Starting phenix.real_space_refine on Mon May 19 01:59:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qoe_18535/05_2025/8qoe_18535_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qoe_18535/05_2025/8qoe_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/cci-nas-00/data/ceres_data/8qoe_18535/05_2025/8qoe_18535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qoe_18535/05_2025/8qoe_18535.map" model { file = "/net/cci-nas-00/data/ceres_data/8qoe_18535/05_2025/8qoe_18535_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qoe_18535/05_2025/8qoe_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-5687/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: 22.66, per 1000 atoms: 1.27 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: 4.68 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: 1.25 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: 6.13 Time building geometry restraints manager: 5.59 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: 0.05 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: 1.570 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: 0.310 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 52.520 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.590 ------------------------------------------------------------------------------- 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= 1.316 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 Details of bonding type rmsd hydrogen bonds : bond 0.21350 ( 510) hydrogen bonds : angle 7.36138 ( 1506) covalent geometry : bond 0.01879 ( 8878) covalent geometry : angle 2.44035 (12018) *********************** 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 to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 1.483 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: 0.4966 time to fit residues: 77.8758 Evaluate side-chains 61 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.108630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.079583 restraints weight = 52558.474| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.24 r_work: 0.3177 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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= 0.181 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 Details of bonding type rmsd hydrogen bonds : bond 0.06335 ( 510) hydrogen bonds : angle 5.12149 ( 1506) covalent geometry : bond 0.00403 ( 8878) covalent geometry : angle 0.67878 (12018) *********************** 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 to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 1.301 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: A 336 ASN cc_start: 0.8808 (t0) cc_final: 0.8597 (t0) outliers start: 7 outliers final: 4 residues processed: 68 average time/residue: 0.3967 time to fit residues: 39.8942 Evaluate side-chains 56 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 55 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.107636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.079281 restraints weight = 53967.683| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.22 r_work: 0.3195 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8878 Z= 0.141 Angle : 0.557 6.143 12018 Z= 0.302 Chirality : 0.038 0.147 1454 Planarity : 0.003 0.032 1510 Dihedral : 5.123 21.522 1216 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.52 % Allowed : 8.87 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1132 helix: 0.96 (0.19), residues: 742 sheet: -0.05 (0.67), residues: 70 loop : -1.46 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 164 HIS 0.008 0.003 HIS B 561 PHE 0.017 0.001 PHE B 390 TYR 0.010 0.001 TYR B 570 ARG 0.002 0.000 ARG B 126 Details of bonding type rmsd hydrogen bonds : bond 0.05240 ( 510) hydrogen bonds : angle 4.64158 ( 1506) covalent geometry : bond 0.00303 ( 8878) covalent geometry : angle 0.55673 (12018) *********************** 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 62 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 1.309 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: A 336 ASN cc_start: 0.8810 (t0) cc_final: 0.8610 (t0) outliers start: 5 outliers final: 3 residues processed: 60 average time/residue: 0.4252 time to fit residues: 37.6566 Evaluate side-chains 54 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 46 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 57 optimal weight: 0.0470 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 96 optimal weight: 0.6980 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.109334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.081170 restraints weight = 53420.653| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.18 r_work: 0.3229 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3151 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= 0.103 Angle : 0.500 8.865 12018 Z= 0.265 Chirality : 0.036 0.143 1454 Planarity : 0.003 0.029 1510 Dihedral : 4.679 22.296 1216 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.84 % Allowed : 7.72 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1132 helix: 1.48 (0.19), residues: 746 sheet: -0.25 (0.63), residues: 70 loop : -1.28 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 164 HIS 0.009 0.002 HIS B 561 PHE 0.015 0.001 PHE A 390 TYR 0.007 0.001 TYR B 570 ARG 0.003 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.04280 ( 510) hydrogen bonds : angle 4.22391 ( 1506) covalent geometry : bond 0.00211 ( 8878) covalent geometry : angle 0.50013 (12018) *********************** 