Starting phenix.real_space_refine on Wed Sep 17 22:35:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xra_38600/09_2025/8xra_38600_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xra_38600/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xra_38600/09_2025/8xra_38600_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xra_38600/09_2025/8xra_38600_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xra_38600/09_2025/8xra_38600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xra_38600/09_2025/8xra_38600.map" } resolution = 2.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.93, per 1000 atoms: 0.25 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: 0.67 Conformation dependent library (CDL) restraints added in 429.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.42 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: 1.94 Time building geometry restraints manager: 0.93 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 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.700 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.700 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (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 ARG 0.008 0.001 ARG B 192 TYR 0.016 0.001 TYR A 103 PHE 0.024 0.001 PHE A 116 TRP 0.015 0.001 TRP B 81 HIS 0.007 0.001 HIS B 356 Details of bonding type rmsd covalent geometry : bond 0.00402 (12139) covalent geometry : angle 0.63522 (16429) SS BOND : bond 0.00577 ( 18) SS BOND : angle 1.43739 ( 36) hydrogen bonds : bond 0.13408 ( 485) hydrogen bonds : angle 6.19738 ( 1428) 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) *********************** 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 : 0.375 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: 0.5326 time to fit residues: 209.2373 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 : 0.382 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.2980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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** A 501 ASN B 283 GLN B 360 GLN C 101 ASN C 244 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.152885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.140239 restraints weight = 16375.176| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.69 r_work: 0.3869 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 12168 Z= 0.204 Angle : 0.795 14.868 16498 Z= 0.395 Chirality : 0.048 0.183 1804 Planarity : 0.006 0.067 2118 Dihedral : 10.272 141.438 1924 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.12 % Favored : 95.75 % Rotamer: Outliers : 7.25 % Allowed : 25.15 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.22), residues: 1458 helix: 2.39 (0.27), residues: 381 sheet: 0.02 (0.30), residues: 303 loop : -1.39 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 27 TYR 0.022 0.002 TYR C 168 PHE 0.024 0.002 PHE A 148 TRP 0.010 0.002 TRP C 344 HIS 0.010 0.002 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00452 (12139) covalent geometry : angle 0.77643 (16429) SS BOND : bond 0.00808 ( 18) SS BOND : angle 2.35114 ( 36) hydrogen bonds : bond 0.05387 ( 485) hydrogen bonds : angle 5.06470 ( 1428) link_BETA2-3 : bond 0.04178 ( 2) link_BETA2-3 : angle 6.01028 ( 6) link_NAG-ASN : bond 0.00642 ( 9) link_NAG-ASN : angle 1.97624 ( 27) *********************** 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 425 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 331 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 PHE cc_start: 0.8077 (m-80) cc_final: 0.7509 (m-80) REVERT: A 283 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7507 (mm-40) REVERT: B 60 CYS cc_start: 0.6076 (OUTLIER) cc_final: 0.5624 (p) REVERT: C 230 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8021 (mtt) REVERT: C 248 THR cc_start: 0.8478 (m) cc_final: 0.8061 (p) outliers start: 94 outliers final: 21 residues processed: 389 average time/residue: 0.5623 time to fit residues: 237.1892 Evaluate side-chains 308 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 284 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 111 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 136 SER 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 283 GLN 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 292 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 146 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 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 125 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 95 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 ASN B 186 ASN B 244 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 HIS B 356 HIS B 409 ASN C 13 HIS C 33 HIS C 186 ASN C 444 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.134122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.121636 restraints weight = 16017.901| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.67 r_work: 0.3635 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.6041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 12168 Z= 0.213 Angle : 0.737 12.452 16498 Z= 0.373 Chirality : 0.046 0.242 1804 Planarity : 0.005 0.068 2118 Dihedral : 9.847 152.414 1916 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.43 % Favored : 96.50 % Rotamer: Outliers : 5.63 % Allowed : 27.39 