Starting phenix.real_space_refine on Wed May 14 14:22:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xra_38600/05_2025/8xra_38600_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xra_38600/05_2025/8xra_38600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xra_38600/05_2025/8xra_38600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xra_38600/05_2025/8xra_38600.map" model { file = "/net/cci-nas-00/data/ceres_data/8xra_38600/05_2025/8xra_38600_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xra_38600/05_2025/8xra_38600_neut.cif" } resolution = 2.31 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= 0.001 sd= 0.024 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 72 5.16 5 C 7431 2.51 5 N 2022 2.21 5 O 2356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11881 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3890 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 19, 'TRANS': 470} Chain breaks: 1 Chain: "B" Number of atoms: 3890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3890 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 19, 'TRANS': 470} Chain breaks: 1 Chain: "C" Number of atoms: 3890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3890 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 19, 'TRANS': 470} Chain breaks: 1 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {'NAG': 3, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: F Time building chain proxies: 9.22, per 1000 atoms: 0.78 Number of scatterers: 11881 At special positions: 0 Unit cell: (85.85, 87.55, 150.45, 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 72 16.00 O 2356 8.00 N 2022 7.00 C 7431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 9 " - pdb=" SG CYS A 467 " distance=2.04 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 278 " distance=2.02 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.02 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 467 " distance=2.05 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 72 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 467 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 478 " 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 BETA2-3 " GAL D 1 " - " SIA D 2 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL F 1 " - " SIA F 2 " NAG-ASN " NAG A 601 " - " ASN A 290 " " NAG A 602 " - " ASN A 484 " " NAG A 603 " - " ASN A 169 " " NAG B 601 " - " ASN B 484 " " NAG B 602 " - " ASN B 28 " " NAG B 603 " - " ASN B 169 " " NAG C 701 " - " ASN C 28 " " NAG C 702 " - " ASN C 290 " " NAG C 703 " - " ASN C 484 " Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.7 seconds 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2694 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 34 sheets defined 29.1% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 69 through 77 removed outlier: 3.801A pdb=" N ASP A 73 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ARG A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 75 " --> pdb=" O CYS A 72 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 76 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER A 77 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 112 removed outlier: 3.947A pdb=" N SER A 112 " --> pdb=" O HIS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.597A pdb=" N TRP A 127 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 367 through 388 removed outlier: 3.707A pdb=" N THR A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 457 removed outlier: 3.779A pdb=" N ASP A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 492 through 502 removed outlier: 3.510A pdb=" N ASN A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 69 through 76 removed outlier: 3.968A pdb=" N ASP B 73 " --> pdb=" O PRO B 70 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG B 74 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.800A pdb=" N ARG B 126 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TRP B 127 " --> pdb=" O LYS B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 123 through 127' Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 367 through 387 removed outlier: 3.720A pdb=" N THR B 371 " --> pdb=" O ASP B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 457 removed outlier: 3.559A pdb=" N ASP B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 488 through 502 removed outlier: 4.292A pdb=" N TYR B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLU B 494 " --> pdb=" O PRO B 490 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLU B 495 " --> pdb=" O LYS B 491 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 69 through 76 removed outlier: 3.919A pdb=" N ASP C 73 " --> pdb=" O PRO C 70 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ARG C 74 " --> pdb=" O GLU C 71 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU C 76 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.887A