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 61 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 1.465 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: 0.8269 (tpp) cc_final: 0.7772 (mmm) REVERT: B 501 MET cc_start: 0.8724 (mtt) cc_final: 0.8465 (mmt) REVERT: A 501 MET cc_start: 0.8691 (mtt) cc_final: 0.8434 (mmt) outliers start: 8 outliers final: 6 residues processed: 58 average time/residue: 0.5502 time to fit residues: 43.4823 Evaluate side-chains 53 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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 153 ILE 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 39 optimal weight: 0.0870 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.107994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.079727 restraints weight = 54404.543| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.20 r_work: 0.3217 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8878 Z= 0.112 Angle : 0.481 7.181 12018 Z= 0.258 Chirality : 0.036 0.140 1454 Planarity : 0.003 0.030 1510 Dihedral : 4.428 21.039 1216 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.52 % Allowed : 8.25 % Favored : 91.23 % 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: 1.16 (0.26), residues: 1132 helix: 1.70 (0.19), residues: 746 sheet: -0.39 (0.62), residues: 70 loop : -1.18 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 164 HIS 0.007 0.002 HIS B 561 PHE 0.016 0.001 PHE A 390 TYR 0.006 0.001 TYR A 570 ARG 0.003 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 510) hydrogen bonds : angle 4.13300 ( 1506) covalent geometry : bond 0.00243 ( 8878) covalent geometry : angle 0.48093 (12018) *********************** 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 to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 1.361 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: 0.8280 (tpp) cc_final: 0.7822 (mmm) REVERT: B 501 MET cc_start: 0.8772 (mtt) cc_final: 0.8515 (mmt) REVERT: A 501 MET cc_start: 0.8728 (mtt) cc_final: 0.8470 (mmt) outliers start: 5 outliers final: 4 residues processed: 57 average time/residue: 0.5452 time to fit residues: 42.1874 Evaluate side-chains 53 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 41 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.107445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.079558 restraints weight = 53836.499| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.14 r_work: 0.3201 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8878 Z= 0.142 Angle : 0.487 6.585 12018 Z= 0.261 Chirality : 0.036 0.135 1454 Planarity : 0.003 0.032 1510 Dihedral : 4.304 21.012 1216 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.73 % Allowed : 8.77 % 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: 1.20 (0.25), residues: 1132 helix: 1.74 (0.19), residues: 746 sheet: -0.46 (0.61), residues: 70 loop : -1.20 (0.34), residues: 316 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 0.014 0.001 PHE B 390 TYR 0.007 0.001 TYR B 570 ARG 0.003 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 510) hydrogen bonds : angle 4.10327 ( 1506) covalent geometry : bond 0.00314 ( 8878) covalent geometry : angle 0.48712 (12018) *********************** 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 56 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 1.290 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: 0.8335 (tpp) cc_final: 0.7892 (mmm) outliers start: 7 outliers final: 6 residues processed: 52 average time/residue: 0.6441 time to fit residues: 43.8852 Evaluate side-chains 54 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 1.304 ------------------------------------------------------------------------------- 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 293 ILE 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 67 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 111 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.107040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.078950 restraints weight = 54022.468| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.16 r_work: 0.3200 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8878 Z= 0.114 Angle : 0.473 6.964 12018 Z= 0.251 Chirality : 0.036 0.137 1454 Planarity : 0.003 0.032 1510 Dihedral : 4.205 19.442 1216 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.42 % Allowed : 9.29 % 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: 1.30 (0.26), residues: 1132 helix: 1.82 (0.19), residues: 746 sheet: -0.46 (0.61), residues: 70 loop : -1.15 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 164 HIS 0.006 0.001 HIS B 561 PHE 0.013 0.001 PHE B 390 TYR 0.007 0.001 TYR A 570 ARG 0.003 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 510) hydrogen bonds : angle 4.00466 ( 1506) covalent geometry : bond 0.00248 ( 8878) covalent geometry : angle 0.47324 (12018) *********************** 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 54 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 1.260 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: 0.8308 (tpp) cc_final: 0.7858 (mmm) REVERT: A 501 MET cc_start: 0.8766 (mtt) cc_final: 0.8485 (mmt) outliers start: 4 outliers final: 4 residues processed: 52 average time/residue: 0.6336 time to fit residues: 43.1348 Evaluate side-chains 53 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 91 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.106940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.078813 restraints weight = 