Starting phenix.real_space_refine on Tue Jun 10 18:08:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xra_38600/06_2025/8xra_38600_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xra_38600/06_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_38600/06_2025/8xra_38600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xra_38600/06_2025/8xra_38600.map" model { file = "/net/cci-nas-00/data/ceres_data/8xra_38600/06_2025/8xra_38600_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xra_38600/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.63, per 1000 atoms: 0.73 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: 3.18 Conformation dependent library (CDL) restraints added in 1.3 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: 1.91 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: 3.91 Time building geometry restraints manager: 3.63 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.790 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 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:12.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.050 ------------------------------------------------------------------------------- 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 : 1.242 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: 1.1189 time to fit residues: 438.6862 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 : 1.320 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.148969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.136402 restraints weight = 16233.140| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.66 r_work: 0.3823 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 2.00516 ( 27) hydrogen bonds : bond 0.05532 ( 485) hydrogen bonds : angle 5.06106 ( 1428) SS BOND : bond 0.00953 ( 18) SS BOND : angle 2.60540 ( 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 : 1.372 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: 0.8585 (OUTLIER) cc_final: 0.8359 (mm) REVERT: A 258 PHE cc_start: 0.8267 (m-80) cc_final: 0.7642 (m-80) REVERT: A 323 ASN cc_start: 0.7587 (t0) cc_final: 0.7066 (t0) REVERT: B 60 CYS cc_start: 0.6293 (OUTLIER) cc_final: 0.5802 (p) REVERT: C 230 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8158 (mtt) REVERT: C 248 THR cc_start: 0.8558 (m) cc_final: 0.8166 (p) REVERT: C 349 ASP cc_start: 0.7069 (p0) cc_final: 0.6858 (p0) REVERT: C 405 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7565 (mmp80) outliers start: 94 outliers final: 20 residues processed: 395 average time/residue: 1.1983 time to fit residues: 513.6391 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 : 1.410 ------------------------------------------------------------------------------- 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: 0.9980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3838 r_free = 0.3838 target = 0.129525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.117153 restraints weight = 15822.328| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.65 r_work: 0.3572 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.6654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 12168 Z= 0.232 Angle : 0.768 12.314 16498 Z= 0.389 Chirality : 0.046 0.216 1804 Planarity : 0.005 0.068 2118 Dihedral : 9.993 148.101 1916 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.50 % Favored : 96.43 % Rotamer: Outliers : 4.86 % Allowed : 27.01 % Favored : 68.13 % 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 (0.21), residues: 1458 helix: 2.67 (0.26), residues: 375 sheet: 0.34 (0.29), residues: 312 loop : -1.47 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 127 HIS 0.010 0.002 HIS A 296 PHE 0.028 0.002 PHE B 470 TYR 0.023 0.002 TYR A 487 ARG 0.006 0.001 ARG A 149 Details of bonding type rmsd link_BETA2-3 : bond 0.00661 ( 2) link_BETA2-3 : angle 7.31583 ( 6) link_NAG-ASN : bond 0.00330 ( 9) link_NAG-ASN : angle 1.90690 ( 27) hydrogen bonds : bond 0.06851 ( 485) hydrogen bonds : angle 4.98104 ( 1428) SS BOND : bond 0.01093 ( 18) SS BOND : angle 3.04448 ( 36) covalent geometry : bond 0.00538 (12139) covalent geometry : angle 0.73886 (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 399 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 336 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.8031 (tp) cc_final: 0.7717 (tt) REVERT: A 283 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8033 (mm-40) REVERT: A 393 PHE cc_start: 0.8119 (t80) cc_final: 0.7869 (t80) REVERT: B 8 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7735 (tt) REVERT: B 136 SER cc_start: 0.8615 (p) cc_final: 0.8333 (t) REVERT: B 260 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7490 (mt) REVERT: B 272 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: B 375 PHE cc_start: 0.7910 (t80) cc_final: 0.7671 (t80) REVERT: C 230 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8433 (mtt) REVERT: C 272 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: C 349 ASP cc_start: 0.7357 (p0) cc_final: 0.7068 (p0) REVERT: C 405 ARG cc_start: 0.7863 (mtp85) cc_final: 0.7603 (mmp80) REVERT: C 415 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7164 (mp0) outliers start: 63 outliers final: 16 residues processed: 358 average time/residue: 1.3407 time to fit residues: 515.6269 Evaluate side-chains 319 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 296 time to evaluate : 1.367 ------------------------------------------------------------------------------- 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 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 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 139 CYS Chi-restraints excluded: chain C residue 230 MET 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 446 LYS 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: 0.1980 chunk 126 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 130 optimal weight: 0.0060 chunk 95 optimal weight: 3.