pdb=" N TRP C 127 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 338 through 342 removed outlier: 3.670A pdb=" N GLU C 341 " --> pdb=" O GLY C 338 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY C 342 " --> pdb=" O PHE C 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 338 through 342' Processing helix chain 'C' and resid 367 through 387 Processing helix chain 'C' and resid 404 through 457 removed outlier: 3.722A pdb=" N ASP C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 Processing helix chain 'C' and resid 492 through 502 removed outlier: 3.582A pdb=" N LEU C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG C 500 " --> pdb=" O SER C 496 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN C 501 " --> pdb=" O LYS C 497 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 363 through 364 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 4.292A pdb=" N GLU A 19 " --> pdb=" O VAL A 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AA4, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA5, first strand: chain 'A' and resid 46 through 49 removed outlier: 5.861A pdb=" N LEU A 46 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N CYS A 278 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 55 through 56 removed outlier: 6.686A pdb=" N LEU A 55 " --> pdb=" O MET A 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.705A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 98 through 100 removed outlier: 8.016A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AB1, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.496A pdb=" N ALA A 138 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 9.714A pdb=" N ASN A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB3, first strand: chain 'A' and resid 287 through 289 removed outlier: 4.203A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 361 through 364 removed outlier: 4.272A pdb=" N GLN B 7 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AB6, first strand: chain 'B' and resid 34 through 36 Processing sheet with id=AB7, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AB8, first strand: chain 'B' and resid 46 through 49 removed outlier: 5.739A pdb=" N LEU B 46 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N CYS B 278 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 55 through 56 removed outlier: 6.729A pdb=" N LEU B 55 " --> pdb=" O MET B 85 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE B 84 " --> pdb=" O MET B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.412A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 98 through 100 removed outlier: 7.970A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.899A pdb=" N ALA B 138 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 10.500A pdb=" N ASN B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 164 through 169 removed outlier: 3.741A pdb=" N LEU B 209 " --> pdb=" O THR B 206 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 288 through 289 removed outlier: 4.132A pdb=" N CYS B 282 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 361 through 364 Processing sheet with id=AC7, first strand: chain 'C' and resid 19 through 21 removed outlier: 4.263A pdb=" N GLU C 19 " --> pdb=" O VAL C 31 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AC9, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AD1, first strand: chain 'C' and resid 48 through 49 removed outlier: 6.309A pdb=" N LYS C 48 " --> pdb=" O THR C 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 55 through 56 removed outlier: 6.597A pdb=" N LEU C 55 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE C 84 " --> pdb=" O MET C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.521A pdb=" N PHE C 232 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.521A pdb=" N PHE C 232 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.783A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD7, first strand: chain 'C' and resid 288 through 289 removed outlier: 4.403A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1428 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: 4.20 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3909 1.35 - 1.47: 2950 1.47 - 1.60: 5172 1.60 - 1.72: 0 1.72 - 1.85: 108 Bond restraints: 12139 Sorted by residual: bond pdb=" C3 GAL D 1 " pdb=" O3 GAL D 1 " ideal model delta sigma weight residual 1.406 1.374 0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" C3 GAL F 1 " pdb=" O3 GAL F 1 " ideal model delta sigma weight residual 1.406 1.374 0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" C1 NAG A 603 " pdb=" O5 NAG A 603 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" C5 GAL D 1 " pdb=" O5 GAL D 1 " ideal model delta sigma weight residual 1.412 1.442 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" CG LEU B 456 " pdb=" CD2 LEU B 456 