Starting phenix.real_space_refine on Wed Sep 17 22:24:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xr7_38597/09_2025/8xr7_38597.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xr7_38597/09_2025/8xr7_38597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xr7_38597/09_2025/8xr7_38597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xr7_38597/09_2025/8xr7_38597.map" model { file = "/net/cci-nas-00/data/ceres_data/8xr7_38597/09_2025/8xr7_38597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xr7_38597/09_2025/8xr7_38597.cif" } resolution = 2.62 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= 0.026 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 75 5.16 5 C 7426 2.51 5 N 2006 2.21 5 O 2305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 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: 11812 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3886 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 20, 'TRANS': 467} Chain breaks: 1 Chain: "B" Number of atoms: 3886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3886 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 20, 'TRANS': 467} Chain breaks: 1 Chain: "C" Number of atoms: 3886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3886 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 20, 'TRANS': 467} Chain breaks: 1 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" 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: "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 Time building chain proxies: 2.94, per 1000 atoms: 0.25 Number of scatterers: 11812 At special positions: 0 Unit cell: (87.55, 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 75 16.00 O 2305 8.00 N 2006 7.00 C 7426 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=2.03 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 278 " distance=2.03 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=2.03 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=2.02 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 NAG-ASN " NAG A 601 " - " ASN A 16 " " NAG A 602 " - " ASN A 28 " " NAG A 603 " - " ASN A 169 " " NAG A 604 " - " ASN A 290 " " NAG A 605 " - " ASN A 484 " " NAG B 601 " - " ASN B 16 " " NAG B 602 " - " ASN B 28 " " NAG B 603 " - " ASN B 169 " " NAG C 701 " - " ASN C 28 " " NAG C 702 " - " ASN C 169 " " NAG C 703 " - " ASN C 290 " Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 554.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 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: 28 helices and 32 sheets defined 27.9% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.928A pdb=" N LEU A 75 " --> pdb=" O CYS A 72 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 76 " --> pdb=" O ASP A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 76' Processing helix chain 'A' and resid 102 through 110 Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.880A 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 387 Processing helix chain 'A' and resid 404 through 457 Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 492 through 502 Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 69 through 73 removed outlier: 4.070A pdb=" N ASP B 73 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 110 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.544A pdb=" N TRP B 127 " --> pdb=" O LYS B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 367 through 387 Processing helix chain 'B' and resid 404 through 457 removed outlier: 3.590A pdb=" N GLU B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 3.777A 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 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 492 through 502 Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 72 through 76 removed outlier: 3.800A pdb=" N LEU C 75 " --> pdb=" O CYS C 72 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU C 76 " --> pdb=" O ASP C 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 76' Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.843A 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 368 through 389 removed outlier: 4.296A pdb=" N MET C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 457 removed outlier: 3.631A pdb=" N ASP C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 485 removed outlier: 3.704A pdb=" N ASN C 484 " --> pdb=" O ASP C 480 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 502 removed outlier: 3.683A pdb=" N TYR C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU C 494 " --> pdb=" O PRO C 490 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLU C 495 " --> pdb=" O LYS C 491 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU C 502 " --> pdb=" O LEU C 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 362 through 364 Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 21 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 48 through 49 removed outlier: 6.613A pdb=" N LYS A 48 " --> pdb=" O THR A 