Starting phenix.real_space_refine on Thu May 15 15:26:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p8a_17543/05_2025/8p8a_17543.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p8a_17543/05_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_17543/05_2025/8p8a_17543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p8a_17543/05_2025/8p8a_17543.map" model { file = "/net/cci-nas-00/data/ceres_data/8p8a_17543/05_2025/8p8a_17543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p8a_17543/05_2025/8p8a_17543.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 8575 2.51 5 N 2212 2.21 5 O 2477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13337 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "Z" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 926 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "A" Number of atoms: 4415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4415 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 19, 'TRANS': 547} Chain breaks: 3 Chain: "B" Number of atoms: 4440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4440 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 19, 'TRANS': 551} Chain breaks: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.48, per 1000 atoms: 0.71 Number of scatterers: 13337 At special positions: 0 Unit cell: (141.12, 112.56, 159.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 73 16.00 O 2477 8.00 N 2212 7.00 C 8575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG G 1 " - " ASN A 596 " " NAG H 1 " - " ASN B 596 " Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.6 seconds 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3122 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 14 sheets defined 39.2% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 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: 3.82 Time building geometry restraints manager: 3.53 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: 4.150 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 32.360 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 13641 Z= 0.309 Angle : 1.020 19.740 18491 Z= 0.566 Chirality : 0.057 0.387 2106 Planarity : 0.007 0.078 2311 Dihedral : 17.655 89.726 4931 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.25 % Favored : 92.69 % Rotamer: Outliers : 10.55 % Allowed : 7.66 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.16), residues: 1683 helix: -2.07 (0.16), residues: 613 sheet: -2.02 (0.27), residues: 298 loop : -3.13 (0.18), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 379 HIS 0.018 0.003 HIS A 350 PHE 0.025 0.002 PHE A 489 TYR 0.029 0.002 TYR F 51 ARG 0.005 0.001 ARG B 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 2) link_NAG-ASN : angle 3.73755 ( 6) link_BETA1-4 : bond 0.00449 ( 2) link_BETA1-4 : angle 2.60531 ( 6) hydrogen bonds : bond 0.19045 ( 608) hydrogen bonds : angle 7.04865 ( 1719) SS BOND : bond 0.00642 ( 8) SS BOND : angle 3.03581 ( 16) covalent geometry : bond 0.00649 (13629) covalent geometry : angle 1.01334 (18463) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 307 time to evaluate : 1.324 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: 0.2393 time to fit residues: 146.8658 Evaluate side-chains 274 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 111 ASP Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 563 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 0.0770 chunk 97 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 GLN C 38 GLN D 40 GLN D 77 ASN E 37 GLN E 38 GLN F 40 GLN Z 60 ASN Z 74 ASN A 76 ASN A 271 GLN A 283 HIS A 425 ASN A 437 GLN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN B 222 ASN B 387 ASN B 425 ASN B 437 GLN B 457 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.155576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.125361 restraints weight = 15834.142| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.93 r_work: 0.3070 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13641 Z= 0.152 Angle : 0.615 8.677 18491 Z= 0.321 Chirality : 0.042 0.154 2106 Planarity : 0.005 0.065 2311 Dihedral : 9.032 91.508 1988 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.30 % Favored : 93.64 % Rotamer: Outliers : 4.34 % Allowed : 15.45 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.19), residues: 1683 helix: 0.30 (0.21), residues: 604 sheet: -1.45 (0.28), residues: 302 loop : -2.65 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 627 HIS 0.005 0.001 HIS A 283 PHE 0.021 0.001 PHE F 79 TYR 0.018 0.001 TYR A 276 ARG 0.005 0.000 ARG D 