Starting phenix.real_space_refine on Sun Jun 15 21:54:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qoe_18535/06_2025/8qoe_18535_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qoe_18535/06_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_18535/06_2025/8qoe_18535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qoe_18535/06_2025/8qoe_18535.map" model { file = "/net/cci-nas-00/data/ceres_data/8qoe_18535/06_2025/8qoe_18535_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qoe_18535/06_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-5710/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: 24.80, per 1000 atoms: 1.39 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: 5.27 Conformation dependent library (CDL) restraints added in 2.3 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: 1.33 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: 9.67 Time building geometry restraints manager: 5.61 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: 0.09 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: 75.510 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: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 63.550 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.080 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:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.960 ------------------------------------------------------------------------------- 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 : 1.387 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: 0.4859 time to fit residues: 75.4625 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 : 1.241 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.079569 restraints weight = 52558.481| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.25 r_work: 0.3177 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 : 1.508 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: 0.8789 (t0) cc_final: 0.8583 (t0) outliers start: 7 outliers final: 4 residues processed: 68 average time/residue: 0.4391 time to fit residues: 44.3661 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 : 1.669 ------------------------------------------------------------------------------- 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: 3.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.107551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.079226 restraints weight = 53937.574| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.20 r_work: 0.3194 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2807 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= 0.148 Angle : 0.555 6.351 12018 Z= 0.301 Chirality : 0.038 0.142 1454 Planarity : 0.003 0.033 1510 Dihedral : 5.068 21.152 1216 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.52 % Allowed : 8.66 % 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: 0.36 (0.25), residues: 1132 helix: 1.03 (0.19), residues: 736 sheet: -0.06 (0.66), residues: 70 loop : -1.46 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 164 HIS 0.009 0.003 HIS A 535 PHE 0.016 0.001 PHE B 390 TYR 0.010 0.001 TYR B 570 ARG 0.002 0.000 ARG A 441 Details of bonding type rmsd hydrogen bonds : bond 0.05103 ( 510) hydrogen bonds : angle 4.60327 ( 1506) covalent geometry : bond 0.00301 ( 8878) covalent geometry : angle 0.55477 (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 65 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 1.996 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: 5 outliers final: 3 residues processed: 63 average time/residue: 0.5489 time to fit residues: 51.7916 Evaluate side-chains 53 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 2.226 ------------------------------------------------------------------------------- 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: 1.9990 chunk 42 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.107178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.079069 restraints weight = 53693.789| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.17 r_work: 0.3202 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3121 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= 0.123 Angle : 0.504 7.691 12018 Z= 0.271 Chirality : 0.036 0.142 1454 Planarity : 0.003 0.031 1510 Dihedral : 4.741 21.873 1216 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.94 % Allowed : 8.46 % 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: 0.77 (0.25), residues: 1132 helix: 1.39 (0.19), residues: 746 sheet: -0.38 (0.64), residues: 70 loop : -1.38 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 164 HIS 0.008 0.002 HIS B 561 PHE 0.016 0.001 PHE A 390 TYR 0.008 0.001 TYR B 570 ARG 0.003 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.04471 ( 510) hydrogen bonds : angle 4.32371 ( 1506) covalent geometry : bond 0.00263 ( 8878) covalent geometry : angle 0.50423 (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 60 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 231 MET cc_start: 0.8306 (tpp) cc_final: 0.7802 (mmm) REVERT: B 501 MET cc_start: 0.8782 (mtt) cc_final: 0.8453 (mmt) outliers start: 9 outliers final: 7 residues processed: 57 average time/residue: 0.5589 time to fit residues: 43.4094 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 : 1.307 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.106923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.078746 restraints weight = 54668.369| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.18 r_work: 0.3188 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8878 Z= 0.147 Angle : 0.500 6.678 12018 Z= 0.270 Chirality : 0.037 0.137 1454 Planarity : 0.003 0.033 1510 Dihedral : 4.504 21.414 1216 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.84 % Allowed : 8.46 % Favored : 90.71 % 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: 0.93 (0.25), residues: 1132 helix: 1.56 (0.19), residues: 746 sheet: -0.61 (0.61), residues: 70 loop : -1.36 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 164 HIS 0.007 0.002 HIS B 561 PHE 0.017 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 0.04326 ( 510) hydrogen bonds : angle 4.25314 ( 1506) covalent geometry : bond 0.00321 ( 8878) covalent geometry : angle 0.50031 (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 61 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 1.310 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 REVERT: B 231 MET cc_start: 0.8350 (tpp) cc_final: 0.7868 (mmm) outliers start: 8 outliers final: 4 residues processed: 58 average time/residue: 0.5499 time to fit residues: 43.3209 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 : 1.302 ------------------------------------------------------------------------------- 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: 5.