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 55 through 56 removed outlier: 6.525A pdb=" N LEU A 55 " --> pdb=" O MET A 85 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 84 " --> pdb=" O MET A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.398A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N HIS A 115 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG A 263 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A 113 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 98 through 100 removed outlier: 7.809A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.721A pdb=" N ALA A 138 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 9.891A pdb=" N LYS A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 289 removed outlier: 4.164A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 363 through 364 Processing sheet with id=AB4, first strand: chain 'B' and resid 19 through 22 removed outlier: 4.314A pdb=" N GLU B 19 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 34 through 36 Processing sheet with id=AB6, first strand: chain 'B' and resid 46 through 49 removed outlier: 6.126A pdb=" N LEU B 46 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N CYS B 278 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 55 through 56 removed outlier: 6.627A pdb=" N LEU B 55 " --> pdb=" O MET B 85 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE B 84 " --> pdb=" O MET B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.496A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N HIS B 115 " --> pdb=" O SER B 261 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG B 263 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL B 113 " --> pdb=" O ARG B 263 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 98 through 100 removed outlier: 7.866A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.481A pdb=" N ALA B 138 " --> pdb=" O LYS B 144 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N LYS B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AC3, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AC4, first strand: chain 'C' and resid 362 through 364 removed outlier: 3.575A pdb=" N GLN C 7 " --> pdb=" O SER C 357 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 20 through 21 Processing sheet with id=AC6, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AC7, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AC8, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.134A pdb=" N LEU C 46 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N CYS C 278 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 55 through 56 removed outlier: 6.508A pdb=" N LEU C 55 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE C 84 " --> pdb=" O MET C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 98 through 100 removed outlier: 6.598A pdb=" N SER C 99 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N TRP C 234 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N HIS C 115 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG C 263 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 113 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 98 through 100 removed outlier: 6.598A pdb=" N SER C 99 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N TRP C 234 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.629A pdb=" N ALA C 138 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N LYS C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD5, first strand: chain 'C' and resid 288 through 289 removed outlier: 4.233A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) 497 hydrogen bonds defined for protein. 1392 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: 2.10 Time building geometry restraints manager: 1.07 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: 3865 1.35 - 1.47: 2906 1.47 - 1.59: 5194 1.59 - 1.71: 0 1.71 - 1.83: 114 Bond restraints: 12079 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" C1 NAG C 702 " pdb=" O5 NAG C 702 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" C1 NAG C 703 " pdb=" O5 NAG C 703 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.84e+00 bond pdb=" C1 NAG C 701 " pdb=" O5 NAG C 701 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.72e+00 bond pdb=" C1 NAG A 604 " pdb=" O5 NAG A 604 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.70e+00 ... (remaining 12074 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 16161 2.47 - 4.94: 160 4.94 - 7.41: 11 7.41 - 9.88: 1 9.88 - 12.35: 1 Bond angle restraints: 16334 Sorted by residual: angle pdb=" CA LEU A 419 " pdb=" CB LEU A 419 " pdb=" CG LEU A 419 " ideal model delta sigma weight residual 116.30 128.65 -12.35 3.50e+00 8.16e-02 1.24e+01 angle pdb=" CA GLU C 495 " pdb=" CB GLU C 495 " pdb=" CG GLU C 495 " ideal model delta sigma weight residual 114.10 120.70 -6.60 2.00e+00 2.50e-01 1.09e+01 angle pdb=" CA GLU B 469 " pdb=" CB GLU B 469 " pdb=" CG GLU B 469 " ideal model delta sigma weight residual 114.10 120.10 -6.00 2.00e+00 2.50e-01 9.00e+00 angle pdb=" N CYS A 139 " pdb=" CA CYS A 139 " pdb=" C CYS A 139 " ideal model delta sigma weight residual 109.71 105.59 4.12 1.41e+00 5.03e-01 8.56e+00 angle pdb=" CB GLU B 469 " pdb=" CG GLU B 469 " pdb=" CD GLU B 469 " ideal model delta sigma weight residual 112.60 117.39 -4.79 1.70e+00 3.46e-01 7.93e+00 ... (remaining 16329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6097 17.94 - 35.89: 886 35.89 - 53.83: 341 53.83 - 71.78: 70 71.78 - 89.72: 16 Dihedral angle restraints: 7410 sinusoidal: 3195 harmonic: 4215 Sorted by residual: 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 -86.00 -165.24 79.24 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CA CYS A 139 " pdb=" C CYS A 139 " pdb=" N ALA A 140 " pdb=" CA ALA A 140 " ideal model delta harmonic sigma weight residual -180.00 -161.06 -18.94 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA CYS A 72 " pdb=" C CYS A 72 " pdb=" N ASP A 73 " pdb=" CA ASP A 73 " ideal model delta harmonic sigma weight residual -180.00 -161.53 -18.47 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 7407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1168 0.038 - 0.075: 432 0.075 - 0.113: 141 0.113 - 0.151: 29 0.151 - 0.189: 1 Chirality restraints: 1771 Sorted by residual: chirality pdb=" CA CYS A 139 " pdb=" N CYS A 139 " pdb=" C CYS A 139 " pdb=" CB CYS A 139 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CG LEU A 419 " pdb=" CB LEU A 419 " pdb=" CD1 LEU A 419 " pdb=" CD2 LEU A 419 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CG LEU A 429 " pdb=" CB LEU A 429 " pdb=" CD1 LEU A 429 " pdb=" CD2 LEU A 429 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.11e-01 ... (remaining 1768 not shown) Planarity restraints: 2116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 158 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO B 159 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 159 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 159 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 489 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO A 490 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 490 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 490 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 469 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.18e+00 pdb=" CD GLU B 469 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU B 469 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU B 469 " -0.012 2.00e-02 2.50e+03 ... (remaining 2113 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1880 2.76 - 3.30: 10047 3.30 - 3.83: 19068 3.83 - 4.37: 22191 4.37 - 4.90: 39828 Nonbonded interactions: 93014 Sorted by model distance: nonbonded pdb=" OG SER A 207 " pdb=" OD1 ASP A 241 " model vdw 2.229 3.040 nonbonded pdb=" O TYR C 195 " pdb=" NZ LYS C 197 " model vdw 2.254 3.120 nonbonded pdb=" OD1 ASN B 380 " pdb=" NH2 ARG C 27 " model vdw 2.281 3.120 nonbonded pdb=" O SER C 142 " pdb=" OG SER C 142 " model vdw 2.283 3.040 nonbonded pdb=" N GLU C 495 " pdb=" OE1 GLU C 495 " model vdw 2.289 3.120 ... (remaining 93009 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' and resid 6 through 603) selection = chain 'B' selection = chain 'C' } 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: 2.940 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.120 Find NCS groups from input model: 0.230 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: 0.000 Load rotamer database and sin/cos tables:7.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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 : 0.005 0.041 12108 Z= 0.199 Angle : 0.612 12.346 16403 Z= 0.320 Chirality : 0.044 0.189 1771 Planarity : 0.005 0.064 2105 Dihedral : 19.422 89.721 4662 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.66 % Allowed : 32.56 % Favored : 62.78 % 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: 1452 helix: 2.10 (0.27), residues: 375 sheet: 0.36 (0.30), residues: 315 loop : -1.91 (0.19), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 91 TYR 0.022 0.002 TYR B 424 PHE 0.022 0.002 PHE C 440 TRP 0.009 0.001 TRP B 422 HIS 0.011 0.001 HIS A 356 Details of bonding type rmsd covalent geometry : bond 0.00453 (12079) covalent geometry : angle 0.60663 (16334) SS BOND : bond 0.00511 ( 18) SS BOND : angle 1.57862 ( 36) hydrogen bonds : bond 0.18005 ( 463) hydrogen bonds : angle 6.80408 ( 1392) link_NAG-ASN : bond 0.00169 ( 11) link_NAG-ASN : angle 1.25542 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 377 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 431 LEU cc_start: 0.8608 (mp) cc_final: 0.8387 (mt) outliers start: 60 outliers final: 57 residues processed: 420 average time/residue: 0.6303 time to fit residues: 283.4854 Evaluate side-chains 428 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 371 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 493 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 50 ASN A 283 GLN