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00110 ( 2) link_NAG-ASN : angle 1.95123 ( 6) link_BETA1-4 : bond 0.00342 ( 2) link_BETA1-4 : angle 1.51938 ( 6) hydrogen bonds : bond 0.04857 ( 608) hydrogen bonds : angle 4.67072 ( 1719) SS BOND : bond 0.00497 ( 8) SS BOND : angle 1.29337 ( 16) covalent geometry : bond 0.00345 (13629) covalent geometry : angle 0.61299 (18463) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 258 time to evaluate : 1.350 Fit side-chains REVERT: E 79 GLN cc_start: 0.6750 (mt0) cc_final: 0.6440 (tt0) REVERT: F 78 GLN cc_start: 0.9003 (mt0) cc_final: 0.8686 (mt0) REVERT: F 89 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7439 (mm-30) REVERT: F 111 GLN cc_start: 0.8608 (pm20) cc_final: 0.8382 (pm20) REVERT: A 141 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7936 (mt0) REVERT: A 177 LYS cc_start: 0.7349 (mmtp) cc_final: 0.6729 (mtmt) REVERT: A 226 LEU cc_start: 0.8420 (mm) cc_final: 0.8166 (mp) REVERT: A 285 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6904 (mt-10) REVERT: A 378 ARG cc_start: 0.7396 (ttp-170) cc_final: 0.6148 (mmt-90) REVERT: A 393 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.6404 (mt0) REVERT: A 417 LYS cc_start: 0.8623 (pttt) cc_final: 0.7815 (mmtm) REVERT: A 616 LYS cc_start: 0.8836 (mttp) cc_final: 0.8327 (mtpp) REVERT: B 160 ARG cc_start: 0.6810 (ttt180) cc_final: 0.6502 (ttt180) REVERT: B 162 ASN cc_start: 0.6094 (m-40) cc_final: 0.5678 (m-40) REVERT: B 198 MET cc_start: 0.8281 (mtm) cc_final: 0.8073 (mtp) REVERT: B 222 ASN cc_start: 0.8126 (OUTLIER) cc_final: 0.7849 (t0) REVERT: B 263 ARG cc_start: 0.7921 (mmm-85) cc_final: 0.7404 (mmm160) REVERT: B 348 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6527 (mm-30) REVERT: B 375 HIS cc_start: 0.7739 (t70) cc_final: 0.7171 (t-170) REVERT: B 378 ARG cc_start: 0.7709 (ttp-170) cc_final: 0.7079 (ttp-110) REVERT: B 387 ASN cc_start: 0.8425 (t0) cc_final: 0.8128 (t0) REVERT: B 473 LYS cc_start: 0.8172 (tptp) cc_final: 0.7957 (mmmt) REVERT: B 585 GLU cc_start: 0.8626 (tp30) cc_final: 0.8311 (tp30) outliers start: 63 outliers final: 37 residues processed: 302 average time/residue: 0.2592 time to fit residues: 112.2004 Evaluate side-chains 283 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 243 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 3 GLN Chi-restraints excluded: chain Z residue 53 THR Chi-restraints excluded: chain Z residue 111 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 563 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 52 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 140 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 32 optimal weight: 0.0980 chunk 82 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN D 77 ASN A 629 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.146209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.113931 restraints weight = 16125.048| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.05 r_work: 0.2980 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13641 Z= 0.208 Angle : 0.655 9.716 18491 Z= 0.338 Chirality : 0.044 0.219 2106 Planarity : 0.005 0.064 2311 Dihedral : 7.454 89.754 1954 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.07 % Favored : 92.87 % Rotamer: Outliers : 3.93 % Allowed : 17.03 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1683 helix: 0.97 (0.21), residues: 604 sheet: -0.95 (0.29), residues: 309 loop : -2.44 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 109 HIS 0.005 0.001 HIS A 630 PHE 0.021 0.002 PHE F 79 TYR 0.022 0.002 TYR B 605 ARG 0.002 0.000 ARG A 426 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 2) link_NAG-ASN : angle 2.05308 ( 6) link_BETA1-4 : bond 0.00218 ( 2) link_BETA1-4 : angle 1.43296 ( 6) hydrogen bonds : bond 0.05551 ( 608) hydrogen bonds : angle 4.53369 ( 1719) SS BOND : bond 0.00832 ( 8) SS BOND : angle 1.74636 ( 16) covalent geometry : bond 0.00497 (13629) covalent geometry : angle 0.65200 (18463) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 238 time to evaluate : 1.412 Fit side-chains REVERT: E 79 GLN cc_start: 0.6671 (mt0) cc_final: 0.6270 (tt0) REVERT: F 89 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7449 (mm-30) REVERT: A 177 LYS cc_start: 0.7477 (mmtp) cc_final: 0.6880 (mtmt) REVERT: A 226 LEU cc_start: 0.8492 (mm) cc_final: 0.8207 (mp) REVERT: A 246 ARG cc_start: 0.8016 (mpt180) cc_final: 0.7247 (mtp85) REVERT: A 285 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7136 (mt-10) REVERT: A 378 ARG cc_start: 0.7495 (ttp-170) cc_final: 0.6135 (mmt-90) REVERT: A 393 