Starting phenix.real_space_refine on Sun Nov 17 08:37:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p8a_17543/11_2024/8p8a_17543.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p8a_17543/11_2024/8p8a_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p8a_17543/11_2024/8p8a_17543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p8a_17543/11_2024/8p8a_17543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p8a_17543/11_2024/8p8a_17543.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p8a_17543/11_2024/8p8a_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 9.20, per 1000 atoms: 0.69 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: 2.75 Conformation dependent library (CDL) restraints added in 1.8 seconds 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3122 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 14 sheets defined 39.2% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 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: 4.27 Time building geometry restraints manager: 3.32 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: 5.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 32.990 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.560 ------------------------------------------------------------------------------- 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 13629 Z= 0.419 Angle : 1.013 19.740 18463 Z= 0.564 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 *********************** 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 : 1.526 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: 0.2601 time to fit residues: 158.5960 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 : 1.600 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 13629 Z= 0.225 Angle : 0.613 8.677 18463 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 *********************** 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 : 1.456 Fit side-chains REVERT: F 78 GLN cc_start: 0.8894 (mt0) cc_final: 0.8584 (mt0) REVERT: F 111 GLN cc_start: 0.8058 (pm20) cc_final: 0.7843 (pm20) REVERT: A 141 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7753 (mt0) REVERT: A 177 LYS cc_start: 0.7432 (mmtp) cc_final: 0.6941 (mtmt) REVERT: A 226 LEU cc_start: 0.8550 (mm) cc_final: 0.8304 (mp) REVERT: A 285 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6811 (mt-10) REVERT: A 378 ARG cc_start: 0.7024 (ttp-170) cc_final: 0.6208 (mmt-90) REVERT: A 393 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6442 (mt0) REVERT: A 417 LYS cc_start: 0.8419 (pttt) cc_final: 0.7948 (mmtm) REVERT: A 616 LYS cc_start: 0.8558 (mttp) cc_final: 0.8033 (mtpp) REVERT: B 160 ARG cc_start: 0.6699 (ttt180) cc_final: 0.6417 (ttt180) REVERT: B 162 ASN cc_start: 0.5873 (m-40) cc_final: 0.5492 (m-40) REVERT: B 222 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7930 (t0) REVERT: B 263 ARG cc_start: 0.7536 (mmm-85) cc_final: 0.7237 (mmm160) REVERT: B 375 HIS cc_start: 0.7577 (t70) cc_final: 0.7113 (t-170) REVERT: B 378 ARG cc_start: 0.7134 (ttp-170) cc_final: 0.6902 (ttp-110) REVERT: B 387 ASN cc_start: 0.8321 (t0) cc_final: 0.8039 (t0) REVERT: B 585 GLU cc_start: 0.7880 (tp30) cc_final: 0.7513 (tp30) REVERT: B 616 LYS cc_start: 0.8715 (mttp) cc_final: 0.8490 (mttm) outliers start: 63 outliers final: 37 residues processed: 302 average time/residue: 0.2767 time to fit residues: 119.1692 Evaluate side-chains 282 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 243 time to evaluate : 1.437 ------------------------------------------------------------------------------- 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 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 84 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN A 629 ASN B 629 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 13629 Z= 0.444 Angle : 0.702 9.935 18463 Z= 0.363 Chirality : 0.046 0.167 2106 Planarity : 0.005 0.065 2311 Dihedral : 7.520 87.577 1951 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.43 % Favored : 92.51 % Rotamer: Outliers : 3.86 % Allowed : 17.31 