B 175 GLN B 186 ASN B 355 HIS B 356 HIS C 165 GLN C 191 GLN C 196 GLN C 224 ASN C 296 HIS C 358 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.121616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.109787 restraints weight = 15947.880| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.96 r_work: 0.3349 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12108 Z= 0.151 Angle : 0.537 8.053 16403 Z= 0.289 Chirality : 0.043 0.141 1771 Planarity : 0.004 0.046 2105 Dihedral : 9.010 80.041 1903 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.75 % Allowed : 28.98 % Favored : 65.27 % 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: -0.23 (0.21), residues: 1452 helix: 2.23 (0.27), residues: 381 sheet: 0.82 (0.31), residues: 279 loop : -1.86 (0.19), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 91 TYR 0.013 0.001 TYR C 92 PHE 0.019 0.001 PHE C 440 TRP 0.008 0.001 TRP A 81 HIS 0.011 0.001 HIS A 356 Details of bonding type rmsd covalent geometry : bond 0.00350 (12079) covalent geometry : angle 0.53206 (16334) SS BOND : bond 0.00386 ( 18) SS BOND : angle 1.18381 ( 36) hydrogen bonds : bond 0.05357 ( 463) hydrogen bonds : angle 5.03815 ( 1392) link_NAG-ASN : bond 0.00286 ( 11) link_NAG-ASN : angle 1.29699 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 403 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7546 (ttm110) REVERT: A 190 GLU cc_start: 0.8231 (pt0) cc_final: 0.7971 (pt0) REVERT: A 212 ARG cc_start: 0.8619 (ttt-90) cc_final: 0.8403 (ttm-80) REVERT: A 404 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8017 (mt-10) REVERT: B 111 SER cc_start: 0.8701 (OUTLIER) cc_final: 0.8396 (t) REVERT: B 117 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7237 (tm-30) REVERT: B 272 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: B 276 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7573 (mt-10) REVERT: B 491 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8294 (pptt) REVERT: C 47 CYS cc_start: 0.7016 (m) cc_final: 0.6730 (m) outliers start: 74 outliers final: 39 residues processed: 437 average time/residue: 0.6381 time to fit residues: 297.6548 Evaluate side-chains 412 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 368 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 33 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 77 optimal weight: 0.0970 chunk 135 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN B 175 GLN B 186 ASN B 191 GLN B 356 HIS C 165 GLN C 191 GLN C 196 GLN C 224 ASN ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.121295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.109649 restraints weight = 16163.139| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.96 r_work: 0.3341 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12108 Z= 0.164 Angle : 0.532 6.359 16403 Z= 0.286 Chirality : 0.042 0.139 1771 Planarity : 0.004 0.045 2105 Dihedral : 6.639 58.205 1832 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.75 % Allowed : 28.67 % Favored : 65.58 % 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: 1452 helix: 2.30 (0.27), residues: 381 sheet: 0.90 (0.31), residues: 279 loop : -1.86 (0.19), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 91 TYR 0.016 0.001 TYR B 424 PHE 0.021 0.002 PHE C 440 TRP 0.010 0.001 TRP A 81 HIS 0.013 0.001 HIS A 356 Details of bonding type rmsd covalent geometry : bond 0.00386 (12079) covalent geometry : angle 0.52606 (16334) SS BOND : bond 0.00390 ( 18) SS BOND : angle 1.26844 ( 36) hydrogen bonds : bond 0.05317 ( 463) hydrogen bonds : angle 4.79601 ( 1392) link_NAG-ASN : bond 0.00208 ( 11) link_NAG-ASN : angle 1.42880 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 378 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7558 (ttm110) REVERT: A 428 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8097 (tp) REVERT: B 111 SER cc_start: 0.8694 (OUTLIER) cc_final: 0.8393 (t) REVERT: B 272 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: B 276 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7574 (mt-10) REVERT: B 491 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8175 (pptt) REVERT: C 91 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7764 (ttp80) REVERT: C 367 ASP cc_start: 0.8256 (t0) cc_final: 0.8043 (t70) REVERT: C 488 ASP cc_start: 0.6534 (OUTLIER) cc_final: 0.6235 (t0) outliers start: 74 outliers final: 42 residues processed: 412 average time/residue: 0.6227 time to fit residues: 274.7318 Evaluate side-chains 415 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 366 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 393 PHE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 493 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 114 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 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 165 GLN A 326 GLN B 175 GLN B 191 GLN B 356 HIS C 165 GLN C 191 GLN C 224 ASN ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.121812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.110254 