Starting phenix.real_space_refine on Mon Oct 14 12:36:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qoe_18535/10_2024/8qoe_18535_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qoe_18535/10_2024/8qoe_18535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qoe_18535/10_2024/8qoe_18535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qoe_18535/10_2024/8qoe_18535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qoe_18535/10_2024/8qoe_18535_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qoe_18535/10_2024/8qoe_18535_neut.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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: 5 Type Number sf(0) Gaussians S 34 5.16 5 C 5612 2.51 5 N 1456 2.21 5 O 1642 1.98 5 H 9072 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 17816 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 8908 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 17, 'TRANS': 550} Restraints were copied for chains: B Time building chain proxies: 23.16, per 1000 atoms: 1.30 Number of scatterers: 17816 At special positions: 0 Unit cell: (110.21, 75.97, 133.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 O 1642 8.00 N 1456 7.00 C 5612 6.00 H 9072 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 4.32 Conformation dependent library (CDL) restraints added in 1.4 seconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 64.4% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'B' and resid 12 through 21 removed outlier: 3.659A pdb=" N PHE B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 17 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 44 removed outlier: 3.501A pdb=" N LEU B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 64 through 109 removed outlier: 3.616A pdb=" N GLY B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 117 removed outlier: 3.806A pdb=" N THR B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 113 through 117' Processing helix chain 'B' and resid 120 through 140 removed outlier: 3.556A pdb=" N ARG B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 162 Processing helix chain 'B' and resid 164 through 210 Proline residue: B 175 - end of helix removed outlier: 3.549A pdb=" N ILE B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Proline residue: B 183 - end of helix removed outlier: 3.578A pdb=" N ILE B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 219 Processing helix chain 'B' and resid 222 through 274 removed outlier: 3.648A pdb=" N GLY B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Proline residue: B 252 - end of helix Processing helix chain 'B' and resid 280 through 295 removed outlier: 3.863A pdb=" N PHE B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 322 removed outlier: 3.616A pdb=" N PHE B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 308 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 388 Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.525A pdb=" N GLU B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'B' and resid 446 through 454 removed outlier: 3.767A pdb=" N LYS B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 481 through 495 removed outlier: 3.587A pdb=" N ILE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 525 Processing helix chain 'B' and resid 537 through 540 Processing helix chain 'B' and resid 560 through 566 Processing helix chain 'B' and resid 572 through 577 Processing helix chain 'A' and resid 12 through 21 removed outlier: 3.658A pdb=" N PHE A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 44 removed outlier: 3.502A pdb=" N LEU A 44 " --> pdb=" O THR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 109 removed outlier: 3.616A pdb=" N GLY A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 removed outlier: 3.806A pdb=" N THR A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 117' Processing helix chain 'A' and resid 120 through 140 removed outlier: 3.555A pdb=" N ARG A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 162 Processing helix chain 'A' and resid 164 through 210 Proline residue: A 175 - end of helix removed outlier: 3.550A pdb=" N ILE A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Proline residue: A 183 - end of helix removed outlier: 3.577A pdb=" N ILE A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 219 Processing helix chain 'A' and resid 222 through 274 removed outlier: 3.648A pdb=" N GLY A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 280 through 295 removed outlier: 3.863A pdb=" N PHE A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 322 removed outlier: 3.616A pdb=" N PHE A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 388 Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.525A pdb=" N GLU A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 446 through 454 removed outlier: 3.767A pdb=" N LYS A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 481 through 495 removed outlier: 3.586A pdb=" N ILE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 525 Processing helix chain 'A' and resid 