Starting phenix.real_space_refine on Thu Jan 16 08:20:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ba5_44396/01_2025/9ba5_44396.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ba5_44396/01_2025/9ba5_44396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ba5_44396/01_2025/9ba5_44396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ba5_44396/01_2025/9ba5_44396.map" model { file = "/net/cci-nas-00/data/ceres_data/9ba5_44396/01_2025/9ba5_44396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ba5_44396/01_2025/9ba5_44396.cif" } resolution = 3.51 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 140 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 5666 2.51 5 N 1570 2.21 5 O 1734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 9012 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4436 Classifications: {'peptide': 573} Link IDs: {'PCIS': 6, 'PTRANS': 31, 'TRANS': 535} Chain: "B" Number of atoms: 4436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4436 Classifications: {'peptide': 573} Link IDs: {'PCIS': 6, 'PTRANS': 31, 'TRANS': 535} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.38, per 1000 atoms: 0.71 Number of scatterers: 9012 At special positions: 0 Unit cell: (197.4, 80.85, 99.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1734 8.00 N 1570 7.00 C 5666 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 111 " distance=2.02 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 348 " - pdb=" SG CYS A 395 " distance=2.02 Simple disulfide: pdb=" SG CYS A 440 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 587 " distance=2.02 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 111 " distance=2.02 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 348 " - pdb=" SG CYS B 395 " distance=2.02 Simple disulfide: pdb=" SG CYS B 440 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 587 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 76 " " NAG A 702 " - " ASN A 198 " " NAG A 703 " - " ASN A 461 " " NAG A 704 " - " ASN A 498 " " NAG A 705 " - " ASN A 525 " " NAG B 701 " - " ASN B 76 " " NAG B 702 " - " ASN B 198 " " NAG B 703 " - " ASN B 461 " " NAG B 704 " - " ASN B 498 " " NAG B 705 " - " ASN B 525 " Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 38 sheets defined 4.5% alpha, 43.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 101 through 106 removed outlier: 4.236A pdb=" N ALA A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 removed outlier: 4.226A pdb=" N LEU A 202 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.774A pdb=" N SER A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.936A pdb=" N GLU A 483 " --> pdb=" O ARG A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 4.124A pdb=" N GLY A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 removed outlier: 4.002A pdb=" N ALA B 106 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 3.537A pdb=" N ASP B 201 " --> pdb=" O ASN B 198 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU B 202 " --> pdb=" O ALA B 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 202' Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.845A pdb=" N SER B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 483 removed outlier: 3.701A pdb=" N GLU B 483 " --> pdb=" O ARG B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 582 removed outlier: 4.135A pdb=" N GLY B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 41 removed outlier: 6.275A pdb=" N GLY A 36 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N SER A 66 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG A 62 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 48 Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 56 through 59 Processing sheet with id=AA5, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA6, first strand: chain 'A' and resid 143 through 147 removed outlier: 6.303A pdb=" N VAL A 143 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ALA A 230 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA A 145 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N GLU A 232 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU A 147 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A 206 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 143 through 147 removed outlier: 6.303A pdb=" N VAL A 143 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ALA A 230 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA A 145 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N GLU A 232 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU A 147 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA9, first strand: chain 'A' and resid 248 through 252 removed outlier: 6.142A pdb=" N THR A 249 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN A 324 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA A 251 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 257 through 260 Processing sheet with id=AB2, first strand: chain 'A' and resid 328 through 331 removed outlier: 6.828A pdb=" N ALA A 349 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 336 through 339 removed outlier: 6.499A pdb=" N THR A 336 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLN A 413 " --> pdb=" O THR A 336 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA A 338 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 398 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 344 through 346 Processing sheet with id=AB5, first strand: chain 'A' and resid 415 through 418 removed outlier: 3.656A pdb=" N ALA A 445 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG A 443 " --> pdb=" O PRO A 417 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 427 through 431 Processing sheet with id=AB7, first strand: chain 'A' and resid 435 through 439 Processing sheet with id=AB8, first strand: chain 'A' and resid 510 through 513 removed outlier: 6.687A pdb=" N HIS A 531 " --> pdb=" O THR A 512 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 518 through 519 Processing sheet with id=AC1, first strand: chain 'A' and resid 526 through 528 Processing sheet with id=AC2, first strand: chain 'B' and resid 35 through 41 removed outlier: 6.202A pdb=" N GLY B 36 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N SER B 66 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG B 62 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 46 through 48 removed outlier: 3.551A pdb=" N THR B 78 " --> pdb=" O MET B 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 46 through 48 Processing sheet with id=AC5, first strand: chain 'B' and resid 56 through 59 Processing sheet with id=AC6, first strand: chain 'B' and resid 131 through 132 removed outlier: 3.516A pdb=" N PHE B 131 " --> pdb=" O TYR B 161 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 143 through 147 removed outlier: 6.295A pdb=" N VAL B 143 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ALA B 230 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ALA B 145 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N GLU B 232 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU B 147 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 151 through 153 Processing sheet with id=AC9, first strand: chain 'B' and resid 165 through 168 Processing sheet with id=AD1, first strand: chain 'B' and resid 241 through 244 Processing sheet with id=AD2, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AD3, first strand: chain 'B' and resid 328 through 331 removed outlier: 6.749A pdb=" N ALA B 349 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 336 through 339 removed outlier: 6.573A pdb=" N THR B 336 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLN B 413 " --> pdb=" O THR B 336 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA B 338 " --> pdb=" O GLN B 413 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 357 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 344 through 346 Processing sheet with id=AD6, first strand: chain 'B' and resid 415 through 418 removed outlier: 3.656A pdb=" N ALA B 445 " --> pdb=" O LEU B 415 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG B 443 " --> pdb=" O PRO B 417 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 427 through 431 removed outlier: 6.539A pdb=" N ILE B 428 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ARG B 506 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ALA B 430 " --> pdb=" O ARG B 506 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 435 through 439 Processing sheet with id=AD9, first strand: chain 'B' and resid 510 through 513 removed outlier: 6.783A pdb=" N HIS B 531 " --> pdb=" O THR B 512 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 518 through 519 removed outlier: 3.550A pdb=" N LEU B 603 " --> pdb=" O ALA B 518 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 526 through 528 316 hydrogen bonds defined for protein. 723 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: 3.65 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2901 1.34 - 1.46: 2109 1.46 - 1.58: 4148 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 9218 Sorted by residual: bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.558 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" C1 NAG B 702 " pdb=" O5 NAG B 702 " ideal model delta sigma weight residual 1.406 1.558 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" C1 NAG B 705 " pdb=" O5 NAG B 705 " ideal model delta sigma weight residual 1.406 1.544 -0.138 2.00e-02 2.50e+03 4.74e+01 bond pdb=" C1 NAG B 701 " pdb=" O5 NAG B 701 " ideal model delta sigma weight residual 1.406 1.543 -0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" C1 NAG B 703 " pdb=" O5 NAG B 703 " ideal model delta sigma weight residual 1.406 1.542 -0.136 2.00e-02 2.50e+03 4.62e+01 ... (remaining 9213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 12218 3.60 - 7.21: 295 7.21 - 10.81: 22 10.81 - 14.42: 3 