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.18e+00 ... (remaining 12134 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 16296 2.65 - 5.30: 122 5.30 - 7.95: 2 7.95 - 10.60: 4 10.60 - 13.25: 5 Bond angle restraints: 16429 Sorted by residual: angle pdb=" CA LYS A 281 " pdb=" CB LYS A 281 " pdb=" CG LYS A 281 " ideal model delta sigma weight residual 114.10 123.35 -9.25 2.00e+00 2.50e-01 2.14e+01 angle pdb=" CA CYS B 467 " pdb=" CB CYS B 467 " pdb=" SG CYS B 467 " ideal model delta sigma weight residual 114.40 124.85 -10.45 2.30e+00 1.89e-01 2.07e+01 angle pdb=" C2 GAL D 1 " pdb=" C3 GAL D 1 " pdb=" O3 GAL D 1 " ideal model delta sigma weight residual 107.49 120.74 -13.25 3.00e+00 1.11e-01 1.95e+01 angle pdb=" C2 GAL F 1 " pdb=" C3 GAL F 1 " pdb=" O3 GAL F 1 " ideal model delta sigma weight residual 107.49 120.74 -13.25 3.00e+00 1.11e-01 1.95e+01 angle pdb=" CA CYS A 467 " pdb=" CB CYS A 467 " pdb=" SG CYS A 467 " ideal model delta sigma weight residual 114.40 124.17 -9.77 2.30e+00 1.89e-01 1.80e+01 ... (remaining 16424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.80: 6817 28.80 - 57.61: 603 57.61 - 86.41: 59 86.41 - 115.22: 15 115.22 - 144.02: 6 Dihedral angle restraints: 7500 sinusoidal: 3285 harmonic: 4215 Sorted by residual: dihedral pdb=" CB CYS B 95 " pdb=" SG CYS B 95 " pdb=" SG CYS B 139 " pdb=" CB CYS B 139 " ideal model delta sinusoidal sigma weight residual 93.00 28.46 64.54 1 1.00e+01 1.00e-02 5.47e+01 dihedral pdb=" CB CYS B 9 " pdb=" SG CYS B 9 " pdb=" SG CYS B 467 " pdb=" CB CYS B 467 " ideal model delta sinusoidal sigma weight residual 93.00 29.17 63.83 1 1.00e+01 1.00e-02 5.37e+01 dihedral pdb=" CB CYS A 60 " pdb=" SG CYS A 60 " pdb=" SG CYS A 72 " pdb=" CB CYS A 72 " ideal model delta sinusoidal sigma weight residual 93.00 147.49 -54.49 1 1.00e+01 1.00e-02 4.02e+01 ... (remaining 7497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.279: 1802 0.279 - 0.558: 0 0.558 - 0.837: 0 0.837 - 1.116: 0 1.116 - 1.395: 2 Chirality restraints: 1804 Sorted by residual: chirality pdb=" C2 SIA F 2 " pdb=" O3 GAL F 1 " pdb=" C1 SIA F 2 " pdb=" O6 SIA F 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.66 0.16 2.00e-02 2.50e+03 6.46e+01 chirality pdb=" C2 SIA D 2 " pdb=" O3 GAL D 1 " pdb=" C1 SIA D 2 " pdb=" O6 SIA D 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.66 0.16 2.00e-02 2.50e+03 6.32e+01 chirality pdb=" C3 GAL D 1 " pdb=" C2 GAL D 1 " pdb=" C4 GAL D 1 " pdb=" O3 GAL D 1 " both_signs ideal model delta sigma weight residual False 2.41 1.01 1.40 2.00e-01 2.50e+01 4.87e+01 ... (remaining 1801 not shown) Planarity restraints: 2127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 69 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO C 70 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 70 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 70 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 78 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO C 79 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 79 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 79 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 116 " -0.012 2.00e-02 2.50e+03 1.06e-02 1.98e+00 pdb=" CG PHE A 116 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 116 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 116 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 116 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 116 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 116 " 0.000 2.00e-02 2.50e+03 ... (remaining 2124 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2278 2.77 - 3.31: 9853 3.31 - 3.84: 18997 3.84 - 4.37: 22218 4.37 - 4.90: 39738 Nonbonded interactions: 93084 Sorted by model distance: nonbonded pdb=" O SER C 82 " pdb=" OG SER C 266 " model vdw 2.243 3.040 nonbonded pdb=" OE1 GLU A 394 " pdb=" N ALA A 395 " model vdw 2.252 3.120 nonbonded pdb=" OG SER A 384 " pdb=" NH2 ARG C 27 " model vdw 2.273 3.120 nonbonded pdb=" O THR A 486 " pdb=" OG1 THR A 486 " model vdw 2.277 3.040 nonbonded pdb=" NZ LYS A 107 " pdb=" OE1 GLU A 399 " model vdw 2.288 3.120 ... (remaining 93079 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 6 through 502 or resid 601 through 603)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 1.920 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 33.660 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 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 : 0.004 0.057 12168 Z= 0.182 Angle : 0.720 29.327 16498 Z= 0.346 Chirality : 0.063 1.395 1804 Planarity : 0.004 0.036 2118 Dihedral : 20.281 144.021 4752 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.88 % Favored : 96.91 % Rotamer: Outliers : 3.40 % Allowed : 30.02 % Favored : 66.59 % 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: 0.04 (0.22), residues: 1458 helix: 2.38 (0.27), residues: 375 sheet: 0.25 (0.31), residues: 318 loop : -1.34 