers start: 75 outliers final: 58 residues processed: 292 average time/residue: 0.1303 time to fit residues: 54.2027 Evaluate side-chains 297 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 231 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 52 ILE 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 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 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 99 ARG 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 165 ILE 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 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 143 SER 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 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 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 Chi-restraints excluded: chain B residue 620 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.0000 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 142 optimal weight: 0.4980 chunk 85 optimal weight: 0.3980 chunk 36 optimal weight: 0.3980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.147647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.116005 restraints weight = 16107.818| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.00 r_work: 0.3028 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13641 Z= 0.106 Angle : 0.543 8.275 18491 Z= 0.280 Chirality : 0.040 0.194 2106 Planarity : 0.003 0.050 2311 Dihedral : 5.430 50.951 1937 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.94 % Favored : 94.00 % Rotamer: Outliers : 3.93 % Allowed : 21.59 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.22), residues: 1683 helix: 1.79 (0.22), residues: 614 sheet: -0.34 (0.29), residues: 309 loop : -1.89 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 147 TYR 0.016 0.001 TYR A 276 PHE 0.015 0.001 PHE F 79 TRP 0.013 0.001 TRP B 627 HIS 0.003 0.001 HIS B 375 Details of bonding type rmsd covalent geometry : bond 0.00237 (13629) covalent geometry : angle 0.54074 (18463) SS BOND : bond 0.00441 ( 8) SS BOND : angle 0.85672 ( 16) hydrogen bonds : bond 0.03920 ( 608) hydrogen bonds : angle 4.05843 ( 1719) link_BETA1-4 : bond 0.00319 ( 2) link_BETA1-4 : angle 1.66219 ( 6) link_NAG-ASN : bond 0.00141 ( 2) link_NAG-ASN : angle 1.80343 ( 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 298 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 241 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: C 18 ARG cc_start: 0.7154 (ttp80) cc_final: 0.6696 (ttp-170) REVERT: D 5 GLN cc_start: 0.8281 (mm-40) cc_final: 0.8061 (tp40) REVERT: D 30 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8367 (p) REVERT: D 103 LYS cc_start: 0.9264 (ttpt) cc_final: 0.7886 (mmtt) REVERT: E 79 GLN cc_start: 0.6832 (mt0) cc_final: 0.6315 (tt0) REVERT: F 3 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7617 (mp10) REVERT: F 78 GLN cc_start: 0.8978 (mt0) cc_final: 0.8707 (mt0) REVERT: A 177 LYS cc_start: 0.7419 (mmtp) cc_final: 0.6968 (mtmt) REVERT: A 226 LEU cc_start: 0.8496 (mm) cc_final: 0.8184 (mp) REVERT: A 252 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8405 (pp) REVERT: A 378 ARG cc_start: 0.7366 (ttp-170) cc_final: 0.5951 (mmt-90) REVERT: A 417 LYS cc_start: 0.8592 (pttt) cc_final: 0.7687 (mmtm) REVERT: A 481 MET cc_start: 0.7996 (mmt) cc_final: 0.6737 (ttp) REVERT: B 45 ARG cc_start: 0.4443 (ttt-90) cc_final: 0.3312 (mtp-110) REVERT: B 160 ARG cc_start: 0.6694 (ttt180) cc_final: 0.6387 (ttt180) REVERT: B 165 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7727 (tt) REVERT: B 225 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6727 (mm) REVERT: B 263 ARG cc_start: 0.7792 (mmm-85) cc_final: 0.7398 (mmm160) REVERT: B 276 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.8137 (t80) REVERT: B 348 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6556 (mm-30) REVERT: B 378 ARG cc_start: 0.7621 (ttp-170) cc_final: 0.7047 (ttp-110) REVERT: B 515 MET cc_start: 0.8968 (mmm) cc_final: 0.8713 (mtp) REVERT: B 585 GLU cc_start: 0.8643 (tp30) cc_final: 0.8384 (tp30) REVERT: B 608 CYS cc_start: 0.8648 (m) cc_final: 0.8413 (m) REVERT: B 620 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.8002 (t70) outliers start: 57 outliers final: 41 residues processed: 285 average time/residue: 0.1240 time to fit residues: 51.0755 Evaluate side-chains 282 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 69 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER 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 486 SER Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 276 TYR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 370 THR 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 620 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 22 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS B 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.144675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.112978 restraints weight = 16061.012| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.98 r_work: 0.2982 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13641 Z= 0.174 Angle : 0.600 9.037 18491 Z= 0.309 Chirality : 0.043 0.206 2106 