537 through 540 Processing helix chain 'A' and resid 560 through 566 Processing helix chain 'A' and resid 572 through 577 Processing sheet with id=AA1, first strand: chain 'B' and resid 357 through 364 removed outlier: 6.762A pdb=" N LYS B 358 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N SER B 347 " --> pdb=" O LYS B 358 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL B 360 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR B 397 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 417 through 421 removed outlier: 6.440A pdb=" N GLY B 418 " --> pdb=" O MET B 501 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ASP B 503 " --> pdb=" O GLY B 418 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 420 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU B 500 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE B 533 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU B 502 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 532 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL B 369 " --> pdb=" O GLN B 545 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU B 547 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA B 371 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL B 549 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 373 " --> pdb=" O VAL B 549 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 364 removed outlier: 6.762A pdb=" N LYS A 358 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N SER A 347 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL A 360 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A 397 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 417 through 421 removed outlier: 6.440A pdb=" N GLY A 418 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ASP A 503 " --> pdb=" O GLY A 418 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A 420 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU A 500 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE A 533 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU A 502 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 532 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A 369 " --> pdb=" O GLN A 545 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU A 547 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA A 371 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL A 549 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A 373 " --> pdb=" O VAL A 549 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1506 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: 6.04 Time building geometry restraints manager: 5.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 2980 1.02 - 1.22: 6156 1.22 - 1.42: 3580 1.42 - 1.62: 5168 1.62 - 1.82: 66 Bond restraints: 17950 Sorted by residual: bond pdb=" CZ ARG B 316 " pdb=" NH2 ARG B 316 " ideal model delta sigma weight residual 1.330 1.105 0.225 1.30e-02 5.92e+03 3.01e+02 bond pdb=" CZ ARG A 316 " pdb=" NH2 ARG A 316 " ideal model delta sigma weight residual 1.330 1.105 0.225 1.30e-02 5.92e+03 3.00e+02 bond pdb=" CZ ARG A 126 " pdb=" NH2 ARG A 126 " ideal model delta sigma weight residual 1.330 1.105 0.225 1.30e-02 5.92e+03 2.99e+02 bond pdb=" CZ ARG B 126 " pdb=" NH2 ARG B 126 " ideal model delta sigma weight residual 1.330 1.105 0.225 1.30e-02 5.92e+03 2.99e+02 bond pdb=" CZ ARG A 100 " pdb=" NH2 ARG A 100 " ideal model delta sigma weight residual 1.330 1.108 0.222 1.30e-02 5.92e+03 2.93e+02 ... (remaining 17945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 29624 3.48 - 6.95: 2460 6.95 - 10.43: 422 10.43 - 13.90: 64 13.90 - 17.38: 36 Bond angle restraints: 32606 Sorted by residual: angle pdb=" C GLU B 319 " pdb=" N ILE B 320 " pdb=" CA ILE B 320 " ideal model delta sigma weight residual 120.77 138.03 -17.26 1.31e+00 5.83e-01 1.74e+02 angle pdb=" C GLU A 319 " pdb=" N ILE A 320 " pdb=" CA ILE A 320 " ideal model delta sigma weight residual 120.77 138.00 -17.23 1.31e+00 5.83e-01 1.73e+02 angle pdb=" C ARG B 126 " pdb=" N VAL B 127 " pdb=" CA VAL B 127 " ideal model delta sigma weight residual 120.60 136.83 -16.23 1.29e+00 6.01e-01 1.58e+02 angle pdb=" C ARG A 126 " pdb=" N VAL A 127 " pdb=" CA VAL A 127 " ideal model delta sigma weight residual 120.60 136.82 -16.22 1.29e+00 6.01e-01 1.58e+02 angle pdb=" C SER A 125 " pdb=" N ARG A 126 " pdb=" CA ARG A 126 " ideal model delta sigma weight residual 120.79 137.57 -16.78 1.39e+00 5.18e-01 1.46e+02 ... (remaining 32601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.23: 7683 18.23 - 36.47: 385 36.47 - 54.70: 182 54.70 - 72.94: 72 72.94 - 91.17: 8 Dihedral angle restraints: 8330 sinusoidal: 4650 harmonic: 3680 Sorted by residual: dihedral pdb=" C ILE A 108 " pdb=" N ILE A 108 " pdb=" CA ILE A 108 " pdb=" CB ILE A 108 " ideal model delta harmonic sigma weight residual -122.00 -145.09 23.09 0 2.50e+00 1.60e-01 8.53e+01 dihedral pdb=" C ILE B 108 " pdb=" N ILE B 108 " pdb=" CA ILE B 108 " pdb=" CB ILE B 108 " ideal model delta harmonic sigma weight residual -122.00 -145.06 23.06 0 2.50e+00 