14.42 - 18.02: 2 Bond angle restraints: 12540 Sorted by residual: angle pdb=" CG1 VAL B 91 " pdb=" CB VAL B 91 " pdb=" CG2 VAL B 91 " ideal model delta sigma weight residual 110.80 99.34 11.46 2.20e+00 2.07e-01 2.71e+01 angle pdb=" CA LEU A 376 " pdb=" CB LEU A 376 " pdb=" CG LEU A 376 " ideal model delta sigma weight residual 116.30 134.32 -18.02 3.50e+00 8.16e-02 2.65e+01 angle pdb=" C VAL A 91 " pdb=" CA VAL A 91 " pdb=" CB VAL A 91 " ideal model delta sigma weight residual 112.45 118.70 -6.25 1.24e+00 6.50e-01 2.54e+01 angle pdb=" CA LEU B 376 " pdb=" CB LEU B 376 " pdb=" CG LEU B 376 " ideal model delta sigma weight residual 116.30 133.57 -17.27 3.50e+00 8.16e-02 2.43e+01 angle pdb=" C ASP B 547 " pdb=" N ASP B 548 " pdb=" CA ASP B 548 " ideal model delta sigma weight residual 122.07 128.85 -6.78 1.43e+00 4.89e-01 2.25e+01 ... (remaining 12535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 5246 17.19 - 34.37: 365 34.37 - 51.55: 83 51.55 - 68.74: 15 68.74 - 85.92: 7 Dihedral angle restraints: 5716 sinusoidal: 2418 harmonic: 3298 Sorted by residual: dihedral pdb=" CA ARG B 425 " pdb=" C ARG B 425 " pdb=" N ARG B 426 " pdb=" CA ARG B 426 " ideal model delta harmonic sigma weight residual 180.00 -148.50 -31.50 0 5.00e+00 4.00e-02 3.97e+01 dihedral pdb=" CA MET B 98 " pdb=" C MET B 98 " pdb=" N ASN B 99 " pdb=" CA ASN B 99 " ideal model delta harmonic sigma weight residual -180.00 -150.12 -29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA ARG B 355 " pdb=" C ARG B 355 " pdb=" N PRO B 356 " pdb=" CA PRO B 356 " ideal model delta harmonic sigma weight residual -180.00 -152.95 -27.05 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 5713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1138 0.077 - 0.155: 233 0.155 - 0.232: 39 0.232 - 0.310: 11 0.310 - 0.387: 5 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CB ILE B 404 " pdb=" CA ILE B 404 " pdb=" CG1 ILE B 404 " pdb=" CG2 ILE B 404 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CB VAL B 108 " pdb=" CA VAL B 108 " pdb=" CG1 VAL B 108 " pdb=" CG2 VAL B 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CB THR B 466 " pdb=" CA THR B 466 " pdb=" OG1 THR B 466 " pdb=" CG2 THR B 466 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 1423 not shown) Planarity restraints: 1644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 461 " 0.039 2.00e-02 2.50e+03 3.58e-02 1.60e+01 pdb=" CG ASN B 461 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN B 461 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 461 " -0.029 2.00e-02 2.50e+03 pdb=" C1 NAG B 703 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 115 " -0.066 5.00e-02 4.00e+02 9.95e-02 1.58e+01 pdb=" N PRO B 116 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO B 116 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 116 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 115 " 0.060 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO A 116 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 116 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 116 " 0.051 5.00e-02 4.00e+02 ... (remaining 1641 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 3127 2.89 - 3.39: 6293 3.39 - 3.90: 15071 3.90 - 4.40: 14943 4.40 - 4.90: 27349 Nonbonded interactions: 66783 Sorted by model distance: nonbonded pdb=" OG1 THR B 591 " pdb=" OD1 ASP B 594 " model vdw 2.389 3.040 nonbonded pdb=" OG1 THR A 591 " pdb=" OD1 ASP A 594 " model vdw 2.392 3.040 nonbonded pdb=" OG1 THR B 563 " pdb=" OG1 THR B 573 " model vdw 2.401 3.040 nonbonded pdb=" OG SER A 136 " pdb=" OE1 GLU A 138 " model vdw 2.413 3.040 nonbonded pdb=" OG SER B 136 " pdb=" OE1 GLU B 138 " model vdw 2.414 3.040 ... (remaining 66778 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 group one per residue 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: 8.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.290 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.030 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5751 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 : 0.011 0.152 9218 Z= 0.741 Angle : 1.264 18.022 12540 Z= 0.681 Chirality : 0.070 0.387 1426 Planarity : 0.010 0.100 1634 Dihedral : 12.938 85.924 3552 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 16.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.23), residues: 1142 helix: None (None), residues: 0 sheet: -0.31 (0.20), residues: 594 loop : -1.64 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 346 HIS 0.014 0.002 HIS B 534 PHE 0.031 0.003 PHE A 493 TYR 0.034 0.003 TYR B 393 ARG 0.009 0.001 ARG B 425 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ASN cc_start: 0.5727 (m110) cc_final: 0.5387 (m110) REVERT: A 328 GLU cc_start: 0.6397 (mp0) cc_final: 0.6062 (mp0) REVERT: A 359 ARG cc_start: 0.7784 (tmm160) cc_final: 0.7389 (ttp-110) REVERT: B 75 MET cc_start: 0.7015 (ttt) cc_final: 0.6617 (ttt) REVERT: B 367 LEU cc_start: 0.4956 (tp) cc_final: 0.4152 (tp) REVERT: B 409 GLU cc_start: 0.7198 (tt0) cc_final: 0.6951 (tt0) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2979 time to fit residues: 49.8026 Evaluate side-chains 115 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 47 optimal weight: 0.0370 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 0.0970 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 324 GLN A 326 GLN B 104 GLN B 324 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.257250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.222885 restraints weight = 12380.