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.22), residues: 1458 helix: 2.68 (0.26), residues: 381 sheet: 0.16 (0.29), residues: 318 loop : -1.36 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 405 TYR 0.019 0.002 TYR A 256 PHE 0.020 0.002 PHE B 470 TRP 0.014 0.002 TRP C 127 HIS 0.009 0.002 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00491 (12139) covalent geometry : angle 0.71260 (16429) SS BOND : bond 0.00740 ( 18) SS BOND : angle 2.45443 ( 36) hydrogen bonds : bond 0.06355 ( 485) hydrogen bonds : angle 4.87992 ( 1428) link_BETA2-3 : bond 0.00438 ( 2) link_BETA2-3 : angle 7.14498 ( 6) link_NAG-ASN : bond 0.00395 ( 9) link_NAG-ASN : angle 1.88036 ( 27) *********************** 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 411 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 338 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 SER cc_start: 0.8730 (m) cc_final: 0.8445 (t) REVERT: B 8 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7612 (tt) REVERT: B 136 SER cc_start: 0.8665 (p) cc_final: 0.8329 (t) REVERT: B 272 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: B 470 PHE cc_start: 0.7235 (m-80) cc_final: 0.6736 (m-80) REVERT: C 230 MET cc_start: 0.8608 (ttm) cc_final: 0.8397 (mtt) REVERT: C 272 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: C 415 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7177 (mp0) outliers start: 73 outliers final: 19 residues processed: 373 average time/residue: 0.6178 time to fit residues: 248.1103 Evaluate side-chains 331 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 308 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 94 optimal weight: 0.3980 chunk 21 optimal weight: 0.2980 chunk 132 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 29 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 244 ASN A 283 GLN A 380 ASN B 224 ASN B 283 GLN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN C 13 HIS C 130 HIS C 191 GLN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.132878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.120425 restraints weight = 15851.359| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.65 r_work: 0.3620 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.6427 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= 0.122 Angle : 0.590 8.348 16498 Z= 0.303 Chirality : 0.041 0.146 1804 Planarity : 0.004 0.070 2118 Dihedral : 9.007 138.658 1915 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.50 % Favored : 96.36 % Rotamer: Outliers : 4.63 % Allowed : 28.16 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.22), residues: 1458 helix: 2.90 (0.27), residues: 384 sheet: 0.26 (0.30), residues: 318 loop : -1.31 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 453 TYR 0.013 0.001 TYR A 12 PHE 0.010 0.001 PHE B 470 TRP 0.008 0.001 TRP B 65 HIS 0.006 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00267 (12139) covalent geometry : angle 0.57648 (16429) SS BOND : bond 0.00695 ( 18) SS BOND : angle 1.89103 ( 36) hydrogen bonds : bond 0.05299 ( 485) hydrogen bonds : angle 4.66741 ( 1428) link_BETA2-3 : bond 0.00939 ( 2) link_BETA2-3 : angle 3.91857 ( 6) link_NAG-ASN : bond 0.00206 ( 9) link_NAG-ASN : angle 1.59134 ( 27) *********************** 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 373 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 313 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: A 456 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7302 (mp) REVERT: A 471 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.7490 (m-80) REVERT: B 136 SER cc_start: 0.8633 (p) cc_final: 0.8363 (t) REVERT: B 137 ARG cc_start: 0.8642 (mmt90) cc_final: 0.8431 (mtt90) REVERT: B 272 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: C 136 SER cc_start: 0.8489 (p) cc_final: 0.8275 (t) REVERT: C 272 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7717 (mp0) REVERT: C 415 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7120 (mp0) outliers start: 60 outliers final: 24 residues processed: 346 average time/residue: 0.6418 time to fit residues: 238.3417 Evaluate side-chains 322 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 292 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 62 ILE Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 116 PHE 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 413 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 209 LEU 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 46 optimal weight: 3.9990 chunk 6 optimal weight: 0.0670 chunk 35 optimal weight: 4.9990 chunk 54 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 108 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 283 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.131155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.118914 restraints weight = 15819.953| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.61 r_work: 0.3598 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.6756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12168 Z= 0.121 Angle : 0.566 7.862 16498 Z= 0.291 Chirality : 0.041 0.153 1804 Planarity : 0.004 0.071 2118 Dihedral : 8.530 135.313 1914 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.88 % Favored : 96.98 % Rotamer: Outliers : 4.01 % Allowed : 29.17 