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 380 ASN B 224 ASN B 283 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.129347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.117099 restraints weight = 15567.575| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.63 r_work: 0.3574 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.6963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12168 Z= 0.128 Angle : 0.646 20.855 16498 Z= 0.317 Chirality : 0.049 1.128 1804 Planarity : 0.004 0.068 2118 Dihedral : 9.175 138.359 1914 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.29 % Favored : 96.57 % Rotamer: Outliers : 4.09 % Allowed : 28.86 % Favored : 67.05 % 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: 0.30 (0.22), residues: 1458 helix: 2.81 (0.27), residues: 384 sheet: 0.47 (0.30), residues: 312 loop : -1.39 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 81 HIS 0.007 0.001 HIS A 296 PHE 0.011 0.001 PHE A 440 TYR 0.012 0.001 TYR B 487 ARG 0.008 0.001 ARG B 74 Details of bonding type rmsd link_BETA2-3 : bond 0.00991 ( 2) link_BETA2-3 : angle 3.82901 ( 6) link_NAG-ASN : bond 0.00610 ( 9) link_NAG-ASN : angle 5.29671 ( 27) hydrogen bonds : bond 0.05569 ( 485) hydrogen bonds : angle 4.73770 ( 1428) SS BOND : bond 0.00684 ( 18) SS BOND : angle 1.77335 ( 36) covalent geometry : bond 0.00283 (12139) covalent geometry : angle 0.60045 (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 365 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 312 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 456 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7559 (mp) REVERT: B 136 SER cc_start: 0.8544 (p) cc_final: 0.8334 (t) REVERT: B 272 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: B 283 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8564 (mm-40) REVERT: B 375 PHE cc_start: 0.7875 (t80) cc_final: 0.7555 (t80) REVERT: C 272 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: C 349 ASP cc_start: 0.7291 (p0) cc_final: 0.7010 (p0) REVERT: C 405 ARG cc_start: 0.7757 (mtp85) cc_final: 0.7495 (mmp80) REVERT: C 415 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7059 (mp0) outliers start: 53 outliers final: 19 residues processed: 340 average time/residue: 1.3372 time to fit residues: 488.5675 Evaluate side-chains 328 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 304 time to evaluate : 1.374 ------------------------------------------------------------------------------- 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 111 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 211 LYS 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 410 LEU Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 478 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 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: 0.4980 chunk 62 optimal weight: 0.5980 chunk 122 optimal weight: 0.0270 chunk 138 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS 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 = 0.3822 r_free = 0.3822 target = 0.128410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.116185 restraints weight = 15589.459| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.63 r_work: 0.3561 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.7181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12168 Z= 0.130 Angle : 0.618 17.291 16498 Z= 0.310 Chirality : 0.045 0.787 1804 Planarity : 0.004 0.072 2118 Dihedral : 8.791 136.050 1914 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.88 % Favored : 96.98 % Rotamer: Outliers : 4.24 % Allowed : 28.47 % Favored : 67.28 % 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: 0.37 (0.22), residues: 1458 helix: 2.84 (0.27), residues: 384 sheet: 0.55 (0.30), residues: 312 loop : -1.34 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 65 HIS 0.006 0.001 HIS A 296 PHE 0.012 0.001 PHE A 440 TYR 0.015 0.001 TYR A 256 ARG 0.009 0.001 ARG B 436 Details of bonding type rmsd link_BETA2-3 : bond 0.00714 ( 2) link_BETA2-3 : angle 3.58165 ( 6) link_NAG-ASN : bond 0.00392 ( 9) link_NAG-ASN : angle 4.23852 ( 27) hydrogen bonds : bond 0.05522 ( 485) hydrogen bonds : angle 4.66688 ( 1428) SS BOND : bond 0.00614 ( 18) SS BOND : angle 1.98128 ( 36) covalent geometry : bond 0.00294 (12139) covalent geometry : angle 0.58377 (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 361 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 306 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.8247 (m-30) cc_final: 0.7875 (m-30) REVERT: A 272 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: A 456 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7598 (mp) REVERT: B 375 PHE cc_start: 0.7909 (t80) cc_final: 0.7618 (t80) REVERT: C 349 ASP cc_start: 0.7200 (p0) cc_final: 0.6921 (p0) REVERT: C 405 ARG cc_start: 0.7716 (mtp85) cc_final: 0.7467 (mmp80) REVERT: C 415 