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.221541 restraints weight = 17878.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.223787 restraints weight = 13884.163| |-----------------------------------------------------------------------------| r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5764 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9218 Z= 0.254 Angle : 0.604 12.063 12540 Z= 0.310 Chirality : 0.044 0.226 1426 Planarity : 0.006 0.064 1634 Dihedral : 5.952 35.327 1450 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.73 % Allowed : 5.61 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % 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: -0.90 (0.24), residues: 1142 helix: -5.23 (0.24), residues: 12 sheet: 0.06 (0.20), residues: 582 loop : -1.19 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 346 HIS 0.005 0.001 HIS B 401 PHE 0.012 0.001 PHE B 245 TYR 0.010 0.001 TYR A 486 ARG 0.004 0.000 ARG B 425 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.3432 (mpp) cc_final: 0.2540 (pmm) REVERT: A 255 GLN cc_start: 0.6897 (mp10) cc_final: 0.6661 (mp10) REVERT: B 346 TRP cc_start: 0.7567 (m-10) cc_final: 0.5944 (m-10) REVERT: B 457 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.6357 (pp20) REVERT: B 459 LEU cc_start: 0.8130 (mt) cc_final: 0.7909 (mp) outliers start: 7 outliers final: 5 residues processed: 129 average time/residue: 0.2878 time to fit residues: 48.3734 Evaluate side-chains 119 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 496 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 78 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 64 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.255904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.219372 restraints weight = 11756.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.220603 restraints weight = 16917.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.220022 restraints weight = 16262.430| |-----------------------------------------------------------------------------| r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5897 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 9218 Z= 0.480 Angle : 0.681 10.758 12540 Z= 0.347 Chirality : 0.046 0.211 1426 Planarity : 0.005 0.062 1634 Dihedral : 5.703 31.695 1450 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.46 % Allowed : 9.25 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % 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: -0.73 (0.24), residues: 1142 helix: -5.34 (0.20), residues: 12 sheet: 0.16 (0.21), residues: 556 loop : -1.00 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 346 HIS 0.009 0.001 HIS B 401 PHE 0.019 0.002 PHE A 245 TYR 0.016 0.002 TYR A 486 ARG 0.011 0.001 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.3426 (mpp) cc_final: 0.2445 (pmm) REVERT: B 123 ARG cc_start: 0.7352 (tmm-80) cc_final: 0.7145 (ttp80) REVERT: B 365 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.6126 (pt0) outliers start: 14 outliers final: 10 residues processed: 121 average time/residue: 0.3261 time to fit residues: 50.9520 Evaluate side-chains 126 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 588 MET Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 365 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 2 optimal weight: 0.5980 chunk 111 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.253088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.214976 restraints weight = 12128.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.214448 restraints weight = 15193.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.216963 restraints weight = 12455.553| |-----------------------------------------------------------------------------| r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9218 Z= 0.310 Angle : 0.586 7.178 12540 Z= 0.299 Chirality : 0.043 0.171 1426 Planarity : 0.005 0.050 1634 Dihedral : 5.257 31.294 1450 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.87 % Allowed : 9.88 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % 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: -0.59 (0.24), residues: 1142 helix: -5.34 (0.19), residues: 12 sheet: 0.21 (0.21), residues: 544 loop : -0.83 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 73 HIS 0.004 0.001 HIS B 401 PHE 0.017 0.001 PHE B 173 TYR 0.013 0.002 TYR A 486 ARG 0.005 0.000 ARG B 425 