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.22), residues: 1458 helix: 3.00 (0.27), residues: 384 sheet: 0.31 (0.30), residues: 318 loop : -1.25 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 126 TYR 0.015 0.001 TYR A 256 PHE 0.011 0.001 PHE A 440 TRP 0.008 0.001 TRP B 65 HIS 0.006 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00269 (12139) covalent geometry : angle 0.55414 (16429) SS BOND : bond 0.00584 ( 18) SS BOND : angle 1.69287 ( 36) hydrogen bonds : bond 0.05240 ( 485) hydrogen bonds : angle 4.59985 ( 1428) link_BETA2-3 : bond 0.00694 ( 2) link_BETA2-3 : angle 3.40963 ( 6) link_NAG-ASN : bond 0.00201 ( 9) link_NAG-ASN : angle 1.51379 ( 27) *********************** 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 358 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 306 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: A 456 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7336 (mp) REVERT: A 471 TYR cc_start: 0.7803 (m-10) cc_final: 0.7523 (m-80) REVERT: B 136 SER cc_start: 0.8574 (p) cc_final: 0.8342 (t) REVERT: B 137 ARG cc_start: 0.8668 (mmt90) cc_final: 0.8434 (mtt90) REVERT: B 272 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: B 375 PHE cc_start: 0.7744 (t80) cc_final: 0.7513 (t80) REVERT: C 349 ASP cc_start: 0.7270 (p0) cc_final: 0.6980 (p0) REVERT: C 415 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: C 436 ARG cc_start: 0.7713 (mtp-110) cc_final: 0.7499 (mtp180) outliers start: 52 outliers final: 29 residues processed: 335 average time/residue: 0.6144 time to fit residues: 221.4638 Evaluate side-chains 333 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 300 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 62 ILE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 139 CYS 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 446 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 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 486 THR 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 44 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 HIS C 175 GLN ** 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 = 0.3754 r_free = 0.3754 target = 0.123113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.111012 restraints weight = 15562.113| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.60 r_work: 0.3486 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.7782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 12168 Z= 0.259 Angle : 0.779 20.329 16498 Z= 0.392 Chirality : 0.051 0.729 1804 Planarity : 0.005 0.078 2118 Dihedral : 8.796 132.445 1914 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.91 % Favored : 96.02 % Rotamer: Outliers : 4.86 % Allowed : 28.16 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.21), residues: 1458 helix: 2.51 (0.26), residues: 384 sheet: 0.35 (0.30), residues: 312 loop : -1.46 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 436 TYR 0.020 0.002 TYR B 487 PHE 0.027 0.003 PHE B 440 TRP 0.018 0.002 TRP B 65 HIS 0.008 0.002 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00631 (12139) covalent geometry : angle 0.74360 (16429) SS BOND : bond 0.00887 ( 18) SS BOND : angle 2.47872 ( 36) hydrogen bonds : bond 0.07188 ( 485) hydrogen bonds : angle 5.00151 ( 1428) link_BETA2-3 : bond 0.00681 ( 2) link_BETA2-3 : angle 4.38369 ( 6) link_NAG-ASN : bond 0.00438 ( 9) link_NAG-ASN : angle 4.66311 ( 27) *********************** 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 397 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 334 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: A 456 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8108 (mp) REVERT: B 272 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: B 480 ASN cc_start: 0.6730 (m-40) cc_final: 0.6527 (m110) REVERT: C 415 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7137 (mp0) outliers start: 63 outliers final: 32 residues processed: 369 average time/residue: 0.6355 time to fit residues: 251.8801 Evaluate side-chains 351 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 315 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 443 SER Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 24 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 224 ASN A 472 HIS B 224 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN B 409 ASN C 13 HIS ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 HIS C 447 ASN C 455 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.124452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.112401 restraints weight = 15760.599| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.60 r_work: 0.3507 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.7951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12168 Z= 0.159 Angle : 0.654 14.300 16498 Z= 0.333 Chirality : 0.046 0.706 1804 Planarity : 0.005 0.077 2118 Dihedral : 8.347 132.301 1914 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.02 % Favored : 96.91 % Rotamer: Outliers : 4.01 % Allowed : 29.