1.60e-01 8.51e+01 dihedral pdb=" N PHE A 115 " pdb=" C PHE A 115 " pdb=" CA PHE A 115 " pdb=" CB PHE A 115 " ideal model delta harmonic sigma weight residual 122.80 144.56 -21.76 0 2.50e+00 1.60e-01 7.58e+01 ... (remaining 8327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.209: 1216 0.209 - 0.417: 80 0.417 - 0.626: 120 0.626 - 0.835: 24 0.835 - 1.044: 14 Chirality restraints: 1454 Sorted by residual: chirality pdb=" CA PHE A 115 " pdb=" N PHE A 115 " pdb=" C PHE A 115 " pdb=" CB PHE A 115 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.72e+01 chirality pdb=" CA PHE B 115 " pdb=" N PHE B 115 " pdb=" C PHE B 115 " pdb=" CB PHE B 115 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.72e+01 chirality pdb=" CA TRP A 104 " pdb=" N TRP A 104 " pdb=" C TRP A 104 " pdb=" CB TRP A 104 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.60e+01 ... (remaining 1451 not shown) Planarity restraints: 2610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 456 " -0.141 2.00e-02 2.50e+03 5.56e-02 9.26e+01 pdb=" CG TYR A 456 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 456 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 456 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR A 456 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 456 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 456 " -0.020 2.00e-02 2.50e+03 pdb=" OH TYR A 456 " -0.086 2.00e-02 2.50e+03 pdb=" HD1 TYR A 456 " 0.044 2.00e-02 2.50e+03 pdb=" HD2 TYR A 456 " 0.065 2.00e-02 2.50e+03 pdb=" HE1 TYR A 456 " 0.030 2.00e-02 2.50e+03 pdb=" HE2 TYR A 456 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 456 " 0.140 2.00e-02 2.50e+03 5.55e-02 9.25e+01 pdb=" CG TYR B 456 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 456 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 456 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR B 456 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR B 456 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 456 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR B 456 " 0.086 2.00e-02 2.50e+03 pdb=" HD1 TYR B 456 " -0.044 2.00e-02 2.50e+03 pdb=" HD2 TYR B 456 " -0.065 2.00e-02 2.50e+03 pdb=" HE1 TYR B 456 " -0.030 2.00e-02 2.50e+03 pdb=" HE2 TYR B 456 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 26 " -0.124 2.00e-02 2.50e+03 5.15e-02 7.97e+01 pdb=" CG TYR B 26 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 26 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR B 26 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR B 26 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR B 26 " 0.030 2.00e-02 2.50e+03 pdb=" CZ TYR B 26 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 26 " -0.097 2.00e-02 2.50e+03 pdb=" HD1 TYR B 26 " 0.022 2.00e-02 2.50e+03 pdb=" HD2 TYR B 26 " 0.013 2.00e-02 2.50e+03 pdb=" HE1 TYR B 26 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR B 26 " 0.012 2.00e-02 2.50e+03 ... (remaining 2607 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.87: 102 1.87 - 2.55: 14700 2.55 - 3.24: 54678 3.24 - 3.92: 67689 3.92 - 4.60: 103767 Nonbonded interactions: 240936 Sorted by model distance: nonbonded pdb="HD21 ASN B 220 " pdb=" OE2 GLU A 411 " model vdw 1.188 2.450 nonbonded pdb=" OE2 GLU B 411 " pdb="HD21 ASN A 220 " model vdw 1.193 2.450 nonbonded pdb=" OE1 GLN B 208 " pdb=" HG SER A 428 " model vdw 1.233 2.450 nonbonded pdb=" HE1 MET B 271 " pdb="HD21 LEU A 62 " model vdw 1.265 2.440 nonbonded pdb=" HG2 GLU B 101 " pdb="HD11 ILE A 233 " model vdw 1.306 2.440 ... (remaining 240931 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.300 Extract box with map and model: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 51.990 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 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 : 0.019 0.225 8878 Z= 1.227 Angle : 2.440 17.379 12018 Z= 1.716 Chirality : 0.224 1.044 1454 Planarity : 0.014 0.124 1510 Dihedral : 14.312 91.170 3280 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.84 % Allowed : 4.70 % Favored : 94.47 % Cbeta Deviations : 11.59 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.21), residues: 1132 helix: -1.37 (0.16), residues: 714 sheet: 0.06 (0.66), residues: 64 loop : -1.80 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.012 TRP A 104 HIS 0.009 0.003 HIS B 535 PHE 0.055 0.013 PHE B 286 TYR 0.114 0.020 TYR A 26 ARG 0.016 0.001 ARG B 475 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 1.302 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 outliers start: 8 outliers final: 1 residues processed: 113 average time/residue: 0.5042 time to fit residues: 77.9968 Evaluate side-chains 61 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN A 61 ASN A 220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8878 Z= 0.254 Angle : 0.679 5.826 12018 Z= 0.366 Chirality : 0.041 0.146 1454 Planarity : 0.004 0.036 1510 Dihedral : 6.009 44.090 1220 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.73 % Allowed : 8.46 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.24), residues: 