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.3670 (mpp) cc_final: 0.2950 (pmm) REVERT: A 255 GLN cc_start: 0.7531 (mp10) cc_final: 0.7232 (mm-40) REVERT: A 465 VAL cc_start: 0.7364 (t) cc_final: 0.7011 (m) REVERT: A 482 ASP cc_start: 0.6154 (OUTLIER) cc_final: 0.5818 (t0) REVERT: B 72 ARG cc_start: 0.7564 (mtm180) cc_final: 0.7236 (mtm-85) REVERT: B 365 GLU cc_start: 0.6254 (OUTLIER) cc_final: 0.6038 (pt0) REVERT: B 485 LYS cc_start: 0.7954 (mtpp) cc_final: 0.7627 (mtpp) outliers start: 18 outliers final: 14 residues processed: 128 average time/residue: 0.3096 time to fit residues: 50.9930 Evaluate side-chains 134 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 587 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 27 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 91 optimal weight: 0.3980 chunk 44 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 69 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 80 optimal weight: 0.0870 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.255641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.221884 restraints weight = 12325.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.221939 restraints weight = 16572.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.222867 restraints weight = 13231.611| |-----------------------------------------------------------------------------| r_work (final): 0.4493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5794 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9218 Z= 0.169 Angle : 0.515 8.847 12540 Z= 0.261 Chirality : 0.042 0.151 1426 Planarity : 0.004 0.042 1634 Dihedral : 4.765 31.503 1450 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.87 % Allowed : 11.43 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % 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: -0.46 (0.25), residues: 1142 helix: -5.31 (0.21), residues: 12 sheet: 0.21 (0.21), residues: 542 loop : -0.63 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 73 HIS 0.002 0.000 HIS B 160 PHE 0.011 0.001 PHE B 173 TYR 0.016 0.001 TYR B 109 ARG 0.006 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.3870 (mpp) cc_final: 0.3307 (pmm) REVERT: A 249 THR cc_start: 0.7267 (OUTLIER) cc_final: 0.7052 (t) REVERT: A 328 GLU cc_start: 0.6237 (mp0) cc_final: 0.5974 (mt-10) REVERT: A 345 ARG cc_start: 0.6762 (mtp-110) cc_final: 0.6508 (ttm-80) REVERT: A 465 VAL cc_start: 0.7333 (t) cc_final: 0.7004 (t) REVERT: A 482 ASP cc_start: 0.6082 (OUTLIER) cc_final: 0.5875 (t0) REVERT: B 376 LEU cc_start: 0.6106 (tp) cc_final: 0.5895 (tp) outliers start: 18 outliers final: 12 residues processed: 125 average time/residue: 0.3226 time to fit residues: 51.7758 Evaluate side-chains 128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 425 ARG Chi-restraints excluded: chain B residue 460 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 60 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 78 optimal weight: 0.0870 chunk 22 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.256288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.219992 restraints weight = 11887.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.217564 restraints weight = 19573.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.219119 restraints weight = 14795.979| |-----------------------------------------------------------------------------| r_work (final): 0.4418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5932 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9218 Z= 0.357 Angle : 0.594 9.460 12540 Z= 0.299 Chirality : 0.044 0.185 1426 Planarity : 0.004 0.057 1634 Dihedral : 5.061 31.116 1450 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.66 % Allowed : 12.68 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % 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: -0.51 (0.25), residues: 1142 helix: -5.30 (0.21), residues: 12 sheet: 0.22 (0.22), residues: 528 loop : -0.69 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 73 HIS 0.005 0.001 HIS B 401 PHE 0.015 0.001 PHE A 245 TYR 0.021 0.002 TYR B 109 ARG 0.008 0.000 ARG A 476 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.3575 (mpp) cc_final: 0.3022 (pmm) REVERT: A 476 ARG cc_start: 0.7345 (mtm-85) cc_final: 0.6763 (ptp90) REVERT: A 482 ASP cc_start: 0.6193 (OUTLIER) cc_final: 0.5957 (t0) REVERT: B 80 MET cc_start: 0.5796 (ppp) cc_final: 0.4398 (ptt) REVERT: B 357 THR cc_start: 0.7787 (t) cc_final: 0.7492 (p) REVERT: B 376 LEU cc_start: 0.6174 (tp) cc_final: 0.5929 (tp) REVERT: B 491 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6822 (tt0) outliers start: 16 outliers final: 12 residues processed: 122 average time/residue: 0.3055 time to fit residues: 48.1394 Evaluate side-chains 130 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 425 ARG Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 587 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 26 optimal weight: 0.0980 chunk 108 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.259264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.226577 restraints weight = 12158.