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.106513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.078303 restraints weight = 53821.159| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.16 r_work: 0.3203 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8878 Z= 0.114 Angle : 0.477 5.610 12018 Z= 0.256 Chirality : 0.036 0.138 1454 Planarity : 0.003 0.033 1510 Dihedral : 4.355 20.722 1216 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.42 % Allowed : 8.98 % 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: 1.11 (0.25), residues: 1132 helix: 1.70 (0.19), residues: 746 sheet: -0.59 (0.60), residues: 70 loop : -1.29 (0.33), 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 0.014 0.001 PHE A 390 TYR 0.007 0.001 TYR A 570 ARG 0.005 0.000 ARG B 100 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 510) hydrogen bonds : angle 4.08714 ( 1506) covalent geometry : bond 0.00249 ( 8878) covalent geometry : angle 0.47693 (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 55 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 1.262 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: 0.8323 (tpp) cc_final: 0.7868 (mmm) outliers start: 4 outliers final: 4 residues processed: 53 average time/residue: 0.6369 time to fit residues: 44.5295 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 : 1.424 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 96 optimal weight: 0.0870 chunk 79 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.107285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.079349 restraints weight = 54126.516| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.15 r_work: 0.3199 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8878 Z= 0.115 Angle : 0.468 5.694 12018 Z= 0.250 Chirality : 0.036 0.137 1454 Planarity : 0.003 0.032 1510 Dihedral : 4.247 20.028 1216 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.42 % Allowed : 9.81 % 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: 1.22 (0.25), residues: 1132 helix: 1.79 (0.19), residues: 746 sheet: -0.58 (0.60), residues: 70 loop : -1.24 (0.33), 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 0.015 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 0.03942 ( 510) hydrogen bonds : angle 4.02075 ( 1506) covalent geometry : bond 0.00253 ( 8878) covalent geometry : angle 0.46750 (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 53 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 1.303 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: 0.8322 (tpp) cc_final: 0.7871 (mmm) outliers start: 4 outliers final: 4 residues processed: 51 average time/residue: 0.6544 time to fit residues: 43.8802 Evaluate side-chains 52 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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: 0.3980 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 95 optimal weight: 0.0980 chunk 60 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.106736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.078648 restraints weight = 53900.982| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.16 r_work: 0.3206 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3729 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= 0.104 Angle : 0.464 5.577 12018 Z= 0.245 Chirality : 0.036 0.138 1454 Planarity : 0.003 0.032 1510 Dihedral : 4.130 19.050 1216 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.63 % Allowed : 9.29 % Favored : 90.08 % 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: 1.36 (0.26), residues: 1132 helix: 1.89 (0.19), residues: 748 sheet: -0.57 (0.60), residues: 70 loop : -1.18 (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 0.007 0.001 TYR A 570 ARG 0.003 0.000 ARG B 557 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 510) hydrogen bonds : angle 3.92149 ( 1506) covalent geometry : bond 0.00228 ( 8878) covalent geometry : angle 0.46396 (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 : 1.302 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: B 231 MET cc_start: 0.8335 (tpp) cc_final: 0.7891 (mmm) REVERT: B 501 MET cc_start: 0.8778 (mtt) cc_final: 0.8526 (mmt) outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 0.6375 time to fit residues: 43.4013 Evaluate side-chains 52 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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: 4.9990 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 0.0970 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 0.2980 chunk 109 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.108559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.079054 restraints weight = 55752.677| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.43 r_work: 0.3184 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8878 Z= 0.107 Angle : 0.469 8.809 12018 Z= 0.246 Chirality : 0.036 0.136 1454 Planarity : 0.004 0.090 1510 Dihedral : 4.113 19.280 1216 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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: 1.44 (0.26), residues: 1132 helix: 1.96 (0.19), residues: 748 sheet: -0.59 (0.60), residues: 70 loop : -1.16 (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 0.03740 ( 510) hydrogen bonds : angle 3.91536 ( 1506) covalent geometry : bond 0.00235 ( 8878) covalent geometry : angle 0.46945 (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 51 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 1.540 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: B 231 MET cc_start: 0.8351 (tpp) cc_final: 0.7901 (mmm) REVERT: B 501 MET cc_start: 0.8792 (mtt) cc_final: 0.8542 (mmt) REVERT: A 501 MET cc_start: 0.8773 (mtt) cc_final: 0.8515 (mmt) outliers start: 3 outliers final: 3 residues processed: 49 average time/residue: 0.5675 time to fit residues: 38.3514 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 : 1.466 ------------------------------------------------------------------------------- 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: 0.0980 chunk 1 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.108758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.079223 restraints weight = 55499.069| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.43 r_work: 0.3187 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8878 Z= 0.109 Angle : 0.461 5.631 12018 Z= 0.244 Chirality : 0.036 0.136 1454 Planarity : 0.004 0.099 1510 Dihedral : 4.075 18.472 1216 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.52 % Allowed : 10.02 % 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: 1.48 (0.26), residues: 1132 helix: 2.01 (0.19), residues: 748 sheet: -0.58 (0.61), residues: 70 loop : -1.18 (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 0.007 0.001 TYR A 570 ARG 0.010 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 510) hydrogen bonds : angle 3.89867 ( 1506) covalent geometry : bond 0.00238 ( 8878) covalent geometry : angle 0.46113 (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 55 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 1.335 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: B 231 MET cc_start: 0.8344 (tpp) cc_final: 0.7893 (mmm) REVERT: B 501 MET cc_start: 0.8791 (mtt) cc_final: 0.8541 (mmt) REVERT: A 501 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8522 (mmt) outliers start: 5 outliers final: 4 residues processed: 51 average time/residue: 0.6211 time to fit residues: 42.0017 Evaluate side-chains 53 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 555 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 32 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 80 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.108580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.079311 restraints weight = 56094.251| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.40 r_work: 0.3184 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8878 Z= 0.119 Angle : 0.470 6.529 12018 Z= 0.248 Chirality : 0.036 0.135 1454 Planarity : 0.004 0.097 1510 Dihedral : 4.055 18.262 1216 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.52 % Allowed : 10.02 % 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: 1.50 (0.26), residues: 1132 helix: 2.01 (0.19), residues: 748 sheet: -0.58 (0.61), residues: 70 loop : -1.16 (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 0.006 0.001 TYR B 570 ARG 0.013 0.000 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 510) hydrogen bonds : angle 3.89731 ( 1506) covalent geometry : bond 0.00264 ( 8878) covalent geometry : angle 0.47017 (12018) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7895.85 seconds wall clock time: 136 minutes 26.94 seconds (8186.94 seconds total)