1132 helix: 0.36 (0.19), residues: 738 sheet: 0.03 (0.64), residues: 70 loop : -1.56 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 164 HIS 0.010 0.003 HIS B 561 PHE 0.014 0.002 PHE B 57 TYR 0.011 0.001 TYR A 437 ARG 0.003 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 1.438 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 outliers start: 7 outliers final: 4 residues processed: 68 average time/residue: 0.4334 time to fit residues: 43.2894 Evaluate side-chains 55 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 555 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8878 Z= 0.204 Angle : 0.564 6.740 12018 Z= 0.306 Chirality : 0.038 0.146 1454 Planarity : 0.004 0.033 1510 Dihedral : 5.084 21.533 1216 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.63 % Allowed : 8.56 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1132 helix: 0.95 (0.19), residues: 744 sheet: -0.10 (0.66), residues: 70 loop : -1.45 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 164 HIS 0.009 0.003 HIS B 561 PHE 0.018 0.001 PHE B 390 TYR 0.010 0.001 TYR B 570 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 1.374 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 outliers start: 6 outliers final: 4 residues processed: 59 average time/residue: 0.4464 time to fit residues: 38.6429 Evaluate side-chains 53 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 555 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 519 GLN A 272 GLN A 560 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8878 Z= 0.287 Angle : 0.554 8.043 12018 Z= 0.300 Chirality : 0.038 0.140 1454 Planarity : 0.003 0.038 1510 Dihedral : 4.737 22.419 1216 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.84 % Allowed : 8.66 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1132 helix: 1.13 (0.19), residues: 748 sheet: -0.50 (0.64), residues: 70 loop : -1.51 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 164 HIS 0.009 0.003 HIS B 561 PHE 0.017 0.001 PHE B 390 TYR 0.010 0.001 TYR A 437 ARG 0.004 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 1.408 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: symmetry clash outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 0.6556 time to fit residues: 47.5816 Evaluate side-chains 54 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 557 ARG Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 557 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.5980 chunk 1 optimal weight: 0.0030 chunk 80 optimal weight: 0.1980 chunk 44 optimal weight: 0.6980 chunk 92 optimal weight: 0.0270 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 overall best weight: 0.3048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8878 Z= 0.130 Angle : 0.480 6.401 12018 Z= 0.257 Chirality : 0.036 0.143 1454 Planarity : 0.003 0.033 1510 Dihedral : 4.507 21.839 1216 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.52 % Allowed : 9.19 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1132 helix: 1.56 (0.19), residues: 746 sheet: -0.43 (0.63), residues: 70 loop : -1.32 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 164 HIS 0.007 0.002 HIS B 561 PHE 0.016 0.001 PHE A 390 TYR 0.006 0.001 TYR A 289 ARG 0.002 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 1.227 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 231 MET cc_start: 0.7546 (tpp) cc_final: 0.7309 (mmm) outliers start: 5 outliers final: 4 residues processed: 57 average time/residue: 0.6252 time to fit residues: 47.0083 Evaluate side-chains 53 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 557 ARG Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 557 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 56 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8878 Z= 0.232 Angle : 0.500 5.728 12018 Z= 0.270 Chirality : 0.037 0.136 1454 Planarity : 0.003 0.034 1510 Dihedral : 4.380 21.096 1216 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.84 % Allowed : 8.77 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.25), residues: 1132 helix: 1.55 (0.19), residues: 748 sheet: -0.64 (0.62), residues: 70 loop : -1.33 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 164 HIS 0.006 0.002 HIS B 561 PHE 0.015 0.001 PHE B 390 TYR 0.008 0.001 TYR A 570 ARG 0.003 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 1.352 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: B 231 MET cc_start: 0.7565 (tpp) cc_final: 0.7358 (mmm) REVERT: A 501 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7772 (mtt) outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 0.6465 time to fit residues: 46.0841 Evaluate side-chains 55 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 557 ARG Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 557 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8878 Z= 0.191 Angle : 0.484 5.681 12018 Z= 0.260 Chirality : 0.036 0.138 1454 Planarity : 0.003 0.035 1510 Dihedral : 4.273 20.593 1216 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.52 % Allowed : 9.50 