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.6459 (mt0) REVERT: A 417 LYS cc_start: 0.8693 (pttt) cc_final: 0.7789 (mmtm) REVERT: A 489 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7977 (t80) REVERT: B 198 MET cc_start: 0.8437 (mtm) cc_final: 0.8193 (mtp) REVERT: B 225 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6590 (mm) REVERT: B 263 ARG cc_start: 0.7775 (mmm-85) cc_final: 0.7366 (mmm160) REVERT: B 348 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6585 (mm-30) REVERT: B 378 ARG cc_start: 0.7662 (ttp-170) cc_final: 0.7034 (ttp-110) REVERT: B 387 ASN cc_start: 0.8509 (t0) cc_final: 0.8189 (t0) REVERT: B 585 GLU cc_start: 0.8688 (tp30) cc_final: 0.8413 (tp30) outliers start: 57 outliers final: 41 residues processed: 282 average time/residue: 0.2628 time to fit residues: 105.9860 Evaluate side-chains 277 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 232 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 53 THR Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 111 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 42 optimal weight: 0.0000 chunk 2 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 140 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.152809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.122004 restraints weight = 15796.533| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.93 r_work: 0.3069 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13641 Z= 0.117 Angle : 0.556 7.655 18491 Z= 0.288 Chirality : 0.040 0.146 2106 Planarity : 0.004 0.060 2311 Dihedral : 6.790 83.392 1948 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.12 % Favored : 93.82 % Rotamer: Outliers : 3.79 % Allowed : 18.83 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.21), residues: 1683 helix: 1.49 (0.22), residues: 598 sheet: -0.70 (0.29), residues: 309 loop : -2.25 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 379 HIS 0.002 0.001 HIS B 375 PHE 0.016 0.001 PHE F 79 TYR 0.016 0.001 TYR A 276 ARG 0.003 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00026 ( 2) link_NAG-ASN : angle 1.78845 ( 6) link_BETA1-4 : bond 0.00333 ( 2) link_BETA1-4 : angle 1.59878 ( 6) hydrogen bonds : bond 0.04310 ( 608) hydrogen bonds : angle 4.23466 ( 1719) SS BOND : bond 0.00545 ( 8) SS BOND : angle 1.06286 ( 16) covalent geometry : bond 0.00261 (13629) covalent geometry : angle 0.55344 (18463) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 254 time to evaluate : 1.386 Fit side-chains REVERT: D 103 LYS cc_start: 0.9247 (ttpt) cc_final: 0.7926 (mmtt) REVERT: E 79 GLN cc_start: 0.6815 (mt0) cc_final: 0.6309 (tt0) REVERT: F 78 GLN cc_start: 0.9036 (mt0) cc_final: 0.8744 (mt0) REVERT: Z 11 LEU cc_start: 0.5960 (OUTLIER) cc_final: 0.5725 (pp) REVERT: A 177 LYS cc_start: 0.7474 (mmtp) cc_final: 0.6897 (mtmt) REVERT: A 226 LEU cc_start: 0.8494 (mm) cc_final: 0.8201 (mp) REVERT: A 285 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7223 (mt-10) REVERT: A 378 ARG cc_start: 0.7448 (ttp-170) cc_final: 0.6072 (mmt-90) REVERT: A 393 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.6467 (mt0) REVERT: A 417 LYS cc_start: 0.8635 (pttt) cc_final: 0.7755 (mmtm) REVERT: B 162 ASN cc_start: 0.6212 (m-40) cc_final: 0.5618 (m-40) REVERT: B 198 MET cc_start: 0.8304 (mtm) cc_final: 0.8091 (mtp) REVERT: B 225 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6581 (mm) REVERT: B 263 ARG cc_start: 0.7760 (mmm-85) cc_final: 0.7387 (mmm160) REVERT: B 348 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6598 (mm-30) REVERT: B 378 ARG cc_start: 0.7662 (ttp-170) cc_final: 0.7081 (ttp-110) REVERT: B 387 ASN cc_start: 0.8452 (t0) cc_final: 0.8175 (t0) REVERT: B 481 MET cc_start: 0.7267 (mmt) cc_final: 0.6888 (tpt) REVERT: B 585 GLU cc_start: 0.8610 (tp30) cc_final: 0.8353 (tp30) outliers start: 55 outliers final: 39 residues processed: 298 average time/residue: 0.2457 time to fit residues: 106.3261 Evaluate side-chains 287 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 245 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 53 THR Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 111 ASP Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 165 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 104 optimal weight: 0.0770 chunk 8 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.151372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.121683 restraints weight = 15919.590| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.89 r_work: 0.3012 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13641 Z= 0.140 Angle : 0.563 8.611 18491 Z= 0.291 Chirality : 0.041 0.147 2106 Planarity : 0.004 0.059 2311 Dihedral : 6.199 70.091 1943 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.36 % Favored : 93.58 % Rotamer: Outliers : 4.07 % Allowed : 19.52 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.21), residues: 1683 helix: 1.57 (0.22), residues: 614 sheet: -0.54 (0.30), residues: 310 loop : -2.10 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 379 HIS 0.003 0.001 HIS A 630 PHE 0.017 0.001 PHE F 79 TYR 0.016 0.001 TYR D 51 ARG 0.003 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00098 ( 2) link_NAG-ASN : angle 1.90928 ( 6) link_BETA1-4 : bond 0.00107 ( 2) link_BETA1-4 : angle 1.52736 ( 6) hydrogen bonds : bond 0.04381 ( 608) hydrogen bonds : angle 4.15544 ( 1719) SS BOND : bond 0.00568 ( 8) SS BOND : angle 1.20869 ( 16) covalent geometry : bond 0.00328 (13629) covalent geometry : angle 0.56059 (18463) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 250 time to evaluate : 1.410 Fit side-chains REVERT: D 103 LYS cc_start: 0.9246 (ttpt) cc_final: 0.7932 (mmtt) REVERT: E 42 ASN cc_start: 0.8620 (m-40) cc_final: 0.8372 (m110) REVERT: E 79 GLN cc_start: 0.6793 (mt0) cc_final: 0.6307 (tt0) REVERT: F 78 GLN cc_start: 0.9044 (mt0) cc_final: 0.8792 (mt0) REVERT: Z 11 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5806 (pp) REVERT: A 177 LYS cc_start: 0.7494 (mmtp) cc_final: 0.6927 (mtmt) REVERT: A 226 LEU cc_start: 0.8517 (mm) cc_final: 0.8204 (mp) REVERT: A 252 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8428 (pp) REVERT: A 378 ARG cc_start: 0.7419 (ttp-170) cc_final: 0.6051 (mmt-90) REVERT: A 393 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.7092 (tm-30) REVERT: A 417 LYS cc_start: 0.8646 (pttt) cc_final: 0.7784 (mmtm) REVERT: A 635 CYS cc_start: 0.8626 (m) cc_final: 0.8145 (m) REVERT: B 160 ARG cc_start: 0.6650 (ttt180) cc_final: 0.6329 (ttt180) REVERT: B 165 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7878 (tt) REVERT: B 198 MET cc_start: 0.8376 (mtm) cc_final: 0.8157 (mtp) REVERT: B 225 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6625 (mm) REVERT: B 263 ARG cc_start: 0.7729 (mmm-85) cc_final: 0.7345 (mmm160) REVERT: B 348 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6607 (mm-30) REVERT: B 378 ARG cc_start: 0.7676 (ttp-170) cc_final: 0.7068 (ttp-110) REVERT: B 387 ASN cc_start: 0.8460 (t0) cc_final: 0.8121 (t0) REVERT: B 515 MET cc_start: 0.8997 (mmm) cc_final: 0.8747 (mtp) REVERT: B 585 GLU cc_start: 0.8642 (tp30) cc_final: 0.8382 (tp30) outliers start: 59 outliers final: 48 residues processed: 296 average time/residue: 0.2547 time to fit residues: 108.7788 Evaluate side-chains 294 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 241 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 111 ASP Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 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 510 MET 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 248 SER Chi-restraints excluded: chain B residue 276 TYR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 125 optimal weight: 0.0050 chunk 93 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 104 optimal weight: 0.0970 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 116 optimal weight: 0.0270 chunk 18 optimal weight: 2.9990 overall best weight: 0.3450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.151036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.119943 restraints weight = 16035.147| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.97 r_work: 0.3044 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13641 Z= 0.100 Angle : 0.515 7.865 18491 Z= 0.268 Chirality : 0.039 0.143 2106 Planarity : 0.003 0.052 2311 Dihedral : 5.764 61.519 1942 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.11 % Favored : 94.83 % Rotamer: Outliers : 3.38 % Allowed : 20.62 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.22), residues: 1683 helix: 1.80 (0.22), residues: 614 sheet: -0.36 (0.30), residues: 305 loop : -1.96 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 627 HIS 0.003 0.001 HIS B 375 PHE 0.014 0.001 PHE F 79 TYR 0.015 0.001 TYR A 276 ARG 0.008 0.000 ARG B 147 Details of bonding type rmsd link_NAG-ASN : bond 0.00147 ( 2) link_NAG-ASN : angle 1.68552 ( 6) link_BETA1-4 : bond 0.00205 ( 2) link_BETA1-4 : angle 1.64000 ( 6) hydrogen bonds : bond 0.03650 ( 608) hydrogen bonds : angle 3.97832 ( 1719) SS BOND : bond 0.00441 ( 8) SS BOND : angle 0.86274 ( 16) covalent geometry : bond 0.00218 (13629) covalent geometry : angle 0.51277 (18463) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 