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 81 HIS 0.007 0.001 HIS B 356 PHE 0.024 0.001 PHE A 116 TYR 0.016 0.001 TYR A 103 ARG 0.008 0.001 ARG B 192 Details of bonding type rmsd link_BETA2-3 : bond 0.05746 ( 2) link_BETA2-3 : angle 17.31936 ( 6) link_NAG-ASN : bond 0.00189 ( 9) link_NAG-ASN : angle 1.49497 ( 27) hydrogen bonds : bond 0.13408 ( 485) hydrogen bonds : angle 6.19738 ( 1428) SS BOND : bond 0.00577 ( 18) SS BOND : angle 1.43739 ( 36) covalent geometry : bond 0.00402 (12139) covalent geometry : angle 0.63522 (16429) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 326 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 THR cc_start: 0.6952 (OUTLIER) cc_final: 0.6086 (m) REVERT: C 38 LEU cc_start: 0.8135 (tp) cc_final: 0.7840 (tp) REVERT: C 248 THR cc_start: 0.7353 (m) cc_final: 0.7116 (p) REVERT: C 405 ARG cc_start: 0.7196 (mtp85) cc_final: 0.6958 (mmp80) outliers start: 44 outliers final: 10 residues processed: 360 average time/residue: 1.0645 time to fit residues: 417.9185 Evaluate side-chains 261 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 250 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 244 ASN A 283 GLN A 299 HIS ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 356 HIS C 101 ASN C 244 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.148935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.136225 restraints weight = 16235.794| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.69 r_work: 0.3819 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 12168 Z= 0.215 Angle : 0.804 11.469 16498 Z= 0.403 Chirality : 0.048 0.199 1804 Planarity : 0.006 0.060 2118 Dihedral : 10.402 141.848 1924 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.32 % Favored : 95.54 % Rotamer: Outliers : 7.25 % Allowed : 25.31 % Favored : 67.44 % 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: -0.10 (0.22), residues: 1458 helix: 2.37 (0.26), residues: 381 sheet: 0.01 (0.30), residues: 303 loop : -1.42 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 81 HIS 0.011 0.002 HIS A 33 PHE 0.027 0.002 PHE A 148 TYR 0.023 0.002 TYR C 168 ARG 0.016 0.001 ARG A 27 Details of bonding type rmsd link_BETA2-3 : bond 0.03995 ( 2) link_BETA2-3 : angle 5.78778 ( 6) link_NAG-ASN : bond 0.00697 ( 9) link_NAG-ASN : angle 2.00517 ( 27) hydrogen bonds : bond 0.05532 ( 485) hydrogen bonds : angle 5.06106 ( 1428) SS BOND : bond 0.00953 ( 18) SS BOND : angle 2.60539 ( 36) covalent geometry : bond 0.00482 (12139) covalent geometry : angle 0.78480 (16429) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 335 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8361 (mm) REVERT: A 258 PHE cc_start: 0.8272 (m-80) cc_final: 0.7644 (m-80) REVERT: A 323 ASN cc_start: 0.7598 (t0) cc_final: 0.7073 (t0) REVERT: B 60 CYS cc_start: 0.6311 (OUTLIER) cc_final: 0.5811 (p) REVERT: C 230 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8171 (mtt) REVERT: C 248 THR cc_start: 0.8558 (m) cc_final: 0.8164 (p) REVERT: C 349 ASP cc_start: 0.7099 (p0) cc_final: 0.6879 (p0) REVERT: C 405 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7580 (mmp80) outliers start: 94 outliers final: 20 residues processed: 395 average time/residue: 1.1495 time to fit residues: 493.4284 Evaluate side-chains 316 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 292 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 51 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS A 69 ASN A 283 GLN A 380 ASN A 459 ASN ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 244 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 HIS B 409 ASN C 13 HIS C 33 HIS C 175 GLN C 186 ASN C 191 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.131555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.119134 restraints weight = 15935.891| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.65 r_work: 0.3600 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.6364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 12168 Z= 0.213 Angle : 0.745 10.935 16498 Z= 0.378 Chirality : 0.046 0.196 1804 Planarity : 0.005 0.062 2118 Dihedral : 9.809 147.861 1916 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.22 % Favored : 96.71 % Rotamer: Outliers : 4.94 % Allowed : 26.70 % Favored : 68.36 % 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: 0.14 (0.22), residues: 1458 helix: 2.65 (0.26), residues: 381 sheet: 0.29 (0.30), residues: 297 loop : -1.38 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 127 HIS 0.009 0.002 HIS B 299 PHE 0.032 0.002 PHE B 470 TYR 0.023 0.002 TYR B 487 ARG 0.005 0.001 ARG B 137 Details of bonding type rmsd link_BETA2-3 : bond 0.01104 ( 2) link_BETA2-3 : angle 7.12411 ( 6) link_NAG-ASN : bond 0.00305 ( 9) link_NAG-ASN : angle 1.87872 ( 27) hydrogen bonds : bond 0.06542 ( 485) hydrogen bonds : angle 4.90336 ( 1428) SS BOND : bond 0.00881 ( 18) SS BOND : angle 2.84817 ( 36) covalent