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.225024 restraints weight = 18145.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.226020 restraints weight = 15169.171| |-----------------------------------------------------------------------------| r_work (final): 0.4478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5854 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9218 Z= 0.299 Angle : 0.566 10.625 12540 Z= 0.286 Chirality : 0.043 0.169 1426 Planarity : 0.004 0.044 1634 Dihedral : 4.970 32.234 1450 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.39 % Allowed : 12.16 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % 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: -0.46 (0.25), residues: 1142 helix: -5.30 (0.22), residues: 12 sheet: 0.18 (0.22), residues: 536 loop : -0.60 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 73 HIS 0.004 0.001 HIS B 401 PHE 0.012 0.001 PHE B 245 TYR 0.015 0.001 TYR B 109 ARG 0.007 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.3765 (mpp) cc_final: 0.3430 (pmm) REVERT: A 328 GLU cc_start: 0.6179 (mp0) cc_final: 0.5881 (mt-10) REVERT: A 345 ARG cc_start: 0.6739 (mtp85) cc_final: 0.6512 (mmm160) REVERT: A 381 ARG cc_start: 0.6800 (ptp-110) cc_final: 0.6591 (ptp90) REVERT: B 80 MET cc_start: 0.5733 (ppp) cc_final: 0.4386 (ptt) REVERT: B 357 THR cc_start: 0.7685 (t) cc_final: 0.7402 (p) REVERT: B 376 LEU cc_start: 0.6251 (tp) cc_final: 0.5962 (tp) REVERT: B 457 GLU cc_start: 0.7302 (pp20) cc_final: 0.6778 (pt0) outliers start: 23 outliers final: 18 residues processed: 120 average time/residue: 0.3004 time to fit residues: 46.8214 Evaluate side-chains 128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 425 ARG Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 587 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 77 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 85 optimal weight: 0.3980 chunk 113 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 99 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 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 226 GLN A 228 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.259020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.225427 restraints weight = 12241.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.224364 restraints weight = 15944.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.225629 restraints weight = 13819.149| |-----------------------------------------------------------------------------| r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5856 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9218 Z= 0.300 Angle : 0.570 11.754 12540 Z= 0.286 Chirality : 0.043 0.177 1426 Planarity : 0.004 0.042 1634 Dihedral : 4.960 32.811 1450 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.60 % Allowed : 12.27 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % 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: -0.49 (0.25), residues: 1142 helix: -5.28 (0.22), residues: 12 sheet: 0.15 (0.22), residues: 534 loop : -0.60 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 73 HIS 0.004 0.001 HIS B 401 PHE 0.012 0.001 PHE B 245 TYR 0.023 0.001 TYR B 109 ARG 0.008 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.3726 (mpp) cc_final: 0.3429 (pmm) REVERT: A 328 GLU cc_start: 0.6416 (mp0) cc_final: 0.6120 (mt-10) REVERT: A 345 ARG cc_start: 0.6772 (mtp85) cc_final: 0.6529 (mmm160) REVERT: A 465 VAL cc_start: 0.7456 (t) cc_final: 0.7080 (m) REVERT: A 482 ASP cc_start: 0.6637 (t0) cc_final: 0.6360 (t70) REVERT: B 75 MET cc_start: 0.6708 (OUTLIER) cc_final: 0.6422 (mmm) REVERT: B 80 MET cc_start: 0.5779 (ppp) cc_final: 0.4512 (ptt) REVERT: B 357 THR cc_start: 0.7562 (t) cc_final: 0.7289 (p) REVERT: B 376 LEU cc_start: 0.6300 (tp) cc_final: 0.6003 (tp) REVERT: B 457 GLU cc_start: 0.7315 (pp20) cc_final: 0.6789 (pt0) outliers start: 25 outliers final: 18 residues processed: 126 average time/residue: 0.3058 time to fit residues: 50.0923 Evaluate side-chains 133 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 425 ARG Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 590 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 62 optimal weight: 1.9990 chunk 30 optimal weight: 0.0670 chunk 48 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 32 optimal weight: 0.0870 chunk 105 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 228 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.260660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.228088 restraints weight = 12136.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.226636 restraints weight = 16746.