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (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: -1.48 (0.20), residues: 1683 helix: 0.81 (0.21), residues: 604 sheet: -1.00 (0.29), residues: 308 loop : -2.54 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 109 HIS 0.007 0.001 HIS A 630 PHE 0.022 0.002 PHE F 79 TYR 0.024 0.002 TYR B 605 ARG 0.003 0.000 ARG A 426 *********************** 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 285 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 229 time to evaluate : 1.469 Fit side-chains REVERT: D 82 GLN cc_start: 0.8058 (tp40) cc_final: 0.7805 (tp40) REVERT: F 82 GLN cc_start: 0.8330 (tt0) cc_final: 0.8105 (tt0) REVERT: A 141 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7725 (mt0) REVERT: A 177 LYS cc_start: 0.7589 (mmtp) cc_final: 0.7132 (mtmt) REVERT: A 226 LEU cc_start: 0.8607 (mm) cc_final: 0.8333 (mp) REVERT: A 285 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7146 (mt-10) REVERT: A 378 ARG cc_start: 0.7138 (ttp-170) cc_final: 0.6193 (mmt-90) REVERT: A 393 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.6493 (mt0) REVERT: A 417 LYS cc_start: 0.8509 (pttt) cc_final: 0.7902 (mmtm) REVERT: A 489 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7896 (t80) REVERT: B 225 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6719 (mm) REVERT: B 263 ARG cc_start: 0.7367 (mmm-85) cc_final: 0.7165 (mmm160) REVERT: B 378 ARG cc_start: 0.7099 (ttp-170) cc_final: 0.6807 (ttp-110) REVERT: B 387 ASN cc_start: 0.8416 (t0) cc_final: 0.8116 (t0) REVERT: B 585 GLU cc_start: 0.7920 (tp30) cc_final: 0.7493 (tp30) outliers start: 56 outliers final: 44 residues processed: 272 average time/residue: 0.2724 time to fit residues: 105.2020 Evaluate side-chains 272 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 225 time to evaluate : 1.503 ------------------------------------------------------------------------------- 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 69 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 3 GLN Chi-restraints excluded: chain Z residue 34 MET Chi-restraints excluded: chain Z residue 53 THR Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 111 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 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 491 CYS 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 150 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 72 optimal weight: 0.4980 chunk 102 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 B 222 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13629 Z= 0.193 Angle : 0.556 7.236 18463 Z= 0.290 Chirality : 0.041 0.146 2106 Planarity : 0.004 0.060 2311 Dihedral : 6.554 76.816 1944 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.76 % Favored : 94.18 % Rotamer: Outliers : 3.79 % Allowed : 18.55 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.21), residues: 1683 helix: 1.41 (0.22), residues: 598 sheet: -0.67 (0.29), residues: 308 loop : -2.28 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 379 HIS 0.002 0.001 HIS B 155 PHE 0.016 0.001 PHE F 79 TYR 0.016 0.001 TYR A 276 ARG 0.004 0.000 ARG E 18 *********************** 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 313 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 258 time to evaluate : 1.418 Fit side-chains REVERT: D 103 LYS cc_start: 0.9213 (ttpt) cc_final: 0.7979 (mmtt) REVERT: F 78 GLN cc_start: 0.8925 (mt0) cc_final: 0.8640 (mt0) REVERT: Z 11 LEU cc_start: 0.5906 (OUTLIER) cc_final: 0.5674 (pp) REVERT: A 177 LYS cc_start: 0.7636 (mmtp) cc_final: 0.7175 (mtmt) REVERT: A 226 LEU cc_start: 0.8568 (mm) cc_final: 0.8301 (mp) REVERT: A 252 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8329 (pp) REVERT: A 285 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7212 (mt-10) REVERT: A 378 ARG cc_start: 0.7065 (ttp-170) cc_final: 0.6108 (mmt-90) REVERT: A 393 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.6499 (mt0) REVERT: A 417 LYS cc_start: 0.8437 (pttt) cc_final: 0.7855 (mmtm) REVERT: B 75 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8285 (tt) REVERT: B 160 ARG cc_start: 0.6596 (ttt180) cc_final: 0.6337 (ttt180) REVERT: B 225 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6746 (mm) REVERT: B 263 ARG cc_start: 0.7391 (mmm-85) cc_final: 0.7177 (mmm160) REVERT: B 378 ARG cc_start: 0.7115 (ttp-170) cc_final: 0.6829 (ttp-110) REVERT: B 387 ASN cc_start: 0.8313 (t0) cc_final: 0.8000 (t0) REVERT: B 489 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7851 (t80) REVERT: B 585 GLU cc_start: 0.7890 (tp30) cc_final: 0.7592 (tp30) outliers start: 55 outliers final: 35 residues processed: 296 average time/residue: 0.2846 time to fit residues: 121.9631 Evaluate side-chains 286 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 245 time to evaluate : 1.529 ------------------------------------------------------------------------------- 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 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 111 ASP Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 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 489 PHE Chi-restraints excluded: chain B residue 565 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 134 optimal weight: 1.9990 chunk 91 optimal weight: 0.0970 chunk 2 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13629 Z= 0.244 Angle : 0.582 8.850 18463 Z= 0.301 Chirality : 0.042 0.148 2106 Planarity : 0.004 0.058 2311 Dihedral : 6.207 59.885 1942 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.42 % Favored : 93.52 % Rotamer: Outliers : 4.21 % Allowed : 19.72 % Favored : 76.07 % 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: -0.71 (0.21), residues: 1683 helix: 1.56 (0.22), residues: 605 sheet: -0.51 (0.30), residues: 304 loop : -2.22 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 379 HIS 0.004 0.001 HIS A 630 PHE 0.018 0.001 PHE F 79 TYR 0.018 0.002 TYR B 605 ARG 0.003 0.000 ARG E 18 *********************** 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: 61 poor density : 248 time to evaluate : 1.625 Fit side-chains REVERT: D 103 LYS cc_start: 0.9184 (ttpt) cc_final: 0.8000 (mmtt) REVERT: Z 11 LEU cc_start: 0.5945 (OUTLIER) cc_final: 0.5721 (pp) REVERT: A 141 GLN cc_start: 0.7970 (tt0) cc_final: 0.7723 (tt0) REVERT: A 177 LYS cc_start: 0.7539 (mmtp) cc_final: 0.7144 (mtmt) REVERT: A 226 LEU cc_start: 0.8605 (mm) cc_final: 0.8335 (mp) REVERT: A 378 ARG cc_start: 0.7102 (ttp-170) cc_final: 0.6096 (mmt-90) REVERT: A 393 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6794 (tm-30) REVERT: A 417 LYS cc_start: 0.8439 (pttt) cc_final: 0.7849 (mmtm) REVERT: A 635 CYS cc_start: 0.7874 (m) cc_final: 0.7303 (m) REVERT: B 75 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8283 (tt) REVERT: B 147 ARG cc_start: 0.7504 (mtp180) cc_final: 0.7151 (mtp180) REVERT: B 160 ARG cc_start: 0.6584 (ttt180) cc_final: 0.6363 (ttt180) REVERT: B 165 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7943 (tt) REVERT: B 225 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6756 (mm) REVERT: B 263 ARG cc_start: 0.7424 (mmm-85) cc_final: 0.7199 (mmm160) REVERT: B 378 ARG cc_start: 0.7128 (ttp-170) cc_final: 0.6819 (ttp-110) REVERT: B 387 ASN cc_start: 0.8320 (t0) cc_final: 0.7970 (t0) REVERT: B 489 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7907 (t80) REVERT: B 515 MET cc_start: 0.8590 (mmm) cc_final: 0.8316 (mtp) REVERT: B 585 GLU cc_start: 0.7903 (tp30) cc_final: 0.7591 (tp30) outliers start: 61 outliers final: 44 residues processed: 294 average time/residue: 0.2645 time to fit residues: 112.2692 Evaluate side-chains 290 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 240 time to evaluate : 1.517 ------------------------------------------------------------------------------- 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 114 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 68 ILE 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 111 ASP Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 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 556 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 