251 time to evaluate : 1.531 Fit side-chains REVERT: C 18 ARG cc_start: 0.7116 (ttp80) cc_final: 0.6665 (ttp-170) REVERT: D 103 LYS cc_start: 0.9240 (ttpt) cc_final: 0.7911 (mmtt) REVERT: D 111 GLN cc_start: 0.7777 (pm20) cc_final: 0.7572 (pt0) REVERT: E 79 GLN cc_start: 0.6815 (mt0) cc_final: 0.6315 (tt0) REVERT: F 78 GLN cc_start: 0.9000 (mt0) cc_final: 0.8620 (mt0) REVERT: Z 11 LEU cc_start: 0.6046 (OUTLIER) cc_final: 0.5815 (pp) REVERT: A 177 LYS cc_start: 0.7441 (mmtp) cc_final: 0.6879 (mtmt) REVERT: A 226 LEU cc_start: 0.8492 (mm) cc_final: 0.8174 (mp) REVERT: A 252 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8406 (pp) REVERT: A 285 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7742 (mt-10) REVERT: A 378 ARG cc_start: 0.7366 (ttp-170) cc_final: 0.5999 (mmt-90) REVERT: A 393 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6984 (tm-30) REVERT: A 417 LYS cc_start: 0.8592 (pttt) cc_final: 0.7714 (mmtm) REVERT: A 458 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8553 (mt-10) REVERT: A 481 MET cc_start: 0.8027 (mmt) cc_final: 0.6727 (ttp) REVERT: B 45 ARG cc_start: 0.4371 (ttt-90) cc_final: 0.3209 (mtp-110) REVERT: B 126 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7672 (tm-30) REVERT: B 198 MET cc_start: 0.8305 (mtm) cc_final: 0.8080 (mtp) REVERT: B 225 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.6757 (mm) REVERT: B 263 ARG cc_start: 0.7717 (mmm-85) cc_final: 0.7339 (mmm160) REVERT: B 348 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6579 (mm-30) REVERT: B 378 ARG cc_start: 0.7678 (ttp-170) cc_final: 0.7051 (ttp-110) REVERT: B 481 MET cc_start: 0.7285 (mmt) cc_final: 0.6967 (tpt) REVERT: B 515 MET cc_start: 0.8973 (mmm) cc_final: 0.8722 (mtp) REVERT: B 585 GLU cc_start: 0.8652 (tp30) cc_final: 0.8406 (tp30) outliers start: 49 outliers final: 41 residues processed: 287 average time/residue: 0.2528 time to fit residues: 104.6176 Evaluate side-chains 286 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 241 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 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 94 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 53 THR Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 111 ASP Chi-restraints excluded: chain A residue 102 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 486 SER Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 276 TYR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 109 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN B 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.143000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.110897 restraints weight = 16215.314| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.03 r_work: 0.2937 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 13641 Z= 0.281 Angle : 0.682 10.206 18491 Z= 0.350 Chirality : 0.046 0.170 2106 Planarity : 0.004 0.056 2311 Dihedral : 6.238 50.713 1942 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.19 % Favored : 92.75 % Rotamer: Outliers : 4.62 % Allowed : 20.00 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.21), residues: 1683 helix: 1.47 (0.21), residues: 615 sheet: -0.48 (0.30), residues: 307 loop : -2.10 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 109 HIS 0.007 0.001 HIS A 630 PHE 0.023 0.002 PHE A 39 TYR 0.024 0.002 TYR D 51 ARG 0.006 0.000 ARG B 147 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 2) link_NAG-ASN : angle 2.10254 ( 6) link_BETA1-4 : bond 0.00248 ( 2) link_BETA1-4 : angle 1.26739 ( 6) hydrogen bonds : bond 0.05625 ( 608) hydrogen bonds : angle 4.39063 ( 1719) SS BOND : bond 0.00802 ( 8) SS BOND : angle 1.95346 ( 16) covalent geometry : bond 0.00681 (13629) covalent geometry : angle 0.67893 (18463) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 237 time to evaluate : 1.448 Fit side-chains REVERT: E 42 ASN cc_start: 0.8713 (m-40) cc_final: 0.8423 (m-40) REVERT: E 56 THR cc_start: 0.7675 (OUTLIER) cc_final: 0.7461 (p) REVERT: E 79 GLN cc_start: 0.6865 (mt0) cc_final: 0.6332 (tt0) REVERT: A 177 LYS cc_start: 0.7503 (mmtp) cc_final: 0.6992 (mtmt) REVERT: A 226 LEU cc_start: 0.8529 (mm) cc_final: 0.8195 (mp) REVERT: A 246 ARG cc_start: 0.8132 (mpt180) cc_final: 0.7407 (mtp85) REVERT: A 252 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8533 (pp) REVERT: A 378 ARG cc_start: 0.7556 (ttp-170) cc_final: 0.6140 (mmt-90) REVERT: A 393 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6224 (mt0) REVERT: A 417 LYS cc_start: 0.8675 (pttt) cc_final: 0.7772 (mmtm) REVERT: A 635 CYS cc_start: 0.8643 (m) cc_final: 