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.25), residues: 1132 helix: 1.64 (0.19), residues: 748 sheet: -0.75 (0.60), residues: 70 loop : -1.28 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 164 HIS 0.006 0.001 HIS B 561 PHE 0.017 0.001 PHE B 390 TYR 0.008 0.001 TYR A 570 ARG 0.003 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 1.392 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: B 231 MET cc_start: 0.7595 (tpp) cc_final: 0.7379 (mmm) outliers start: 5 outliers final: 4 residues processed: 50 average time/residue: 0.6652 time to fit residues: 43.8787 Evaluate side-chains 50 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 557 ARG Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 555 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 0.0980 chunk 84 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8878 Z= 0.140 Angle : 0.467 5.700 12018 Z= 0.248 Chirality : 0.036 0.139 1454 Planarity : 0.004 0.092 1510 Dihedral : 4.218 19.794 1216 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.31 % Allowed : 10.02 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.26), residues: 1132 helix: 1.79 (0.19), residues: 748 sheet: -0.71 (0.60), residues: 70 loop : -1.23 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 164 HIS 0.006 0.001 HIS B 561 PHE 0.013 0.001 PHE A 390 TYR 0.007 0.001 TYR A 570 ARG 0.009 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 1.433 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: B 231 MET cc_start: 0.7548 (tpp) cc_final: 0.7339 (mmm) outliers start: 3 outliers final: 3 residues processed: 48 average time/residue: 0.5582 time to fit residues: 37.2971 Evaluate side-chains 47 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 557 ARG Chi-restraints excluded: chain A residue 454 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8878 Z= 0.168 Angle : 0.466 5.629 12018 Z= 0.248 Chirality : 0.036 0.135 1454 Planarity : 0.004 0.091 1510 Dihedral : 4.147 19.239 1216 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.42 % Allowed : 10.13 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.26), residues: 1132 helix: 1.83 (0.19), residues: 748 sheet: -0.69 (0.61), residues: 70 loop : -1.23 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 164 HIS 0.005 0.001 HIS B 561 PHE 0.014 0.001 PHE A 390 TYR 0.006 0.001 TYR B 570 ARG 0.010 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 1.503 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: B 231 MET cc_start: 0.7563 (tpp) cc_final: 0.7359 (mmm) REVERT: A 501 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7782 (mtt) outliers start: 4 outliers final: 3 residues processed: 51 average time/residue: 0.5612 time to fit residues: 40.4080 Evaluate side-chains 53 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 557 ARG Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 501 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 0.0980 chunk 102 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8878 Z= 0.195 Angle : 0.474 5.550 12018 Z= 0.254 Chirality : 0.036 0.134 1454 Planarity : 0.004 0.092 1510 Dihedral : 4.126 19.171 1216 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.52 % Allowed : 10.23 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.26), residues: 1132 helix: 1.83 (0.19), residues: 748 sheet: -0.73 (0.62), residues: 70 loop : -1.22 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 164 HIS 0.005 0.001 HIS B 561 PHE 0.014 0.001 PHE A 390 TYR 0.008 0.001 TYR B 570 ARG 0.011 0.000 ARG A 557 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 1.297 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: B 231 MET cc_start: 0.7595 (tpp) cc_final: 0.7390 (mmm) REVERT: A 501 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7812 (mtt) outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 0.6079 time to fit residues: 44.1303 Evaluate side-chains 55 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 557 ARG Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 501 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.0770 chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 0.0770 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.106558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.078661 restraints weight = 53939.231| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.14 r_work: 0.3203 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8878 Z= 0.132 Angle : 0.454 5.484 12018 Z= 0.240 Chirality : 0.035 0.138 1454 Planarity : 0.004 0.091 1510 Dihedral : 4.068 18.298 1216 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.42 % Allowed : 10.33 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.26), residues: 1132 helix: 2.01 (0.19), residues: 746 sheet: -0.66 (0.62), residues: 70 loop : -1.13 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 164 HIS 0.005 0.001 HIS B 561 PHE 0.014 0.001 PHE A 390 TYR 0.005 0.001 TYR A 289 ARG 0.014 0.000 ARG B 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3634.28 seconds wall clock time: 65 minutes 35.73 seconds (3935.73 seconds total)