geometry : bond 0.00508 (12139) covalent geometry : angle 0.71794 (16429) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 328 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7923 (tp) cc_final: 0.7609 (tt) REVERT: A 136 SER cc_start: 0.8664 (m) cc_final: 0.8461 (t) REVERT: A 393 PHE cc_start: 0.7919 (t80) cc_final: 0.7649 (t80) REVERT: B 8 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7726 (tt) REVERT: B 136 SER cc_start: 0.8629 (p) cc_final: 0.8330 (t) REVERT: B 260 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7444 (mt) REVERT: B 272 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: B 375 PHE cc_start: 0.7779 (t80) cc_final: 0.7565 (t80) REVERT: B 470 PHE cc_start: 0.7364 (m-80) cc_final: 0.6975 (m-80) REVERT: C 230 MET cc_start: 0.8595 (ttm) cc_final: 0.8386 (mtt) REVERT: C 272 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: C 349 ASP cc_start: 0.7313 (p0) cc_final: 0.7018 (p0) REVERT: C 405 ARG cc_start: 0.7843 (mtp85) cc_final: 0.7584 (mmp80) REVERT: C 415 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7164 (mp0) outliers start: 64 outliers final: 17 residues processed: 354 average time/residue: 1.3470 time to fit residues: 513.2633 Evaluate side-chains 320 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 298 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 55 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 130 optimal weight: 0.3980 chunk 95 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 210 ASN A 380 ASN B 224 ASN B 283 GLN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN C 13 HIS ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.129248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.116918 restraints weight = 15587.534| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.63 r_work: 0.3571 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.6830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12168 Z= 0.143 Angle : 0.602 8.845 16498 Z= 0.311 Chirality : 0.042 0.156 1804 Planarity : 0.004 0.072 2118 Dihedral : 8.936 137.180 1915 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.36 % Favored : 96.50 % Rotamer: Outliers : 4.09 % Allowed : 28.55 % Favored : 67.36 % 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: 0.31 (0.22), residues: 1458 helix: 2.83 (0.27), residues: 384 sheet: 0.43 (0.30), residues: 312 loop : -1.37 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 81 HIS 0.007 0.001 HIS A 296 PHE 0.012 0.001 PHE A 440 TYR 0.014 0.002 TYR A 168 ARG 0.009 0.001 ARG A 453 Details of bonding type rmsd link_BETA2-3 : bond 0.00872 ( 2) link_BETA2-3 : angle 3.79901 ( 6) link_NAG-ASN : bond 0.00302 ( 9) link_NAG-ASN : angle 1.54730 ( 27) hydrogen bonds : bond 0.05658 ( 485) hydrogen bonds : angle 4.71451 ( 1428) SS BOND : bond 0.00673 ( 18) SS BOND : angle 1.91548 ( 36) covalent geometry : bond 0.00329 (12139) covalent geometry : angle 0.58850 (16429) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 327 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7111 (ptt90) REVERT: A 92 ASP cc_start: 0.8182 (m-30) cc_final: 0.7845 (m-30) REVERT: A 272 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: A 456 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7535 (mp) REVERT: B 136 SER cc_start: 0.8570 (p) cc_final: 0.8345 (t) REVERT: B 272 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: B 283 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8562 (mm-40) REVERT: B 375 PHE cc_start: 0.7839 (t80) cc_final: 0.7549 (t80) REVERT: C 197 ASN cc_start: 0.8247 (p0) cc_final: 0.8030 (p0) REVERT: C 272 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: C 349 ASP cc_start: 0.7298 (p0) cc_final: 0.7016 (p0) REVERT: C 405 ARG cc_start: 0.7763 (mtp85) cc_final: 0.7505 (mmp80) REVERT: C 415 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7101 (mp0) outliers start: 53 outliers final: 15 residues processed: 357 average time/residue: 1.3648 time to fit residues: 522.4904 Evaluate side-chains 324 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 302 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 30 optimal weight: 0.0270 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN B 244 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 HIS ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.125164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.113055 restraints weight = 15449.007| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.61 r_work: 0.3514 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.7406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 12168 Z= 0.210 Angle : 0.717 20.512 16498 Z= 0.355 Chirality : 0.053 1.193 1804 Planarity : 0.005 0.074 2118 Dihedral : 8.904 135.616 1914 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.57 % Favored : 96.36 % Rotamer: Outliers : 4.32 % Allowed : 28.09 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.20 (0.22), residues: 1458 helix: 2.69 (0.27), residues: 384 sheet: 0.39 (0.30), residues: 297 loop : -1.39 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 81 HIS 0.007 0.002 HIS A 296 PHE 0.021 0.002 PHE B 440 TYR 0.018 0.002 TYR B 487 ARG 0.007 0.001 ARG C 126 Details of bonding type rmsd link_BETA2-3 : bond 0.00724 ( 2) link_BETA2-3 : angle 4.27699 ( 6) link_NAG-ASN : bond 0.00314 ( 9) link_NAG-ASN : angle 5.32555 ( 27) hydrogen bonds : bond 0.06474 ( 485) hydrogen bonds : angle 4.83071 ( 1428) SS BOND : bond 0.00878 ( 18) SS BOND : angle 2.29119 ( 36) covalent geometry : bond 0.00509 (12139) covalent geometry : angle 0.67239 (16429) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 316 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: A 456 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7934 (mp) REVERT: B 206 THR cc_start: 0.8614 (p) cc_final: 0.8389 (p) REVERT: B 272 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: B 375 PHE cc_start: 0.8003 (t80) cc_final: 0.7792 (t80) REVERT: C 272 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: C 405 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7555 (mmp80) REVERT: C 415 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: C 491 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7927 (tptm) outliers start: 56 outliers final: 33 residues processed: 344 average time/residue: 1.2890 time to fit residues: 476.8697 Evaluate side-chains 342 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 303 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 491 LYS Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 97 optimal weight: 0.0770 chunk 138 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 77 optimal weight: 0.0870 chunk 135 optimal weight: 2.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 224 ASN A 472 HIS ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 HIS C 13 HIS C 33 HIS ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.125228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.113232 restraints weight = 15765.503| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.60 r_work: 0.3523 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.7688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12168 Z= 0.151 Angle : 0.624 16.234 16498 Z= 0.318 Chirality : 0.045 0.653 1804 Planarity : 0.004 0.075 2118 Dihedral : 8.455 133.973 1914 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.29 % Favored : 96.64 % Rotamer: Outliers : 5.25 % Allowed : 27.01 % Favored : 67.75 % 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: 0.29 (0.22), residues: 1458 helix: 2.73 (0.27), residues: 384 sheet: 0.48 (0.30), residues: 297 loop : -1.32 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 65 HIS 0.012 0.001 HIS B 356 PHE 0.016 0.001 PHE A 116 TYR 0.013 0.002 TYR A 12 ARG 0.012 0.001 ARG B 436 Details of bonding type rmsd link_BETA2-3 : bond 0.00593 ( 2) link_BETA2-3 : angle 2.94226 ( 6) link_NAG-ASN : bond 0.00610 ( 9) link_NAG-ASN : angle 3.93747 ( 27) hydrogen bonds : bond 0.05963 ( 485) hydrogen bonds : angle 4.71194 ( 1428) SS BOND : bond 0.00664 ( 18) SS BOND : angle 2.07797 ( 36) covalent geometry : bond 0.00348 (12139) covalent geometry : angle 0.59394 (16429) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 307 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7160 (ptt90) REVERT: A 272 GLU cc_start: 0.7720 (mp0) cc_final: 0.7488 (mp0) REVERT: A 456 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7932 (mp) REVERT: B 272 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: B 375 PHE cc_start: 0.8015 (t80) cc_final: 0.7719 (t80) REVERT: C 415 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7075 (mp0) outliers start: 68 outliers final: 32 residues processed: 347 average time/residue: 1.3372 time to fit residues: 501.9730 Evaluate side-chains 339 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 303 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 224 ASN A 380 ASN A 472 HIS ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN B 244 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN B 356 HIS C 13 HIS C 33 HIS ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.124343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.112394 restraints weight = 15758.607| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.59 r_work: 0.3509 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.7917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12168 Z= 0.162 Angle : 0.652 13.986 16498 Z= 0.333 Chirality : 0.045 0.621 1804 Planarity : 0.004 0.077 2118 Dihedral : 8.296 133.643 1914 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.29 % Favored : 96.64 % Rotamer: Outliers : 4.40 % Allowed : 28.01 % Favored : 67.59 % 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: 0.27 (0.21), residues: 1458 helix: 2.69 (0.27), residues: 384 sheet: 0.50 (0.30), residues: 