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.21), residues: 1458 helix: 2.76 (0.27), residues: 381 sheet: 0.35 (0.30), residues: 297 loop : -1.37 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 126 TYR 0.015 0.002 TYR A 12 PHE 0.019 0.001 PHE A 116 TRP 0.012 0.001 TRP B 65 HIS 0.011 0.001 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00370 (12139) covalent geometry : angle 0.62517 (16429) SS BOND : bond 0.00755 ( 18) SS BOND : angle 2.59272 ( 36) hydrogen bonds : bond 0.06153 ( 485) hydrogen bonds : angle 4.79746 ( 1428) link_BETA2-3 : bond 0.00571 ( 2) link_BETA2-3 : angle 2.90558 ( 6) link_NAG-ASN : bond 0.00340 ( 9) link_NAG-ASN : angle 3.60601 ( 27) *********************** 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 369 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 317 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: B 272 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: B 480 ASN cc_start: 0.6976 (m-40) cc_final: 0.6746 (m110) REVERT: C 415 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7133 (mp0) outliers start: 52 outliers final: 32 residues processed: 344 average time/residue: 0.7407 time to fit residues: 272.7248 Evaluate side-chains 344 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 309 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 188 GLU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 446 LYS 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 116 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 39 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 106 optimal weight: 0.0570 chunk 138 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- 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 455 GLN A 472 HIS ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 HIS C 13 HIS C 33 HIS ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.123582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.111641 restraints weight = 15642.326| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.60 r_work: 0.3494 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.8123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12168 Z= 0.179 Angle : 0.672 13.050 16498 Z= 0.343 Chirality : 0.046 0.528 1804 Planarity : 0.005 0.078 2118 Dihedral : 8.245 133.445 1914 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.57 % Favored : 96.36 % Rotamer: Outliers : 4.01 % Allowed : 28.63 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.21), residues: 1458 helix: 2.72 (0.27), residues: 381 sheet: 0.24 (0.30), residues: 303 loop : -1.36 (0.19), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 453 TYR 0.015 0.002 TYR A 12 PHE 0.020 0.002 PHE B 440 TRP 0.013 0.002 TRP C 81 HIS 0.010 0.002 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00429 (12139) covalent geometry : angle 0.64784 (16429) SS BOND : bond 0.00685 ( 18) SS BOND : angle 2.54206 ( 36) hydrogen bonds : bond 0.06407 ( 485) hydrogen bonds : angle 4.78152 ( 1428) link_BETA2-3 : bond 0.00495 ( 2) link_BETA2-3 : angle 2.91987 ( 6) link_NAG-ASN : bond 0.00463 ( 9) link_NAG-ASN : angle 3.20761 ( 27) *********************** 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 368 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 316 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8037 (mp) REVERT: B 206 THR cc_start: 0.8602 (p) cc_final: 0.8377 (p) REVERT: B 272 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: C 415 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7134 (mp0) outliers start: 52 outliers final: 37 residues processed: 341 average time/residue: 0.6920 time to fit residues: 253.3523 Evaluate side-chains 350 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 310 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 410 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 15 ASN 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 116 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 394 GLU Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 chunk 102 optimal weight: 0.0170 chunk 101 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 455 GLN A 472 HIS ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN B 244 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 HIS B 480 ASN C 13 HIS C 33 HIS ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.123942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.112420 restraints weight = 15775.065| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.60 r_work: 0.3512 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.8212 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= 0.137 Angle : 0.623 11.793 16498 Z= 0.320 Chirality : 0.044 0.494 1804 Planarity : 0.004 0.079 2118 Dihedral : 8.071 133.366 1914 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.98 % Rotamer: Outliers : 3.55 % Allowed : 29.48 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.22), residues: 1458 helix: 2.47 (0.27), residues: 399 sheet: 0.29 (0.31), residues: 303 loop : -1.31 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 453 TYR 0.014 0.001 TYR A 12 PHE 0.018 0.001 PHE A 116 TRP 0.009 0.001 TRP B 65 HIS 0.016 0.002 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00313 (12139) covalent geometry : angle 0.60238 (16429) SS BOND : bond 0.00592 ( 18) SS BOND : angle 2.25069 ( 36) hydrogen bonds : bond 0.05864 ( 485) hydrogen bonds : angle 4.68967 ( 1428) link_BETA2-3 : bond 0.00423 ( 2) link_BETA2-3 : angle 2.13811 ( 6) link_NAG-ASN : bond 0.00445 ( 9) link_NAG-ASN : angle 2.93951 ( 27) *********************** 