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7074 (mp0) outliers start: 55 outliers final: 29 residues processed: 334 average time/residue: 1.4006 time to fit residues: 501.1699 Evaluate side-chains 321 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 289 time to evaluate : 1.351 ------------------------------------------------------------------------------- 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 141 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 443 SER 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 211 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 261 SER 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 146 SER 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 345 GLN 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 497 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 97 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 96 optimal weight: 0.0870 chunk 10 optimal weight: 0.1980 chunk 79 optimal weight: 0.7980 chunk 77 optimal weight: 0.2980 chunk 135 optimal weight: 1.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 B 224 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 = 0.3820 r_free = 0.3820 target = 0.127782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.115577 restraints weight = 15970.438| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.64 r_work: 0.3558 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.7471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12168 Z= 0.120 Angle : 0.578 14.068 16498 Z= 0.295 Chirality : 0.043 0.580 1804 Planarity : 0.004 0.073 2118 Dihedral : 8.196 134.060 1914 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.22 % Favored : 96.64 % Rotamer: Outliers : 3.94 % Allowed : 28.24 % Favored : 67.82 % 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: 0.47 (0.22), residues: 1458 helix: 2.88 (0.27), residues: 384 sheet: 0.67 (0.30), residues: 312 loop : -1.29 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 81 HIS 0.006 0.001 HIS A 296 PHE 0.011 0.001 PHE A 440 TYR 0.011 0.001 TYR B 487 ARG 0.010 0.001 ARG A 453 Details of bonding type rmsd link_BETA2-3 : bond 0.00595 ( 2) link_BETA2-3 : angle 2.71841 ( 6) link_NAG-ASN : bond 0.00502 ( 9) link_NAG-ASN : angle 3.43503 ( 27) hydrogen bonds : bond 0.05327 ( 485) hydrogen bonds : angle 4.57271 ( 1428) SS BOND : bond 0.00581 ( 18) SS BOND : angle 1.84616 ( 36) covalent geometry : bond 0.00267 (12139) covalent geometry : angle 0.55336 (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 365 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 314 time to evaluate : 1.460 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: 0.7642 (mp0) cc_final: 0.7399 (mp0) REVERT: A 456 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7591 (mp) REVERT: B 375 PHE cc_start: 0.7966 (t80) cc_final: 0.7682 (t80) REVERT: B 436 ARG cc_start: 0.7239 (mtp85) cc_final: 0.7039 (mtp85) REVERT: C 272 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: C 405 ARG cc_start: 0.7726 (mtp85) cc_final: 0.7469 (mmp80) REVERT: C 415 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7059 (mp0) outliers start: 51 outliers final: 27 residues processed: 342 average time/residue: 1.3253 time to fit residues: 491.6053 Evaluate side-chains 336 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 306 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 111 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 456 LEU 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 211 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 261 SER 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 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 413 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 118 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 85 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 224 ASN ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 HIS B 224 ASN B 244 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 HIS C 33 HIS C 283 GLN ** 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 = 0.3801 r_free = 0.3801 target = 0.126435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.114331 restraints weight = 15841.023| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.61 r_work: 0.3538 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.7673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12168 Z= 0.142 Angle : 0.616 12.541 16498 Z= 0.314 Chirality : 0.044 0.504 1804 Planarity : 0.004 0.076 2118 Dihedral : 8.055 132.752 1914 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.88 % Favored : 96.98 % Rotamer: Outliers : 3.70 % Allowed : 28.78 % Favored : 67.52 % 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: 0.38 (0.22), residues: 1458 helix: 2.48 (0.27), residues: 402 sheet: 0.75 (0.30), residues: 312 loop : -1.32 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 65 HIS 0.005 0.001 HIS A 296 PHE 0.016 0.001 PHE A 116 TYR 0.018 0.001 TYR A 256 ARG 0.007 0.001 ARG C 74 Details of bonding type rmsd link_BETA2-3 : bond 0.00591 ( 2) link_BETA2-3 : angle 2.72287 ( 6) link_NAG-ASN : bond 0.00506 ( 9) link_NAG-ASN : angle 3.11042 ( 27) hydrogen bonds : bond 0.05636 ( 485) hydrogen bonds : angle 4.61718 ( 1428) SS BOND : bond 0.00648 ( 18) SS BOND : angle 2.23071 ( 36) covalent geometry : bond 0.00330 (12139) covalent geometry : angle 0.59267 (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 353 