restraints weight = 16132.779| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.92 r_work: 0.3347 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12108 Z= 0.145 Angle : 0.523 5.802 16403 Z= 0.280 Chirality : 0.042 0.141 1771 Planarity : 0.004 0.043 2105 Dihedral : 6.017 57.420 1823 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.36 % Allowed : 29.91 % Favored : 64.72 % 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: -0.09 (0.21), residues: 1452 helix: 2.39 (0.27), residues: 381 sheet: 0.98 (0.31), residues: 279 loop : -1.83 (0.19), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 91 TYR 0.017 0.001 TYR B 424 PHE 0.019 0.001 PHE C 440 TRP 0.009 0.001 TRP A 81 HIS 0.013 0.001 HIS A 356 Details of bonding type rmsd covalent geometry : bond 0.00340 (12079) covalent geometry : angle 0.51555 (16334) SS BOND : bond 0.00347 ( 18) SS BOND : angle 1.54190 ( 36) hydrogen bonds : bond 0.05021 ( 463) hydrogen bonds : angle 4.69117 ( 1392) link_NAG-ASN : bond 0.00208 ( 11) link_NAG-ASN : angle 1.42856 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 374 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8288 (mptp) cc_final: 0.8051 (mptp) REVERT: A 27 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7550 (ttm110) REVERT: A 428 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8090 (tp) REVERT: A 458 ASP cc_start: 0.7953 (t0) cc_final: 0.7722 (t0) REVERT: B 111 SER cc_start: 0.8713 (OUTLIER) cc_final: 0.8401 (t) REVERT: B 216 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6879 (mt-10) REVERT: B 272 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: B 276 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: B 477 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7860 (tm-30) REVERT: B 491 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8246 (pptt) REVERT: C 91 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7732 (ttp80) REVERT: C 197 LYS cc_start: 0.8573 (mtmm) cc_final: 0.8301 (mtmm) REVERT: C 367 ASP cc_start: 0.8227 (t0) cc_final: 0.8017 (t70) REVERT: C 479 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7872 (mtt) outliers start: 69 outliers final: 42 residues processed: 404 average time/residue: 0.6346 time to fit residues: 274.4407 Evaluate side-chains 405 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 356 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 493 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 76 optimal weight: 0.3980 chunk 92 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 93 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 53 optimal weight: 0.0670 chunk 129 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN B 175 GLN B 191 GLN B 356 HIS C 165 GLN C 191 GLN C 196 GLN C 224 ASN C 244 ASN ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.123030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.111320 restraints weight = 16187.091| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.96 r_work: 0.3372 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12108 Z= 0.103 Angle : 0.490 5.913 16403 Z= 0.262 Chirality : 0.041 0.143 1771 Planarity : 0.004 0.042 2105 Dihedral : 5.624 56.135 1821 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.21 % Allowed : 30.69 % Favored : 64.10 % 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: 0.03 (0.22), residues: 1452 helix: 2.56 (0.27), residues: 381 sheet: 0.76 (0.31), residues: 291 loop : -1.70 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 74 TYR 0.017 0.001 TYR B 424 PHE 0.017 0.001 PHE B 295 TRP 0.009 0.001 TRP B 422 HIS 0.011 0.001 HIS A 356 Details of bonding type rmsd covalent geometry : bond 0.00233 (12079) covalent geometry : angle 0.48271 (16334) SS BOND : bond 0.00279 ( 18) SS BOND : angle 1.31374 ( 36) hydrogen bonds : bond 0.04551 ( 463) hydrogen bonds : angle 4.53833 ( 1392) link_NAG-ASN : bond 0.00220 ( 11) link_NAG-ASN : angle 1.38529 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 367 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8223 (mptp) cc_final: 0.7997 (mptp) REVERT: A 27 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7561 (ttm110) REVERT: A 458 ASP cc_start: 0.7948 (t0) cc_final: 0.7693 (t0) REVERT: B 74 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8289 (mtm-85) REVERT: B 276 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: B 477 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7903 (tm-30) REVERT: B 491 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8252 (pptt) REVERT: C 47 CYS cc_start: 0.7054 (m) cc_final: 0.6691 (m) REVERT: C 91 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7747 (ttp80) REVERT: C 191 GLN cc_start: 0.8719 (tp40) cc_final: 0.8501 (tp-100) REVERT: C 458 ASP cc_start: 0.7912 (t0) cc_final: 0.7461 (t0) outliers start: 67 outliers final: 39 residues processed: 393 average time/residue: 0.6129 time to fit residues: 257.9404 Evaluate side-chains 394 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 