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 354 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 308 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 272 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: C 76 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8244 (mp) REVERT: C 192 ARG cc_start: 0.8498 (mtm-85) cc_final: 0.8200 (mtt-85) REVERT: C 272 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: C 415 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7118 (mp0) outliers start: 46 outliers final: 32 residues processed: 331 average time/residue: 0.7018 time to fit residues: 249.1986 Evaluate side-chains 335 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 299 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 111 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 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 116 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 265 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 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 145 optimal weight: 0.0980 chunk 100 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 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 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.123585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.111979 restraints weight = 15881.897| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.62 r_work: 0.3505 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.8283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12168 Z= 0.150 Angle : 0.639 11.447 16498 Z= 0.327 Chirality : 0.044 0.455 1804 Planarity : 0.004 0.079 2118 Dihedral : 7.993 133.263 1914 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.22 % Favored : 96.71 % Rotamer: Outliers : 3.01 % Allowed : 30.79 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.22), residues: 1458 helix: 2.33 (0.27), residues: 399 sheet: 0.31 (0.31), residues: 303 loop : -1.30 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 453 TYR 0.014 0.001 TYR A 12 PHE 0.018 0.001 PHE B 440 TRP 0.011 0.001 TRP C 81 HIS 0.012 0.002 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00351 (12139) covalent geometry : angle 0.61979 (16429) SS BOND : bond 0.00604 ( 18) SS BOND : angle 2.25036 ( 36) hydrogen bonds : bond 0.05995 ( 485) hydrogen bonds : angle 4.72861 ( 1428) link_BETA2-3 : bond 0.00431 ( 2) link_BETA2-3 : angle 2.27099 ( 6) link_NAG-ASN : bond 0.00444 ( 9) link_NAG-ASN : angle 2.81320 ( 27) ********************** 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 349 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 310 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 272 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: C 192 ARG cc_start: 0.8506 (mtm-85) cc_final: 0.8204 (mtt-85) REVERT: C 415 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7103 (mp0) outliers start: 39 outliers final: 29 residues processed: 332 average time/residue: 0.7273 time to fit residues: 258.3385 Evaluate side-chains 329 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 298 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 111 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 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 116 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 356 HIS Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain C residue 26 GLU 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 278 CYS 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 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 5 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 136 optimal weight: 0.0060 chunk 79 optimal weight: 0.0870 chunk 32 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 112 optimal weight: 0.5980 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 455 GLN A 472 HIS B 13 HIS B 33 HIS ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN C 13 HIS ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.124472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.113071 restraints weight = 15878.941| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.59 r_work: 0.3523 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.8322 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= 0.125 Angle : 0.609 11.213 16498 Z= 0.313 Chirality : 0.043 0.443 1804 Planarity : 0.005 0.077 2118 Dihedral : 7.885 132.827 1914 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.61 % Favored : 97.26 % Rotamer: Outliers : 2.93 % Allowed : 31.17 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.22), residues: 1458 helix: 2.43 (0.27), residues: 399 sheet: 0.37 (0.31), residues: 303 loop : -1.29 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 74 TYR 0.014 0.001 TYR A 12 PHE 0.014 0.001 PHE B 440 TRP 0.008 0.001 TRP C 422 HIS 0.012 0.002 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00276 (12139) covalent geometry : angle 0.59081 (16429) SS BOND : bond 0.00575 ( 18) SS BOND : angle 2.06577 ( 36) hydrogen bonds : bond 0.05643 ( 485) hydrogen bonds : angle 4.65189 ( 1428) link_BETA2-3 : bond 0.00435 ( 2) link_BETA2-3 : angle 1.87358 ( 6) link_NAG-ASN : bond 0.00440 ( 9) link_NAG-ASN : angle 2.74523 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6244.25 seconds wall clock time: 106 minutes 52.11 seconds (6412.11 seconds total)