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 305 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 GLU cc_start: 0.7739 (mp0) cc_final: 0.7527 (mp0) REVERT: A 456 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7686 (mp) REVERT: B 375 PHE cc_start: 0.8005 (t80) cc_final: 0.7704 (t80) REVERT: C 76 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8217 (mp) REVERT: C 272 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: C 415 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7056 (mp0) outliers start: 48 outliers final: 29 residues processed: 333 average time/residue: 1.3571 time to fit residues: 484.7333 Evaluate side-chains 332 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 299 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 60 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 292 THR 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 211 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 292 THR 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 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 413 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 27 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 99 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 HIS C 13 HIS C 33 HIS C 196 GLN C 224 ASN ** 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 = 0.3743 r_free = 0.3743 target = 0.122022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.110230 restraints weight = 15645.810| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.56 r_work: 0.3475 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.8164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 12168 Z= 0.249 Angle : 0.744 11.700 16498 Z= 0.383 Chirality : 0.049 0.461 1804 Planarity : 0.005 0.081 2118 Dihedral : 8.221 129.431 1914 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.91 % Favored : 96.02 % Rotamer: Outliers : 4.09 % Allowed : 28.09 % Favored : 67.82 % 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: 0.18 (0.21), residues: 1458 helix: 2.52 (0.27), residues: 381 sheet: 0.60 (0.30), residues: 312 loop : -1.43 (0.19), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 81 HIS 0.013 0.002 HIS B 356 PHE 0.029 0.002 PHE B 440 TYR 0.017 0.002 TYR B 487 ARG 0.007 0.001 ARG C 74 Details of bonding type rmsd link_BETA2-3 : bond 0.00493 ( 2) link_BETA2-3 : angle 3.80470 ( 6) link_NAG-ASN : bond 0.00535 ( 9) link_NAG-ASN : angle 2.96887 ( 27) hydrogen bonds : bond 0.07232 ( 485) hydrogen bonds : angle 4.99890 ( 1428) SS BOND : bond 0.00763 ( 18) SS BOND : angle 2.92500 ( 36) covalent geometry : bond 0.00610 (12139) covalent geometry : angle 0.71914 (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 381 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 328 time to evaluate : 1.430 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: 0.7813 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: A 415 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: A 456 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8157 (mp) REVERT: C 76 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8271 (mp) REVERT: C 415 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7138 (mp0) outliers start: 53 outliers final: 30 residues processed: 359 average time/residue: 1.4521 time to fit residues: 558.6353 Evaluate side-chains 354 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 319 time to evaluate : 1.318 ------------------------------------------------------------------------------- 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 415 GLU 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 211 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 261 SER 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 436 ARG Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 47 CYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 87 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 105 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 1 optimal weight: 0.0870 chunk 65 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 409 ASN C 13 HIS C 33 HIS ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.123384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.111782 restraints weight = 15689.924| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.60 r_work: 0.3506 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.8241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12168 Z= 0.141 Angle : 0.632 11.575 16498 Z= 0.326 Chirality : 0.044 0.448 1804 Planarity : 0.004 0.077 2118 Dihedral : 7.944 131.114 1914 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.98 % Rotamer: Outliers : 3.24 % Allowed : 29.48 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1458 helix: 2.41 (0.27), residues: 399 sheet: 0.61 (0.31), residues: 297 loop : -1.32 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 81 HIS 0.014 0.002 HIS A 356 PHE 0.013 0.001 PHE B 440 TYR 0.013 0.001 TYR A 168 ARG 0.008 0.001 ARG A 74 Details of bonding type rmsd link_BETA2-3 : bond 0.00614 ( 2) link_BETA2-3 : angle 2.26394 ( 6) link_NAG-ASN : bond 0.00528 ( 9) link_NAG-ASN : angle 2.91961 ( 27) hydrogen bonds : bond 0.06053 ( 485) hydrogen bonds : angle 4.78914 ( 1428) SS BOND : bond 0.00704 ( 18) SS BOND : angle 2.35207 ( 36) covalent geometry : bond 0.00319 (12139) covalent geometry : angle 0.61057 (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: 42 poor