0.8215 (m) REVERT: B 45 ARG cc_start: 0.4449 (ttt-90) cc_final: 0.3387 (mtp-110) REVERT: B 160 ARG cc_start: 0.6641 (ttt180) cc_final: 0.6357 (ttt180) REVERT: B 165 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7803 (tt) REVERT: B 222 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.7996 (m-40) REVERT: B 225 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6541 (mm) REVERT: B 251 LYS cc_start: 0.8832 (pttm) cc_final: 0.8546 (pttm) REVERT: B 263 ARG cc_start: 0.7807 (mmm-85) cc_final: 0.7428 (mmm160) REVERT: B 348 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6626 (mm-30) REVERT: B 378 ARG cc_start: 0.7691 (ttp-170) cc_final: 0.7040 (ttp-110) outliers start: 67 outliers final: 53 residues processed: 289 average time/residue: 0.2558 time to fit residues: 106.4945 Evaluate side-chains 293 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 234 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 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 252 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 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 393 GLN Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 147 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 46 optimal weight: 0.0010 chunk 65 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 165 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN A 68 ASN B 222 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.152477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.122784 restraints weight = 15915.113| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.91 r_work: 0.3026 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13641 Z= 0.119 Angle : 0.554 9.046 18491 Z= 0.287 Chirality : 0.041 0.162 2106 Planarity : 0.003 0.053 2311 Dihedral : 5.860 51.185 1941 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.29 % Favored : 94.65 % Rotamer: Outliers : 3.79 % Allowed : 21.03 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.21), residues: 1683 helix: 1.72 (0.22), residues: 615 sheet: -0.34 (0.30), residues: 306 loop : -1.94 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 379 HIS 0.002 0.001 HIS B 375 PHE 0.014 0.001 PHE F 79 TYR 0.016 0.001 TYR A 276 ARG 0.006 0.000 ARG B 147 Details of bonding type rmsd link_NAG-ASN : bond 0.00076 ( 2) link_NAG-ASN : angle 1.69368 ( 6) link_BETA1-4 : bond 0.00079 ( 2) link_BETA1-4 : angle 1.52977 ( 6) hydrogen bonds : bond 0.04178 ( 608) hydrogen bonds : angle 4.09202 ( 1719) SS BOND : bond 0.00419 ( 8) SS BOND : angle 0.94545 ( 16) covalent geometry : bond 0.00271 (13629) covalent geometry : angle 0.55257 (18463) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 248 time to evaluate : 1.381 Fit side-chains revert: symmetry clash REVERT: D 5 GLN cc_start: 0.8245 (mm-40) cc_final: 0.8019 (tp40) REVERT: D 103 LYS cc_start: 0.9244 (ttpt) cc_final: 0.7897 (mmtt) REVERT: E 56 THR cc_start: 0.7656 (OUTLIER) cc_final: 0.7449 (p) REVERT: E 79 GLN cc_start: 0.6796 (mt0) cc_final: 0.6273 (tt0) REVERT: F 3 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7675 (mp10) REVERT: F 78 GLN cc_start: 0.8994 (mt0) cc_final: 0.8740 (mt0) REVERT: A 177 LYS cc_start: 0.7452 (mmtp) cc_final: 0.6982 (mtmt) REVERT: A 226 LEU cc_start: 0.8517 (mm) cc_final: 0.8186 (mp) REVERT: A 252 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8425 (pp) REVERT: A 378 ARG cc_start: 0.7396 (ttp-170) cc_final: 0.5983 (mmt-90) REVERT: A 393 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6178 (mt0) REVERT: A 417 LYS cc_start: 0.8593 (pttt) cc_final: 0.7699 (mmtm) REVERT: A 635 CYS cc_start: 0.8603 (m) cc_final: 0.8160 (m) REVERT: B 45 ARG cc_start: 0.4601 (ttt-90) cc_final: 0.3525 (mtp-110) REVERT: B 126 GLN cc_start: 0.7987 (tm-30) cc_final: 0.7717 (tm-30) REVERT: B 160 ARG cc_start: 0.6590 (ttt180) cc_final: 0.6273 (ttt180) REVERT: B 222 ASN cc_start: 0.8099 (OUTLIER) cc_final: 0.7832 (m-40) REVERT: B 225 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.6710 (mm) REVERT: B 263 ARG cc_start: 0.7783 (mmm-85) cc_final: 0.7382 (mmm160) REVERT: B 348 GLU cc_start: 0.6793 (mt-10) cc_final: 0.6510 (mm-30) REVERT: B 378 ARG cc_start: 0.7645 (ttp-170) cc_final: 0.7041 (ttp-110) REVERT: B 531 GLN cc_start: 0.6978 (mm110) cc_final: 0.6589 (mm-40) REVERT: B 608 CYS cc_start: 0.8506 (m) cc_final: 0.8210 (m) outliers start: 55 outliers final: 44 residues processed: 292 average time/residue: 0.2579 time to fit residues: 108.3190 Evaluate side-chains 296 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 246 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 