Planarity : 0.004 0.051 2311 Dihedral : 5.488 49.526 1934 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.01 % Favored : 92.93 % Rotamer: Outliers : 4.00 % Allowed : 21.59 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.21), residues: 1683 helix: 1.65 (0.22), residues: 617 sheet: -0.29 (0.29), residues: 302 loop : -1.92 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 147 TYR 0.017 0.002 TYR D 51 PHE 0.018 0.001 PHE B 489 TRP 0.010 0.002 TRP A 379 HIS 0.003 0.001 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00416 (13629) covalent geometry : angle 0.59791 (18463) SS BOND : bond 0.00599 ( 8) SS BOND : angle 1.38156 ( 16) hydrogen bonds : bond 0.04709 ( 608) hydrogen bonds : angle 4.17314 ( 1719) link_BETA1-4 : bond 0.00101 ( 2) link_BETA1-4 : angle 1.46105 ( 6) link_NAG-ASN : bond 0.00097 ( 2) link_NAG-ASN : angle 1.99370 ( 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 293 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 235 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: C 18 ARG cc_start: 0.7113 (ttp80) cc_final: 0.6615 (ttp-170) REVERT: D 5 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8130 (tp40) REVERT: D 30 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8382 (p) REVERT: D 103 LYS cc_start: 0.9260 (ttpt) cc_final: 0.7873 (mmtt) REVERT: E 79 GLN cc_start: 0.6802 (mt0) cc_final: 0.6299 (tt0) REVERT: F 3 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7650 (mp10) REVERT: A 177 LYS cc_start: 0.7421 (mmtp) cc_final: 0.6949 (mtmt) REVERT: A 226 LEU cc_start: 0.8460 (mm) cc_final: 0.8156 (mp) REVERT: A 252 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8423 (pp) REVERT: A 378 ARG cc_start: 0.7392 (ttp-170) cc_final: 0.5925 (mmt-90) REVERT: A 417 LYS cc_start: 0.8641 (pttt) cc_final: 0.7728 (mmtm) REVERT: A 635 CYS cc_start: 0.8627 (m) cc_final: 0.8193 (m) REVERT: B 45 ARG cc_start: 0.4504 (ttt-90) cc_final: 0.3387 (mtp-110) REVERT: B 160 ARG cc_start: 0.6706 (ttt180) cc_final: 0.6390 (ttt180) REVERT: B 165 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7684 (tt) REVERT: B 225 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.6645 (mm) REVERT: B 263 ARG cc_start: 0.7785 (mmm-85) cc_final: 0.7351 (mmm160) REVERT: B 301 ASP cc_start: 0.7482 (m-30) cc_final: 0.7254 (m-30) REVERT: B 342 TYR cc_start: 0.7406 (t80) cc_final: 0.6767 (t80) REVERT: B 348 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6578 (mm-30) REVERT: B 378 ARG cc_start: 0.7620 (ttp-170) cc_final: 0.7004 (ttp-110) REVERT: B 481 MET cc_start: 0.7223 (mmp) cc_final: 0.6937 (tpt) REVERT: B 515 MET cc_start: 0.8984 (mmm) cc_final: 0.8711 (mtp) REVERT: B 585 GLU cc_start: 0.8648 (tp30) cc_final: 0.8384 (tp30) REVERT: B 608 CYS cc_start: 0.8641 (m) cc_final: 0.8404 (m) REVERT: B 620 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.8025 (t70) outliers start: 58 outliers final: 49 residues processed: 279 average time/residue: 0.1289 time to fit residues: 51.6180 Evaluate side-chains 289 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 234 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 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 5 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 81 LEU 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 165 ILE Chi-restraints excluded: chain A residue 180 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 435 THR 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 226 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 370 THR Chi-restraints excluded: chain B residue 445 VAL 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 620 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 114 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 166 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 153 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN B 436 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.145954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.114857 restraints weight = 16002.697| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.03 r_work: 0.3000 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13641 Z= 0.141 Angle : 0.572 8.457 18491 Z= 0.295 Chirality : 0.042 0.207 2106 Planarity : 0.004 0.051 2311 Dihedral : 5.408 49.983 1934 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.30 % Favored : 93.64 % Rotamer: Outliers : 4.21 % Allowed : 21.52 % Favored : 74.28 % 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 aren not related in a simple way. whole: -0.28 (0.22), residues: 1683 helix: 1.72 (0.22), residues: 617 sheet: -0.18 (0.30), residues: 301 loop : -1.87 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 covalent geometry : bond 0.00332 (13629) covalent geometry : angle 0.57023 (18463) SS BOND : bond 0.00471 ( 8) SS BOND : angle 1.11028 ( 16) hydrogen bonds : bond 0.04340 ( 608) hydrogen bonds : angle 4.09678 ( 1719) link_BETA1-4 : bond 0.00123 ( 2) link_BETA1-4 : angle 1.51331 ( 6) link_NAG-ASN : bond 0.00018 ( 2) link_NAG-ASN : angle 1.87286 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4260.06 seconds wall clock time: 73 minutes 35.33 seconds (4415.33 seconds total)