density : 311 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7977 (mp) REVERT: A 479 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7466 (mtm) REVERT: B 74 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7715 (ttp80) REVERT: B 206 THR cc_start: 0.8612 (p) cc_final: 0.8370 (p) REVERT: C 415 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7127 (mp0) outliers start: 42 outliers final: 29 residues processed: 334 average time/residue: 1.3173 time to fit residues: 473.4734 Evaluate side-chains 331 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 298 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 48 LYS 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 415 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 479 MET 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 211 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 292 THR 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 20 THR 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 265 SER Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 399 GLU 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: 1.9990 chunk 99 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 0.0270 chunk 55 optimal weight: 0.0970 chunk 84 optimal weight: 0.0980 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- 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 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 197 ASN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.125189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.113720 restraints weight = 15637.182| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.58 r_work: 0.3532 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.8291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12168 Z= 0.122 Angle : 0.604 10.959 16498 Z= 0.312 Chirality : 0.043 0.427 1804 Planarity : 0.004 0.081 2118 Dihedral : 7.798 132.260 1914 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.02 % Favored : 96.84 % Rotamer: Outliers : 2.85 % Allowed : 29.63 % Favored : 67.52 % 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: 0.38 (0.22), residues: 1458 helix: 2.46 (0.27), residues: 399 sheet: 0.73 (0.31), residues: 297 loop : -1.23 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 422 HIS 0.014 0.002 HIS A 356 PHE 0.019 0.001 PHE A 116 TYR 0.014 0.001 TYR A 256 ARG 0.007 0.001 ARG C 126 Details of bonding type rmsd link_BETA2-3 : bond 0.00432 ( 2) link_BETA2-3 : angle 1.74424 ( 6) link_NAG-ASN : bond 0.00477 ( 9) link_NAG-ASN : angle 2.79384 ( 27) hydrogen bonds : bond 0.05539 ( 485) hydrogen bonds : angle 4.65628 ( 1428) SS BOND : bond 0.00606 ( 18) SS BOND : angle 2.05159 ( 36) covalent geometry : bond 0.00269 (12139) covalent geometry : angle 0.58537 (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 356 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 319 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7788 (tp) cc_final: 0.7496 (tp) REVERT: A 456 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7844 (mp) REVERT: C 415 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7052 (mp0) outliers start: 37 outliers final: 27 residues processed: 341 average time/residue: 1.2942 time to fit residues: 475.1887 Evaluate side-chains 336 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 307 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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 415 GLU 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 211 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 292 THR 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 20 THR 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: 4.9990 chunk 33 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 345 GLN A 356 HIS A 380 ASN A 455 GLN A 472 HIS A 501 ASN B 13 HIS B 33 HIS ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 HIS B 409 ASN C 13 HIS C 33 HIS C 197 ASN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 ASN C 455 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.121941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.110634 restraints weight = 15723.040| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.57 r_work: 0.3486 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.8409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12168 Z= 0.212 Angle : 0.698 10.990 16498 Z= 0.361 Chirality : 0.047 0.415 1804 Planarity : 0.005 0.079 2118 Dihedral : 7.933 131.199 1914 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.09 % Favored : 96.84 % Rotamer: Outliers : 3.32 % Allowed : 29.78 % 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: 0.22 (0.22), residues: 1458 helix: 2.26 (0.27), residues: 399 sheet: 0.66 (0.31), residues: 297 loop : -1.29 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 81 HIS 0.014 0.002 HIS C 356 PHE 0.024 0.002 PHE B 440 TYR 0.015 0.002 TYR B 487 ARG 0.007 0.001 ARG A 126 Details of bonding type rmsd link_BETA2-3 : bond 0.00471 ( 2) link_BETA2-3 : angle 2.78201 ( 6) link_NAG-ASN : bond 0.00478 ( 9) link_NAG-ASN : angle 2.71473 ( 27) hydrogen bonds : bond 0.06692 ( 485) hydrogen bonds : angle 4.86166 ( 1428) SS BOND : bond 0.00733 ( 18) SS BOND : angle 2.58167 ( 36) covalent geometry : bond 0.00515 (12139) covalent geometry : angle 0.67778 (16429) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12482.93 seconds wall clock time: 213 minutes 9.19 seconds (12789.19 seconds total)