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 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 370 THR 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 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 222 ASN Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 276 TYR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 161 optimal weight: 0.5980 chunk 131 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 79 optimal weight: 0.0570 chunk 120 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.147106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.115573 restraints weight = 15966.766| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.99 r_work: 0.2997 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3301 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= 0.129 Angle : 0.563 10.328 18491 Z= 0.291 Chirality : 0.041 0.153 2106 Planarity : 0.004 0.047 2311 Dihedral : 5.714 51.430 1941 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.18 % Favored : 93.76 % Rotamer: Outliers : 4.07 % Allowed : 20.90 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.22), residues: 1683 helix: 1.69 (0.22), residues: 622 sheet: -0.31 (0.30), residues: 306 loop : -1.88 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.002 0.001 HIS A 630 PHE 0.016 0.001 PHE F 79 TYR 0.015 0.001 TYR A 276 ARG 0.007 0.000 ARG B 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00055 ( 2) link_NAG-ASN : angle 1.85352 ( 6) link_BETA1-4 : bond 0.00156 ( 2) link_BETA1-4 : angle 1.57160 ( 6) hydrogen bonds : bond 0.04207 ( 608) hydrogen bonds : angle 4.05144 ( 1719) SS BOND : bond 0.00453 ( 8) SS BOND : angle 1.06028 ( 16) covalent geometry : bond 0.00301 (13629) covalent geometry : angle 0.56089 (18463) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 245 time to evaluate : 1.504 Fit side-chains revert: symmetry clash REVERT: D 103 LYS cc_start: 0.9242 (ttpt) cc_final: 0.7880 (mmtt) REVERT: E 79 GLN cc_start: 0.6857 (mt0) cc_final: 0.6325 (tt0) REVERT: F 3 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7693 (mp10) REVERT: F 78 GLN cc_start: 0.9018 (mt0) cc_final: 0.8773 (mt0) REVERT: A 177 LYS cc_start: 0.7516 (mmtp) cc_final: 0.7036 (mtmt) REVERT: A 226 LEU cc_start: 0.8498 (mm) cc_final: 0.8181 (mp) REVERT: A 252 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8444 (pp) REVERT: A 378 ARG cc_start: 0.7454 (ttp-170) cc_final: 0.6007 (mmt-90) REVERT: A 393 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.6601 (tm-30) REVERT: A 417 LYS cc_start: 0.8617 (pttt) cc_final: 0.7727 (mmtm) REVERT: A 635 CYS cc_start: 0.8639 (m) cc_final: 0.8201 (m) REVERT: B 45 ARG cc_start: 0.4678 (ttt-90) cc_final: 0.3574 (mtp-110) REVERT: B 126 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7778 (tm-30) REVERT: B 160 ARG cc_start: 0.6650 (ttt180) cc_final: 0.6325 (ttt180) REVERT: B 165 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7724 (tt) REVERT: B 225 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.6652 (mm) REVERT: B 263 ARG cc_start: 0.7852 (mmm-85) cc_final: 0.7443 (mmm160) REVERT: B 348 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6568 (mm-30) REVERT: B 378 ARG cc_start: 0.7689 (ttp-170) cc_final: 0.7072 (ttp-110) REVERT: B 481 MET cc_start: 0.7307 (mmt) cc_final: 0.7042 (tpt) REVERT: B 515 MET cc_start: 0.9003 (mmm) cc_final: 0.8781 (mtp) REVERT: B 531 GLN cc_start: 0.6922 (mm110) cc_final: 0.6519 (mm-40) REVERT: B 608 CYS cc_start: 0.8661 (m) cc_final: 0.8388 (m) outliers start: 59 outliers final: 51 residues processed: 291 average time/residue: 0.2567 time to fit residues: 107.9309 Evaluate side-chains 297 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 241 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 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 57 SER Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 111 ASP Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 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 446 GLU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 276 TYR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 27 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 61 optimal weight: 0.0270 chunk 38 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.147901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.116250 restraints weight = 15878.269| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.98 r_work: 0.3021 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13641 Z= 0.122 Angle : 0.553 10.321 18491 Z= 0.286 Chirality : 0.041 0.158 2106 Planarity : 0.003 0.046 2311 Dihedral : 5.598 