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.227523 restraints weight = 14519.516| |-----------------------------------------------------------------------------| r_work (final): 0.4480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5829 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9218 Z= 0.229 Angle : 0.544 12.461 12540 Z= 0.272 Chirality : 0.042 0.183 1426 Planarity : 0.004 0.045 1634 Dihedral : 4.781 33.690 1450 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.98 % Allowed : 12.79 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % 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: -0.37 (0.25), residues: 1142 helix: -5.27 (0.23), residues: 12 sheet: 0.23 (0.22), residues: 544 loop : -0.51 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 73 HIS 0.003 0.001 HIS B 401 PHE 0.010 0.001 PHE B 245 TYR 0.019 0.001 TYR B 109 ARG 0.010 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.3662 (mpp) cc_final: 0.3428 (pmm) REVERT: A 328 GLU cc_start: 0.6179 (mp0) cc_final: 0.5847 (mt-10) REVERT: A 465 VAL cc_start: 0.7399 (t) cc_final: 0.7138 (m) REVERT: A 482 ASP cc_start: 0.6572 (t0) cc_final: 0.6312 (t70) REVERT: B 343 ASN cc_start: 0.6323 (m-40) cc_final: 0.5984 (m-40) REVERT: B 357 THR cc_start: 0.7577 (t) cc_final: 0.7296 (p) REVERT: B 376 LEU cc_start: 0.6140 (tp) cc_final: 0.5906 (tp) REVERT: B 457 GLU cc_start: 0.7276 (pp20) cc_final: 0.6779 (pt0) outliers start: 19 outliers final: 17 residues processed: 125 average time/residue: 0.2990 time to fit residues: 48.3251 Evaluate side-chains 131 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 425 ARG Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 590 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 0.0060 chunk 89 optimal weight: 0.5980 chunk 48 optimal weight: 0.0470 chunk 63 optimal weight: 0.0270 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 overall best weight: 0.3352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 228 ASN ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.261705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.228224 restraints weight = 12256.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.226123 restraints weight = 17441.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.228344 restraints weight = 14086.781| |-----------------------------------------------------------------------------| r_work (final): 0.4508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5817 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9218 Z= 0.198 Angle : 0.532 12.459 12540 Z= 0.266 Chirality : 0.042 0.184 1426 Planarity : 0.004 0.043 1634 Dihedral : 4.676 33.538 1450 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.35 % Allowed : 12.99 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % 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: -0.25 (0.25), residues: 1142 helix: -5.25 (0.24), residues: 12 sheet: 0.32 (0.22), residues: 544 loop : -0.45 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 73 HIS 0.002 0.000 HIS B 401 PHE 0.009 0.001 PHE B 245 TYR 0.018 0.001 TYR B 109 ARG 0.012 0.000 ARG B 359 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.3667 (mpp) cc_final: 0.3414 (pmm) REVERT: A 328 GLU cc_start: 0.6036 (mp0) cc_final: 0.5724 (mt-10) REVERT: A 465 VAL cc_start: 0.7335 (t) cc_final: 0.7126 (m) REVERT: B 357 THR cc_start: 0.7458 (t) cc_final: 0.7226 (p) REVERT: B 376 LEU cc_start: 0.6076 (tp) cc_final: 0.5825 (tp) outliers start: 13 outliers final: 13 residues processed: 121 average time/residue: 0.3054 time to fit residues: 48.0165 Evaluate side-chains 131 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 425 ARG Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 590 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 40 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 95 optimal weight: 0.0470 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.259481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.225866 restraints weight = 12106.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.225605 restraints weight = 17005.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.223732 restraints weight = 14652.540| |-----------------------------------------------------------------------------| r_work (final): 0.4458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5896 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9218 Z= 0.296 Angle : 0.580 12.269 12540 Z= 0.290 Chirality : 0.043 0.208 1426 Planarity : 0.004 0.047 1634 Dihedral : 4.841 32.763 1450 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.77 % Allowed : 12.68 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % 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: -0.23 (0.26), residues: 1142 helix: -5.22 (0.26), residues: 12 sheet: 0.31 (0.23), residues: 536 loop : -0.41 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 73 HIS 0.004 0.001 HIS B 401 PHE 0.012 0.001 PHE A 245 TYR 0.019 0.001 TYR B 109 ARG 0.012 0.001 ARG B 359 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2997.32 seconds wall clock time: 56 minutes 22.45 seconds (3382.45 seconds total)