53844.258| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.17 r_work: 0.3207 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8878 Z= 0.108 Angle : 0.467 7.541 12018 Z= 0.246 Chirality : 0.036 0.136 1454 Planarity : 0.003 0.032 1510 Dihedral : 4.092 18.300 1216 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.63 % Allowed : 8.98 % 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: 1.42 (0.26), residues: 1132 helix: 1.90 (0.19), residues: 748 sheet: -0.40 (0.61), residues: 70 loop : -1.11 (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 0.013 0.001 PHE B 390 TYR 0.007 0.001 TYR B 570 ARG 0.003 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 510) hydrogen bonds : angle 3.90352 ( 1506) covalent geometry : bond 0.00236 ( 8878) covalent geometry : angle 0.46740 (12018) *********************** 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 55 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 1.900 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: B 231 MET cc_start: 0.8317 (tpp) cc_final: 0.7860 (mmm) REVERT: B 501 MET cc_start: 0.8767 (mtt) cc_final: 0.8513 (mmt) REVERT: A 501 MET cc_start: 0.8752 (mtt) cc_final: 0.8491 (mmt) outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 0.6610 time to fit residues: 45.8347 Evaluate side-chains 51 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 1.399 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 5 optimal weight: 0.0050 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN A 519 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.106428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.078426 restraints weight = 54153.587| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.16 r_work: 0.3200 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3821 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= 0.127 Angle : 0.491 9.457 12018 Z= 0.255 Chirality : 0.036 0.136 1454 Planarity : 0.004 0.093 1510 Dihedral : 4.097 18.419 1216 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.31 % Allowed : 9.92 % Favored : 89.77 % 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: 1.43 (0.26), residues: 1132 helix: 1.93 (0.19), residues: 748 sheet: -0.49 (0.61), residues: 70 loop : -1.14 (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 0.013 0.001 PHE A 390 TYR 0.005 0.001 TYR B 570 ARG 0.009 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 510) hydrogen bonds : angle 3.94070 ( 1506) covalent geometry : bond 0.00283 ( 8878) covalent geometry : angle 0.49084 (12018) *********************** 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 50 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 1.541 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: B 231 MET cc_start: 0.8345 (tpp) cc_final: 0.7903 (mmm) outliers start: 3 outliers final: 3 residues processed: 48 average time/residue: 0.5667 time to fit residues: 36.8556 Evaluate side-chains 50 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 0.0010 chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.106650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.078557 restraints weight = 53645.566| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.15 r_work: 0.3208 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8878 Z= 0.111 Angle : 0.470 7.745 12018 Z= 0.247 Chirality : 0.036 0.136 1454 Planarity : 0.004 0.098 1510 Dihedral : 4.068 18.315 1216 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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: 1.48 (0.26), residues: 1132 helix: 1.99 (0.19), residues: 748 sheet: -0.48 (0.61), residues: 70 loop : -1.19 (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 0.013 0.001 PHE B 390 TYR 0.007 0.001 TYR A 570 ARG 0.010 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 510) hydrogen bonds : angle 3.90130 ( 1506) covalent geometry : bond 0.00243 ( 8878) covalent geometry : angle 0.46975 (12018) ********************** 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 52 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 1.241 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: B 231 MET cc_start: 0.8329 (tpp) cc_final: 0.7886 (mmm) REVERT: B 345 ARG cc_start: 0.8966 (mtm-85) cc_final: 0.8608 (mtm-85) outliers start: 3 outliers final: 3 residues processed: 50 average time/residue: 0.6091 time to fit residues: 40.5081 Evaluate side-chains 51 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 32 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.106183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.078184 restraints weight = 54315.626| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.15 r_work: 0.3193 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8878 Z= 0.130 Angle : 0.485 7.411 12018 Z= 0.254 Chirality : 0.036 0.134 1454 Planarity : 0.004 0.098 1510 Dihedral : 4.045 18.586 1216 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.42 % Allowed : 9.71 % Favored : 89.87 % 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: 1.47 (0.26), residues: 1132 helix: 1.98 (0.19), residues: 748 sheet: -0.50 (0.62), residues: 70 loop : -1.16 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 164 HIS 0.005 0.001 HIS B 561 PHE 0.013 0.001 PHE B 390 TYR 0.006 0.001 TYR A 570 ARG 0.011 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 510) hydrogen bonds : angle 3.93843 ( 1506) covalent geometry : bond 0.00290 ( 8878) covalent geometry : angle 0.48453 (12018) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6996.64 seconds wall clock time: 121 minutes 13.73 seconds (7273.73 seconds total)