351 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 493 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 83 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 63 optimal weight: 0.0060 chunk 89 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN B 175 GLN B 191 GLN B 283 GLN B 356 HIS C 165 GLN C 196 GLN C 224 ASN ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.122040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.110301 restraints weight = 16151.804| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.95 r_work: 0.3377 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12108 Z= 0.133 Angle : 0.519 7.278 16403 Z= 0.275 Chirality : 0.042 0.162 1771 Planarity : 0.004 0.041 2105 Dihedral : 5.439 54.564 1821 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.13 % Allowed : 31.39 % Favored : 63.48 % 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: 1452 helix: 2.61 (0.27), residues: 381 sheet: 0.62 (0.31), residues: 297 loop : -1.64 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 91 TYR 0.011 0.001 TYR A 354 PHE 0.019 0.001 PHE B 295 TRP 0.008 0.001 TRP A 81 HIS 0.012 0.001 HIS A 356 Details of bonding type rmsd covalent geometry : bond 0.00312 (12079) covalent geometry : angle 0.51177 (16334) SS BOND : bond 0.00377 ( 18) SS BOND : angle 1.46555 ( 36) hydrogen bonds : bond 0.04732 ( 463) hydrogen bonds : angle 4.49672 ( 1392) link_NAG-ASN : bond 0.00206 ( 11) link_NAG-ASN : angle 1.32944 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 360 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8274 (mptp) cc_final: 0.8033 (mptp) REVERT: A 27 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7581 (ttm110) REVERT: A 394 GLU cc_start: -0.0110 (OUTLIER) cc_final: -0.0369 (pp20) REVERT: A 428 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8108 (tp) REVERT: A 458 ASP cc_start: 0.8019 (t0) cc_final: 0.7689 (t0) REVERT: B 74 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8297 (mtm-85) REVERT: B 111 SER cc_start: 0.8687 (OUTLIER) cc_final: 0.8381 (t) REVERT: B 276 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: B 477 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7933 (tm-30) REVERT: B 491 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8269 (pptt) REVERT: C 91 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7781 (ttp80) REVERT: C 92 TYR cc_start: 0.7592 (m-80) cc_final: 0.6477 (m-80) REVERT: C 278 CYS cc_start: 0.6163 (p) cc_final: 0.5849 (p) REVERT: C 458 ASP cc_start: 0.7920 (t0) cc_final: 0.7494 (t0) outliers start: 66 outliers final: 42 residues processed: 390 average time/residue: 0.5945 time to fit residues: 248.6036 Evaluate side-chains 401 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 352 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 493 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 140 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 101 optimal weight: 0.2980 chunk 112 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 326 GLN B 175 GLN B 191 GLN B 283 GLN B 356 HIS C 165 GLN C 191 GLN C 196 GLN C 224 ASN ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.122096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.110353 restraints weight = 16107.276| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.95 r_work: 0.3377 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12108 Z= 0.128 Angle : 0.525 11.554 16403 Z= 0.277 Chirality : 0.042 0.161 1771 Planarity : 0.004 0.040 2105 Dihedral : 5.271 54.824 1821 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.13 % Allowed : 31.31 % Favored : 63.56 % 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: 0.07 (0.22), residues: 1452 helix: 2.60 (0.27), residues: 381 sheet: 0.63 (0.31), residues: 297 loop : -1.62 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 91 TYR 0.010 0.001 TYR A 12 PHE 0.020 0.001 PHE B 295 TRP 0.008 0.001 TRP A 81 HIS 0.012 0.001 HIS A 356 Details of bonding type rmsd covalent geometry : bond 0.00301 (12079) covalent geometry : angle 0.51759 (16334) SS BOND : bond 0.00391 ( 18) SS BOND : angle 1.47093 ( 36) hydrogen bonds : bond 0.04685 ( 463) hydrogen bonds : angle 4.47232 ( 1392) link_NAG-ASN : bond 0.00217 ( 11) link_NAG-ASN : angle 1.37264 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 361 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8261 (mptp) cc_final: 0.8055 (mptp) REVERT: A 27 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7575 (ttm110) REVERT: A 39 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: A 394 GLU cc_start: -0.0089 (OUTLIER) cc_final: -0.0346 (pp20) REVERT: A 428 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8114 (tp) REVERT: A 458 ASP cc_start: 0.8047 (t0) cc_final: 0.7654 (t0) REVERT: B 27 ARG cc_start: 0.8076 (mmt-90) cc_final: 0.7753 (mmt90) REVERT: B 74 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8321 (mtm-85) REVERT: B 111 SER cc_start: 0.8667 (OUTLIER) cc_final: 0.8367 (t) REVERT: B 276 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7469 (mt-10) REVERT: B 477 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7912 (tm-30) REVERT: B 491 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8251 (pptt) REVERT: C 91 ARG cc_start: 0.7988 (ttp80) cc_final: 0.7765 (ttp80) REVERT: C 458 ASP cc_start: 0.7879 (t0) cc_final: 0.7462 (t0) outliers start: 66 outliers final: 40 residues processed: 387 average time/residue: 0.6129 time to fit residues: 254.5905 Evaluate side-chains 396 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 348 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 493 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 0.0060 chunk 112 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN B 175 GLN B 191 GLN B 283 GLN B 356 HIS C 165 GLN C 191 GLN C 196 GLN C 224 ASN ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.122226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.110472 restraints weight = 16080.751| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.95 r_work: 0.3364 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12108 Z= 0.133 Angle : 0.561 13.930 16403 Z= 0.293 Chirality : 0.043 0.301 1771 Planarity : 0.004 0.061 2105 Dihedral : 5.173 56.098 1817 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.90 % Allowed : 32.63 % Favored : 62.47 % 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: 0.08 (0.22), residues: 1452 helix: 2.58 (0.27), residues: 381 sheet: 0.65 (0.31), residues: 297 loop : -1.60 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 91 TYR 0.012 0.001 TYR B 354 PHE 0.022 0.001 PHE B 295 TRP 0.008 0.001 TRP A 81 HIS 0.011 0.001 HIS A 356 Details of bonding type rmsd covalent geometry : bond 0.00314 (12079) covalent geometry : angle 0.54925 (16334) SS BOND : bond 0.00376 ( 18) SS BOND : angle 2.09010 ( 36) hydrogen bonds : bond 0.04682 ( 463) hydrogen bonds : angle 4.48362 ( 1392) link_NAG-ASN : bond 0.00305 ( 11) link_NAG-ASN : angle 1.50771 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 361 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7581 (ttm110) REVERT: A 39 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7204 (tt0) REVERT: A 394 GLU cc_start: -0.0052 (OUTLIER) cc_final: -0.0313 (pp20) REVERT: A 428 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8109 (tp) REVERT: A 458 ASP cc_start: 0.8112 (t0) cc_final: 0.7708 (t0) REVERT: B 27 ARG cc_start: 0.8045 (mmt-90) cc_final: 0.7741 (mmt90) REVERT: B 74 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8326 (mtm-85) REVERT: B 92 TYR cc_start: 0.6707 (m-10) cc_final: 0.6455 (m-10) REVERT: B 111 SER cc_start: 0.8666 (OUTLIER) cc_final: 0.8370 (t) REVERT: B 276 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: B 477 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7926 (tm-30) REVERT: B 491 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8245 (pptt) REVERT: C 458 ASP cc_start: 0.7938 (t0) cc_final: 0.7522 (t0) outliers start: 63 outliers final: 45 residues processed: 387 average time/residue: 0.6046 time to fit residues: 251.4181 Evaluate side-chains 413 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 360 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 493 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 111 optimal weight: 0.4980 chunk 114 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN B 175 GLN B 191 GLN B 356 HIS B 360 GLN C 165 GLN C 191 GLN C 196 GLN C 224 ASN ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.122309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.110497 restraints weight = 15966.410| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.95 r_work: 0.3380 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12108 Z= 0.132 Angle : 0.573 16.928 16403 Z= 0.297 Chirality : 0.043 0.299 1771 Planarity : 0.004 0.042 2105 Dihedral : 5.072 57.020 1817 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.35 % Allowed : 33.10 % Favored : 62.55 % 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: 0.10 (0.22), residues: 1452 helix: 2.57 (0.27), residues: 381 sheet: 0.68 (0.31), residues: 297 loop : -1.60 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 453 TYR 0.017 0.001 TYR C 92 PHE 0.022 0.001 PHE B 295 TRP 0.008 0.001 TRP A 81 HIS 0.011 0.001 HIS A 356 Details of bonding type rmsd covalent geometry : bond 0.00311 (12079) covalent geometry : angle 0.56164 (16334) SS BOND : bond 0.00381 ( 18) SS BOND : angle 2.14416 ( 36) hydrogen bonds : bond 0.04657 ( 463) hydrogen bonds : angle 4.48174 ( 1392) link_NAG-ASN : bond 0.00303 ( 11) link_NAG-ASN : angle 1.44419 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 364 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7268 (mpt90) REVERT: A 39 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7237 (tt0) REVERT: A 394 GLU cc_start: -0.0053 (OUTLIER) cc_final: -0.0315 (pp20) REVERT: A 428 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8116 (tp) REVERT: A 458 ASP cc_start: 0.8095 (t0) cc_final: 0.7699 (t0) REVERT: B 27 ARG cc_start: 