297 loop : -1.33 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 81 HIS 0.013 0.002 HIS C 356 PHE 0.018 0.002 PHE B 440 TYR 0.018 0.002 TYR A 256 ARG 0.008 0.001 ARG A 453 Details of bonding type rmsd link_BETA2-3 : bond 0.00557 ( 2) link_BETA2-3 : angle 3.00563 ( 6) link_NAG-ASN : bond 0.00450 ( 9) link_NAG-ASN : angle 3.50152 ( 27) hydrogen bonds : bond 0.06116 ( 485) hydrogen bonds : angle 4.75769 ( 1428) SS BOND : bond 0.00669 ( 18) SS BOND : angle 2.61726 ( 36) covalent geometry : bond 0.00383 (12139) covalent geometry : angle 0.62335 (16429) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 316 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7949 (mp) REVERT: B 142 SER cc_start: 0.8494 (m) cc_final: 0.8279 (t) REVERT: B 206 THR cc_start: 0.8628 (p) cc_final: 0.8406 (p) REVERT: B 272 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: B 375 PHE cc_start: 0.8053 (t80) cc_final: 0.7787 (t80) REVERT: B 436 ARG cc_start: 0.7267 (mtp85) cc_final: 0.7013 (mtp85) REVERT: C 76 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8265 (mp) REVERT: C 415 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7084 (mp0) outliers start: 57 outliers final: 33 residues processed: 347 average time/residue: 1.3052 time to fit residues: 486.8962 Evaluate side-chains 340 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 303 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 27 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 HIS A 472 HIS ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 HIS C 13 HIS C 33 HIS C 224 ASN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.121559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.109726 restraints weight = 15609.695| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.59 r_work: 0.3467 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.8251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 12168 Z= 0.263 Angle : 0.740 12.935 16498 Z= 0.381 Chirality : 0.049 0.498 1804 Planarity : 0.005 0.084 2118 Dihedral : 8.353 131.980 1914 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.77 % Favored : 96.16 % Rotamer: Outliers : 4.40 % Allowed : 27.85 % Favored : 67.75 % 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: 0.12 (0.21), residues: 1458 helix: 2.53 (0.27), residues: 381 sheet: 0.44 (0.30), residues: 297 loop : -1.40 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 81 HIS 0.011 0.002 HIS C 356 PHE 0.035 0.003 PHE A 116 TYR 0.018 0.002 TYR A 492 ARG 0.008 0.001 ARG A 453 Details of bonding type rmsd link_BETA2-3 : bond 0.00384 ( 2) link_BETA2-3 : angle 3.80483 ( 6) link_NAG-ASN : bond 0.00539 ( 9) link_NAG-ASN : angle 3.22629 ( 27) hydrogen bonds : bond 0.07277 ( 485) hydrogen bonds : angle 4.98060 ( 1428) SS BOND : bond 0.00883 ( 18) SS BOND : angle 2.91746 ( 36) covalent geometry : bond 0.00644 (12139) covalent geometry : angle 0.71293 (16429) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 313 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.7038 (ptt-90) REVERT: A 272 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: A 456 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8143 (mp) REVERT: B 272 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: C 76 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8293 (mp) REVERT: C 415 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7160 (mp0) outliers start: 57 outliers final: 33 residues processed: 342 average time/residue: 1.3357 time to fit residues: 490.8512 Evaluate side-chains 346 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 307 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 87 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 356 HIS A 455 GLN A 472 HIS ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 HIS B 480 ASN C 13 HIS C 33 HIS ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.122191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.110692 restraints weight = 15770.581| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.60 r_work: 0.3489 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.8323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12168 Z= 0.167 Angle : 0.663 12.452 16498 Z= 0.342 Chirality : 0.046 0.489 1804 Planarity : 0.005 0.079 2118 Dihedral : 8.192 132.715 1914 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.43 % Favored : 96.50 % Rotamer: Outliers : 3.47 % Allowed : 29.78 % Favored : 66.74 % 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: 0.23 (0.21), residues: 1458 helix: 2.67 (0.27), residues: 381 sheet: 0.49 (0.30), residues: 297 loop : -1.36 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 65 HIS 0.014 0.002 HIS A 356 PHE 0.020 0.002 PHE B 440 TYR 0.016 0.002 TYR A 492 ARG 0.010 0.001 ARG A 453 Details of bonding type rmsd link_BETA2-3 : bond 0.00422 ( 2) link_BETA2-3 : angle 2.75446 ( 6) link_NAG-ASN : bond 0.00517 ( 9) link_NAG-ASN : angle 