51.478 1941 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.06 % Favored : 93.88 % Rotamer: Outliers : 3.72 % Allowed : 21.45 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1683 helix: 1.70 (0.22), residues: 624 sheet: -0.27 (0.30), residues: 306 loop : -1.82 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 627 HIS 0.004 0.001 HIS A 155 PHE 0.016 0.001 PHE F 79 TYR 0.015 0.001 TYR A 276 ARG 0.005 0.000 ARG B 147 Details of bonding type rmsd link_NAG-ASN : bond 0.00063 ( 2) link_NAG-ASN : angle 1.74841 ( 6) link_BETA1-4 : bond 0.00190 ( 2) link_BETA1-4 : angle 1.54125 ( 6) hydrogen bonds : bond 0.04048 ( 608) hydrogen bonds : angle 3.99964 ( 1719) SS BOND : bond 0.00430 ( 8) SS BOND : angle 1.00960 ( 16) covalent geometry : bond 0.00283 (13629) covalent geometry : angle 0.55146 (18463) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 240 time to evaluate : 1.305 Fit side-chains REVERT: D 5 GLN cc_start: 0.8382 (mm-40) cc_final: 0.8158 (tp40) REVERT: D 103 LYS cc_start: 0.9237 (ttpt) cc_final: 0.7879 (mmtt) REVERT: E 79 GLN cc_start: 0.6838 (mt0) cc_final: 0.6343 (tt0) REVERT: F 3 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7684 (mp10) REVERT: F 78 GLN cc_start: 0.9009 (mt0) cc_final: 0.8764 (mt0) REVERT: A 177 LYS cc_start: 0.7551 (mmtp) cc_final: 0.7091 (mtmt) REVERT: A 226 LEU cc_start: 0.8487 (mm) cc_final: 0.8166 (mp) REVERT: A 252 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8466 (pp) REVERT: A 378 ARG cc_start: 0.7403 (ttp-170) cc_final: 0.6002 (mmt-90) REVERT: A 393 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.6566 (tm-30) REVERT: A 417 LYS cc_start: 0.8599 (pttt) cc_final: 0.7727 (mmtm) REVERT: A 458 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8615 (mt-10) REVERT: A 481 MET cc_start: 0.7965 (mmt) cc_final: 0.6718 (ttp) REVERT: A 635 CYS cc_start: 0.8647 (m) cc_final: 0.8182 (m) REVERT: B 45 ARG cc_start: 0.4607 (ttt-90) cc_final: 0.3540 (mtp-110) REVERT: B 126 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7768 (tm-30) REVERT: B 160 ARG cc_start: 0.6688 (ttt180) cc_final: 0.6359 (ttt180) REVERT: B 165 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7725 (tt) REVERT: B 225 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.6757 (mm) REVERT: B 251 LYS cc_start: 0.8815 (pttm) cc_final: 0.8552 (pttm) REVERT: B 263 ARG cc_start: 0.7828 (mmm-85) cc_final: 0.7435 (mmm160) REVERT: B 348 GLU cc_start: 0.6836 (mt-10) cc_final: 0.6555 (mm-30) REVERT: B 378 ARG cc_start: 0.7719 (ttp-170) cc_final: 0.7110 (ttp-110) REVERT: B 481 MET cc_start: 0.7465 (mmt) cc_final: 0.7118 (tpt) REVERT: B 515 MET cc_start: 0.8988 (mmm) cc_final: 0.8762 (mtp) REVERT: B 531 GLN cc_start: 0.6891 (mm110) cc_final: 0.6490 (mm-40) REVERT: B 608 CYS cc_start: 0.8652 (m) cc_final: 0.8385 (m) outliers start: 54 outliers final: 46 residues processed: 281 average time/residue: 0.2464 time to fit residues: 99.8711 Evaluate side-chains 289 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 238 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 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 57 SER Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 276 TYR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 76 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.142114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.110080 restraints weight = 16060.142| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.08 r_work: 0.2945 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 13641 Z= 0.269 Angle : 0.692 12.178 18491 Z= 0.355 Chirality : 0.046 0.162 2106 Planarity : 0.004 0.049 2311 Dihedral : 6.007 51.329 1936 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.37 % Favored : 92.57 % Rotamer: Outliers : 4.14 % Allowed : 21.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.21), residues: 1683 helix: 1.36 (0.21), residues: 617 sheet: -0.46 (0.30), residues: 307 loop : -1.99 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 624 HIS 0.006 0.001 HIS A 630 PHE 0.024 0.002 PHE A 39 TYR 0.024 0.002 TYR B 605 ARG 0.005 0.000 ARG B 147 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 2) link_NAG-ASN : angle 2.13440 ( 6) link_BETA1-4 : bond 0.00263 ( 2) link_BETA1-4 : angle 1.28498 ( 6) hydrogen bonds : bond 0.05633 ( 608) hydrogen bonds : angle 4.35986 ( 1719) SS BOND : bond 0.00819 ( 8) SS BOND : angle 1.96760 ( 16) covalent geometry : bond 0.00653 (13629) covalent geometry : angle 0.68853 (18463) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7957.37 seconds wall clock time: 138 minutes 37.68 seconds (8317.68 seconds total)