0.8053 (mmt-90) cc_final: 0.7733 (mmt90) REVERT: B 74 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8312 (mtm-85) REVERT: B 92 TYR cc_start: 0.6622 (m-10) cc_final: 0.6213 (m-10) REVERT: B 111 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8376 (t) REVERT: B 276 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: B 477 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7957 (tm-30) REVERT: B 491 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8234 (pptt) REVERT: C 41 THR cc_start: 0.8820 (p) cc_final: 0.8615 (t) REVERT: C 144 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7585 (mppt) REVERT: C 458 ASP cc_start: 0.7861 (t0) cc_final: 0.7469 (t0) outliers start: 56 outliers final: 47 residues processed: 384 average time/residue: 0.5939 time to fit residues: 245.0962 Evaluate side-chains 413 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 357 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 493 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 82 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 196 GLN B 175 GLN B 191 GLN B 356 HIS C 165 GLN C 191 GLN C 196 GLN C 224 ASN ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.120765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.108986 restraints weight = 16272.778| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.96 r_work: 0.3346 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12108 Z= 0.202 Angle : 0.611 11.336 16403 Z= 0.320 Chirality : 0.045 0.271 1771 Planarity : 0.004 0.049 2105 Dihedral : 5.118 58.999 1817 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.27 % Allowed : 33.33 % Favored : 62.39 % 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: -0.03 (0.22), residues: 1452 helix: 2.36 (0.27), residues: 381 sheet: 0.90 (0.31), residues: 285 loop : -1.72 (0.19), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 91 TYR 0.015 0.002 TYR A 12 PHE 0.024 0.002 PHE B 295 TRP 0.010 0.001 TRP A 65 HIS 0.012 0.001 HIS A 356 Details of bonding type rmsd covalent geometry : bond 0.00485 (12079) covalent geometry : angle 0.59738 (16334) SS BOND : bond 0.00498 ( 18) SS BOND : angle 2.37140 ( 36) hydrogen bonds : bond 0.05199 ( 463) hydrogen bonds : angle 4.60239 ( 1392) link_NAG-ASN : bond 0.00276 ( 11) link_NAG-ASN : angle 1.60865 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 359 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7953 (mpt90) cc_final: 0.7325 (mpt90) REVERT: A 39 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7227 (tt0) REVERT: A 394 GLU cc_start: -0.0047 (OUTLIER) cc_final: -0.0311 (pp20) REVERT: A 428 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8135 (tp) REVERT: A 458 ASP cc_start: 0.8164 (t0) cc_final: 0.7804 (t0) REVERT: B 27 ARG cc_start: 0.8043 (mmt-90) cc_final: 0.7738 (mmt90) REVERT: B 74 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8341 (mtm-85) REVERT: B 92 TYR cc_start: 0.6652 (m-10) cc_final: 0.6380 (m-80) REVERT: B 276 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: B 477 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7947 (tm-30) REVERT: B 491 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8175 (pptt) REVERT: C 144 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7693 (mppt) REVERT: C 458 ASP cc_start: 0.7982 (t0) cc_final: 0.7548 (t0) outliers start: 55 outliers final: 40 residues processed: 382 average time/residue: 0.5890 time to fit residues: 241.4470 Evaluate side-chains 403 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 356 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 86 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN B 175 GLN B 191 GLN B 356 HIS B 360 GLN C 165 GLN C 191 GLN C 196 GLN C 224 ASN ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.121116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.109249 restraints weight = 16173.002| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.97 r_work: 0.3351 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12108 Z= 0.166 Angle : 0.604 15.198 16403 Z= 0.313 Chirality : 0.044 0.301 1771 Planarity : 0.004 0.042 2105 Dihedral : 5.046 57.734 1817 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.96 % Allowed : 33.88 % Favored : 62.16 % 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: -0.07 (0.22), residues: 1452 helix: 2.32 (0.27), residues: 381 sheet: 0.66 (0.31), residues: 297 loop : -1.67 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 453 TYR 0.017 0.002 TYR C 161 PHE 0.026 0.002 PHE B 295 TRP 0.009 0.001 TRP A 81 HIS 0.012 0.001 HIS A 356 Details of bonding type rmsd covalent geometry : bond 0.00397 (12079) covalent geometry : angle 0.59239 (16334) SS BOND : bond 0.00506 ( 18) SS BOND : angle 2.25216 ( 36) hydrogen bonds : bond 0.05015 ( 463) hydrogen bonds : angle 4.58234 ( 1392) link_NAG-ASN : bond 0.00285 ( 11) link_NAG-ASN : angle 1.53341 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5479.70 seconds wall clock time: 93 minutes 48.80 seconds (5628.80 seconds total)