3.14699 ( 27) hydrogen bonds : bond 0.06487 ( 485) hydrogen bonds : angle 4.85882 ( 1428) SS BOND : bond 0.00709 ( 18) SS BOND : angle 2.41032 ( 36) covalent geometry : bond 0.00393 (12139) covalent geometry : angle 0.64011 (16429) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 308 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8094 (mp) REVERT: B 55 LEU cc_start: 0.7937 (tt) cc_final: 0.7699 (tp) REVERT: B 206 THR cc_start: 0.8607 (p) cc_final: 0.8396 (p) REVERT: B 272 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: C 415 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7138 (mp0) outliers start: 45 outliers final: 29 residues processed: 331 average time/residue: 1.3458 time to fit residues: 477.7424 Evaluate side-chains 336 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 304 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 109 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 70 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 77 optimal weight: 0.0010 chunk 55 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 356 HIS A 455 GLN A 472 HIS ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 HIS C 13 HIS C 33 HIS ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.123503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.111965 restraints weight = 15647.202| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.61 r_work: 0.3506 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.8378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12168 Z= 0.141 Angle : 0.623 11.934 16498 Z= 0.322 Chirality : 0.044 0.465 1804 Planarity : 0.005 0.085 2118 Dihedral : 8.041 133.800 1914 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.36 % Favored : 96.50 % Rotamer: Outliers : 2.93 % Allowed : 30.17 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.33 (0.21), residues: 1458 helix: 2.81 (0.27), residues: 381 sheet: 0.55 (0.30), residues: 297 loop : -1.33 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 81 HIS 0.014 0.002 HIS C 356 PHE 0.018 0.001 PHE B 440 TYR 0.016 0.001 TYR A 492 ARG 0.010 0.001 ARG C 126 Details of bonding type rmsd link_BETA2-3 : bond 0.00484 ( 2) link_BETA2-3 : angle 2.09957 ( 6) link_NAG-ASN : bond 0.00506 ( 9) link_NAG-ASN : angle 2.98903 ( 27) hydrogen bonds : bond 0.06001 ( 485) hydrogen bonds : angle 4.75208 ( 1428) SS BOND : bond 0.00651 ( 18) SS BOND : angle 2.07915 ( 36) covalent geometry : bond 0.00321 (12139) covalent geometry : angle 0.60292 (16429) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 303 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7989 (mp) REVERT: B 206 THR cc_start: 0.8627 (p) cc_final: 0.8398 (p) REVERT: B 272 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: C 192 ARG cc_start: 0.8562 (mtm-85) cc_final: 0.8279 (mtt-85) REVERT: C 415 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7084 (mp0) outliers start: 38 outliers final: 29 residues processed: 325 average time/residue: 1.3689 time to fit residues: 476.9173 Evaluate side-chains 322 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 290 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 122 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 135 optimal weight: 0.2980 chunk 112 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 356 HIS A 472 HIS ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 HIS ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 HIS C 13 HIS C 33 HIS ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.123308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.111751 restraints weight = 15683.438| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.60 r_work: 0.3508 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.8419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12168 Z= 0.149 Angle : 0.639 12.688 16498 Z= 0.329 Chirality : 0.044 0.448 1804 Planarity : 0.005 0.083 2118 Dihedral : 7.977 133.295 1914 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.22 % Favored : 96.64 % Rotamer: Outliers : 3.16 % Allowed : 30.17 % Favored : 66.67 % 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: 0.35 (0.21), residues: 1458 helix: 2.80 (0.27), residues: 381 sheet: 0.60 (0.30), residues: 297 loop : -1.32 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 81 HIS 0.018 0.002 HIS C 356 PHE 0.020 0.001 PHE B 440 TYR 0.017 0.001 TYR A 492 ARG 0.010 0.001 ARG A 453 Details of bonding type rmsd link_BETA2-3 : bond 0.00437 ( 2) link_BETA2-3 : angle 2.08630 ( 6) link_NAG-ASN : bond 0.00481 ( 9) link_NAG-ASN : angle 2.89088 ( 27) hydrogen bonds : bond 0.06051 ( 485) hydrogen bonds : angle 4.73310 ( 1428) SS BOND : bond 0.00637 ( 18) SS BOND : angle 2.23577 ( 36) covalent geometry : bond 0.00344 (12139) covalent geometry : angle 0.61904 (16429) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11759.49 seconds wall clock time: 202 minutes 19.57 seconds (12139.57 seconds total)