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 408 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 4.9990 chunk 145 optimal weight: 0.3980 chunk 31 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 161 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13629 Z= 0.250 Angle : 0.580 8.201 18463 Z= 0.301 Chirality : 0.042 0.150 2106 Planarity : 0.004 0.054 2311 Dihedral : 6.063 50.623 1942 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.18 % Favored : 93.76 % Rotamer: Outliers : 4.76 % Allowed : 19.59 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.21), residues: 1683 helix: 1.64 (0.22), residues: 606 sheet: -0.41 (0.29), residues: 305 loop : -2.12 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 379 HIS 0.004 0.001 HIS A 630 PHE 0.018 0.001 PHE F 79 TYR 0.017 0.002 TYR B 605 ARG 0.003 0.000 ARG B 137 *********************** 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 313 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 244 time to evaluate : 1.458 Fit side-chains revert: symmetry clash REVERT: D 103 LYS cc_start: 0.9186 (ttpt) cc_final: 0.7992 (mmtt) REVERT: D 111 GLN cc_start: 0.7480 (pm20) cc_final: 0.7258 (pt0) REVERT: Z 11 LEU cc_start: 0.6183 (OUTLIER) cc_final: 0.5971 (pp) REVERT: A 177 LYS cc_start: 0.7583 (mmtp) cc_final: 0.7188 (mtmt) REVERT: A 226 LEU cc_start: 0.8613 (mm) cc_final: 0.8334 (mp) REVERT: A 252 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8364 (pp) REVERT: A 378 ARG cc_start: 0.7120 (ttp-170) cc_final: 0.6129 (mmt-90) REVERT: A 393 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6106 (mt0) REVERT: A 417 LYS cc_start: 0.8419 (pttt) cc_final: 0.7851 (mmtm) REVERT: A 635 CYS cc_start: 0.7865 (m) cc_final: 0.7279 (m) REVERT: B 45 ARG cc_start: 0.4488 (ttt-90) cc_final: 0.3588 (mtp-110) REVERT: B 75 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8276 (tt) REVERT: B 147 ARG cc_start: 0.7519 (mtp180) cc_final: 0.7130 (mtp180) REVERT: B 160 ARG cc_start: 0.6542 (ttt180) cc_final: 0.6290 (ttt180) REVERT: B 165 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7840 (tt) REVERT: B 222 ASN cc_start: 0.8245 (t0) cc_final: 0.8024 (m-40) REVERT: B 225 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6707 (mm) REVERT: B 263 ARG cc_start: 0.7465 (mmm-85) cc_final: 0.7211 (mmm160) REVERT: B 378 ARG cc_start: 0.7119 (ttp-170) cc_final: 0.6793 (ttp-110) REVERT: B 387 ASN cc_start: 0.8282 (t0) cc_final: 0.7930 (t0) REVERT: B 489 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7901 (t80) REVERT: B 515 MET cc_start: 0.8606 (mmm) cc_final: 0.8295 (mtp) REVERT: B 585 GLU cc_start: 0.7904 (tp30) cc_final: 0.7592 (tp30) outliers start: 69 outliers final: 57 residues processed: 296 average time/residue: 0.2687 time to fit residues: 113.7521 Evaluate side-chains 305 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 241 time to evaluate : 1.430 ------------------------------------------------------------------------------- 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 36 ASN Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 111 ASP Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 276 TYR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13629 Z= 0.337 Angle : 0.628 9.036 18463 Z= 0.325 Chirality : 0.044 0.154 2106 Planarity : 0.004 0.052 2311 Dihedral : 6.174 50.935 1942 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.89 % Favored : 93.05 % Rotamer: Outliers : 5.38 % Allowed : 19.86 % Favored : 74.76 % 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: -0.66 (0.21), residues: 1683 helix: 1.49 (0.22), residues: 613 sheet: -0.41 (0.30), residues: 302 loop : -2.14 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 109 HIS 0.005 0.001 HIS A 630 PHE 0.020 0.002 PHE F 79 TYR 0.019 0.002 TYR D 51 ARG 0.003 0.000 ARG E 18 *********************** 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 314 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 236 time to evaluate : 1.461 Fit side-chains revert: symmetry clash REVERT: C 18 ARG cc_start: 0.7126 (ttp80) cc_final: 0.6650 (ttp-170) REVERT: D 103 LYS cc_start: 0.9198 (ttpt) cc_final: 0.7972 (mmtt) REVERT: D 111 GLN cc_start: 0.7539 (pm20) cc_final: 0.7314 (pt0) REVERT: F 3 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7392 (mp10) REVERT: A 168 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7840 (mp) REVERT: A 177 LYS cc_start: 0.7631 (mmtp) cc_final: 0.7241 (mtmt) REVERT: A 226 LEU cc_start: 0.8616 (mm) cc_final: 0.8329 (mp) REVERT: A 252 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8457 (pp) REVERT: A 351 GLN cc_start: 0.6556 (tm-30) cc_final: 0.6254 (tm-30) REVERT: A 378 ARG cc_start: 0.7147 (ttp-170) cc_final: 0.6140 (mmt-90) REVERT: A 393 GLN cc_start: 0.7094 (OUTLIER) cc_final: 0.6251 (mt0) REVERT: A 417 LYS cc_start: 0.8451 (pttt) cc_final: 0.7861 (mmtm) REVERT: A 635 CYS cc_start: 0.7896 (m) cc_final: 0.7352 (m) REVERT: B 45 ARG cc_start: 0.4485 (ttt-90) cc_final: 0.3600 (mtp-110) REVERT: B 75 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8318 (tt) REVERT: B 147 ARG cc_start: 0.7609 (mtp180) cc_final: 0.7182 (mtp180) REVERT: B 160 ARG cc_start: 0.6562 (ttt180) cc_final: 0.6288 (ttt180) REVERT: B 225 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.6772 (mm) REVERT: B 263 ARG cc_start: 0.7484 (mmm-85) cc_final: 0.7207 (mmm160) REVERT: B 378 ARG cc_start: 0.7130 (ttp-170) cc_final: 0.6784 (ttp-110) REVERT: B 489 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7971 (t80) REVERT: B 585 GLU cc_start: 0.7909 (tp30) cc_final: 0.7559 (tp30) outliers start: 78 outliers final: 61 residues processed: 297 average time/residue: 0.2661 time to fit residues: 113.0216 Evaluate side-chains 297 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 229 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 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 65 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 111 ASP Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 126 optimal weight: 0.0870 chunk 146 optimal weight: 4.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13629 Z= 0.181 Angle : 0.548 7.221 18463 Z= 0.285 Chirality : 0.040 0.155 2106 Planarity : 0.003 0.047 2311 Dihedral : 5.825 51.273 1941 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.70 % Favored : 94.24 % Rotamer: Outliers : 4.14 % Allowed : 20.83 % 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: -0.37 (0.22), residues: 1683 helix: 1.74 (0.22), residues: 614 sheet: -0.25 (0.30), residues: 299 loop : -1.99 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 627 HIS 0.003 0.001 HIS B 375 PHE 0.015 0.001 PHE F 79 TYR 0.016 0.001 TYR A 276 ARG 0.004 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 248 time to evaluate : 1.304 Fit side-chains revert: symmetry clash REVERT: C 18 ARG cc_start: 0.7131 (ttp80) cc_final: 0.6673 (ttp-170) REVERT: D 5 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7606 (tp40) REVERT: D 103 LYS cc_start: 0.9160 (ttpt) cc_final: 0.7944 (mmtt) REVERT: F 3 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7332 (mp10) REVERT: F 78 GLN cc_start: 0.8911 (mt0) cc_final: 0.8673 (mt0) REVERT: A 177 LYS cc_start: 0.7599 (mmtp) cc_final: 0.7211 (mtmt) REVERT: A 226 LEU cc_start: 0.8593 (mm) cc_final: 0.8310 (mp) REVERT: A 252 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8395 (pp) REVERT: A 378 ARG cc_start: 0.7036 (ttp-170) cc_final: 0.6048 (mmt-90) REVERT: A 393 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6394 (tm-30) REVERT: A 417 LYS cc_start: 0.8384 (pttt) cc_final: 0.7795 (mmtm) REVERT: A 635 CYS cc_start: 0.7875 (m) cc_final: 0.7290 (m) REVERT: B 45 ARG cc_start: 0.4614 (ttt-90) cc_final: 0.3716 (mtp-110) REVERT: B 75 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8269 (tt) REVERT: B 147 ARG cc_start: 0.7528 (mtp180) cc_final: 0.7151 (mtp180) REVERT: B 160 ARG cc_start: 0.6544 (ttt180) cc_final: 0.6266 (ttt180) REVERT: B 165 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7752 (tt) REVERT: B 225 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.6821 (mm) REVERT: B 263 ARG cc_start: 0.7461 (mmm-85) cc_final: 0.7207 (mmm160) REVERT: B 276 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.8180 (t80) REVERT: B 378 ARG cc_start: 0.7125 (ttp-170) cc_final: 0.6805 (ttp-110) REVERT: B 489 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7915 (t80) REVERT: B 515 MET cc_start: 0.8583 (mmm) cc_final: 0.8261 (mtp) REVERT: B 531 GLN cc_start: 0.7098 (mm110) cc_final: 0.6759 (mm-40) REVERT: B 585 GLU cc_start: 0.7890 (tp30) cc_final: 0.7594 (tp30) REVERT: B 608 CYS cc_start: 0.7260 (m) cc_final: 0.6994 (m) outliers start: 60 outliers final: 45 residues processed: 294 average time/residue: 0.2719 time to fit residues: 113.7359 Evaluate side-chains 293 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 240 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 111 ASP Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 276 TYR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 0.9990 chunk 140 optimal weight: 0.5980 chunk 149 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 46 optimal weight: 0.0060 chunk 135 optimal weight: 0.9980 chunk 141 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 158 optimal weight: 0.0170 overall best weight: 0.4234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13629 Z= 0.159 Angle : 0.538 9.068 18463 Z= 0.279 Chirality : 0.040 0.151 2106 Planarity : 0.003 0.046 2311 Dihedral : 5.461 51.698 1938 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.30 % Favored : 93.64 % Rotamer: Outliers : 3.59 % Allowed : 21.79 % Favored : 74.62 % 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: -0.24 (0.22), residues: 1683 helix: 1.80 (0.22), residues: 617 sheet: -0.20 (0.30), residues: 301 loop : -1.87 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 627 HIS 0.003 0.001 HIS B 375 PHE 0.015 0.001 PHE F 79 TYR 0.015 0.001 TYR A 276 ARG 0.004 0.000 ARG E 18 *********************** 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 300 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 248 time to evaluate : 1.463 Fit side-chains revert: symmetry clash REVERT: C 18 ARG cc_start: 0.7131 (ttp80) cc_final: 0.6682 (ttp-170) REVERT: D 103 LYS cc_start: 0.9147 (ttpt) cc_final: 0.7934 (mmtt) REVERT: F 3 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7310 (mp10) REVERT: F 78 GLN cc_start: 0.8908 (mt0) cc_final: 0.8641 (mt0) REVERT: A 177 LYS cc_start: 0.7554 (mmtp) cc_final: 0.7188 (mtmt) REVERT: A 226 LEU cc_start: 0.8577 (mm) cc_final: 0.8290 (mp) REVERT: A 252 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8418 (pp) REVERT: A 378 ARG cc_start: 0.7006 (ttp-170) cc_final: 0.6029 (mmt-90) REVERT: A 417 LYS cc_start: 0.8397 (pttt) cc_final: 0.7828 (mmtm) REVERT: A 458 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8093 (mt-10) REVERT: A 481 MET cc_start: 0.7233 (mmt) cc_final: 0.6814 (ttp) REVERT: B 45 ARG cc_start: 0.4673 (ttt-90) cc_final: 0.3771 (mtp-110) REVERT: B 147 ARG cc_start: 0.7443 (mtp180) cc_final: 0.7119 (mtp180) REVERT: B 160 ARG cc_start: 0.6581 (ttt180) cc_final: 0.6298 (ttt180) REVERT: B 165 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7725 (tt) REVERT: B 225 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6734 (mm) REVERT: B 263 ARG cc_start: 0.7474 (mmm-85) cc_final: 0.7212 (mmm160) REVERT: B 378 ARG cc_start: 0.7119 (ttp-170) cc_final: 0.6778 (ttp-110) REVERT: B 489 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7882 (t80) REVERT: B 515 MET cc_start: 0.8530 (mmm) cc_final: 0.8251 (mtp) REVERT: B 531 GLN cc_start: 0.7007 (mm110) cc_final: 0.6629 (mm-40) REVERT: B 585 GLU cc_start: 0.7879 (tp30) cc_final: 0.7588 (tp30) REVERT: B 608 CYS cc_start: 0.7294 (m) cc_final: 0.7012 (m) outliers start: 52 outliers final: 45 residues processed: 287 average time/residue: 0.2685 time to fit residues: 110.2191 Evaluate side-chains 291 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 241 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 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 165 ILE Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 276 TYR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 0.9980 chunk 75 optimal weight: 0.0470 chunk 110 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 141 optimal weight: 0.3980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13629 Z= 0.188 Angle : 0.552 10.143 18463 Z= 0.286 Chirality : 0.040 0.158 2106 Planarity : 0.004 0.045 2311 Dihedral : 5.276 51.642 1933 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.18 % Favored : 93.76 % Rotamer: Outliers : 3.66 % Allowed : 21.52 % 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: -0.21 (0.22), residues: 1683 helix: 1.81 (0.22), residues: 617 sheet: -0.18 (0.30), residues: 301 loop : -1.84 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 627 HIS 0.002 0.001 HIS B 375 PHE 0.016 0.001 PHE F 79 TYR 0.015 0.001 TYR A 276 ARG 0.013 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 240 time to evaluate : 1.449 Fit side-chains revert: symmetry clash REVERT: C 18 ARG cc_start: 0.7128 (ttp80) cc_final: 0.6684 (ttp-170) REVERT: D 103 LYS cc_start: 0.9150 (ttpt) cc_final: 0.7942 (mmtt) REVERT: F 3 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7314 (mp10) REVERT: F 78 GLN cc_start: 0.8922 (mt0) cc_final: 0.8683 (mt0) REVERT: A 177 LYS cc_start: 0.7556 (mmtp) cc_final: 0.7189 (mtmt) REVERT: A 226 LEU cc_start: 0.8580 (mm) cc_final: 0.8300 (mp) REVERT: A 252 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8415 (pp) REVERT: A 378 ARG cc_start: 0.7001 (ttp-170) cc_final: 0.6024 (mmt-90) REVERT: A 417 LYS cc_start: 0.8386 (pttt) cc_final: 0.7827 (mmtm) REVERT: A 458 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8093 (mt-10) REVERT: A 481 MET cc_start: 0.7206 (mmt) cc_final: 0.6795 (ttp) REVERT: A 635 CYS cc_start: 0.7867 (m) cc_final: 0.7270 (m) REVERT: B 45 ARG cc_start: 0.4690 (ttt-90) cc_final: 0.3803 (mtp-110) REVERT: B 147 ARG cc_start: 0.7469 (mtp180) cc_final: 0.7139 (mtp180) REVERT: B 160 ARG cc_start: 0.6593 (ttt180) cc_final: 0.6304 (ttt180) REVERT: B 165 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7746 (tt) REVERT: B 225 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6664 (mm) REVERT: B 263 ARG cc_start: 0.7467 (mmm-85) cc_final: 0.7195 (mmm160) REVERT: B 378 ARG cc_start: 0.7133 (ttp-170) cc_final: 0.6781 (ttp-110) REVERT: B 489 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7874 (t80) REVERT: B 515 MET cc_start: 0.8548 (mmm) cc_final: 0.8263 (mtp) REVERT: B 531 GLN cc_start: 0.6988 (mm110) cc_final: 0.6624 (mm-40) REVERT: B 585 GLU cc_start: 0.7887 (tp30) cc_final: 0.7591 (tp30) REVERT: B 608 CYS cc_start: 0.7289 (m) cc_final: 0.7013 (m) REVERT: B 620 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.7161 (t70) outliers start: 53 outliers final: 46 residues processed: 281 average time/residue: 0.2695 time to fit residues: 109.1574 Evaluate side-chains 291 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 239 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 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 B residue 36 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 276 TYR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 620 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 136 optimal weight: 0.0970 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.146804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.114741 restraints weight = 15884.385| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.04 r_work: 0.2997 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13629 Z= 0.199 Angle : 0.559 10.030 18463 Z= 0.289 Chirality : 0.041 0.153 2106 Planarity : 0.003 0.040 2311 Dihedral : 5.321 51.640 1933 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.42 % Favored : 93.52 % Rotamer: Outliers : 3.86 % Allowed : 21.45 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.22), residues: 1683 helix: 1.81 (0.22), residues: 617 sheet: -0.17 (0.30), residues: 301 loop : -1.84 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Z 36 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 0.009 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3451.78 seconds wall clock time: 63 minutes 30.66 seconds (3810.66 seconds total)