Starting phenix.real_space_refine on Thu Jun 5 22:16:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j98_61255/06_2025/9j98_61255.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j98_61255/06_2025/9j98_61255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j98_61255/06_2025/9j98_61255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j98_61255/06_2025/9j98_61255.map" model { file = "/net/cci-nas-00/data/ceres_data/9j98_61255/06_2025/9j98_61255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j98_61255/06_2025/9j98_61255.cif" } resolution = 3.33 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= 0.003 sd= 0.092 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 P 2 5.49 5 S 32 5.16 5 C 4558 2.51 5 N 1062 2.21 5 O 1098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6752 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3301 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 14, 'TRANS': 382} Chain breaks: 1 Chain: "B" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3301 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 14, 'TRANS': 382} Chain breaks: 1 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'8PE': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'8PE': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.60, per 1000 atoms: 0.68 Number of scatterers: 6752 At special positions: 0 Unit cell: (68.481, 125.005, 80.438, 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 32 16.00 P 2 15.00 O 1098 8.00 N 1062 7.00 C 4558 6.00 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: 1.84 Conformation dependent library (CDL) restraints added in 937.6 milliseconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1508 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 73.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 232 through 258 removed outlier: 3.810A pdb=" N VAL A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 294 removed outlier: 3.785A pdb=" N ILE A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.556A pdb=" N ILE A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 336 removed outlier: 3.744A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N CYS A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 358 removed outlier: 3.783A pdb=" N TYR A 352 " --> pdb=" O PRO A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 382 removed outlier: 3.654A pdb=" N PHE A 372 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 402 removed outlier: 3.682A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 removed outlier: 4.483A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N MET A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 419 " --> pdb=" O CYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 453 removed outlier: 4.120A pdb=" N CYS A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 471 Processing helix chain 'A' and resid 473 through 503 removed outlier: 3.684A pdb=" N THR A 485 " --> pdb=" O GLY A 481 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A 502 " --> pdb=" O THR A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 531 removed outlier: 3.612A pdb=" N TRP A 514 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TRP A 528 " --> pdb=" O TYR A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 Processing helix chain 'A' and resid 556 through 569 removed outlier: 4.024A pdb=" N TYR A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 removed outlier: 3.928A pdb=" N GLN A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 577 " --> pdb=" O TRP A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 619 removed outlier: 3.591A pdb=" N ILE A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) Proline residue: A 598 - end of helix removed outlier: 4.222A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 613 " --> pdb=" O PHE A 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 258 removed outlier: 3.810A pdb=" N VAL B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 294 removed outlier: 3.784A pdb=" N ILE B 269 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 removed outlier: 3.557A pdb=" N ILE B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 336 removed outlier: 3.743A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N CYS B 334 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 358 removed outlier: 3.784A pdb=" N TYR B 352 " --> pdb=" O PRO B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 382 removed outlier: 3.653A pdb=" N PHE B 372 " --> pdb=" O TYR B 368 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 402 removed outlier: 3.682A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 removed outlier: 4.485A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N MET B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 419 " --> pdb=" O CYS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 453 removed outlier: 4.120A pdb=" N CYS B 453 " --> pdb=" O ALA B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 471 Processing helix chain 'B' and resid 473 through 503 removed outlier: 3.685A pdb=" N THR B 485 " --> pdb=" O GLY B 481 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG B 502 " --> pdb=" O THR B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 531 removed outlier: 3.612A pdb=" N TRP B 514 " --> pdb=" O PHE B 510 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TRP B 528 " --> pdb=" O TYR B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 545 Processing helix chain 'B' and resid 556 through 569 removed outlier: 4.024A pdb=" N TYR B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 580 removed outlier: 3.849A pdb=" N GLN B 576 " --> pdb=" O ALA B 572 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 577 " --> pdb=" O TRP B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 596 removed outlier: 3.811A pdb=" N ILE B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 619 removed outlier: 3.933A pdb=" N PHE B 602 " --> pdb=" O PRO B 598 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 613 " --> pdb=" O PHE B 609 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1134 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: 1.60 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.26: 956 1.26 - 1.40: 2052 1.40 - 1.54: 3798 1.54 - 1.67: 126 1.67 - 1.81: 44 Bond restraints: 6976 Sorted by residual: bond pdb=" C ALA B 597 " pdb=" O ALA B 597 " ideal model delta sigma weight residual 1.244 1.146 0.098 1.00e-02 1.00e+04 9.65e+01 bond pdb=" C PRO B 598 " pdb=" O PRO B 598 " ideal model delta sigma weight residual 1.237 1.128 0.110 1.32e-02 5.74e+03 6.89e+01 bond pdb=" C SER B 578 " pdb=" N ILE B 579 " ideal model delta sigma weight residual 1.335 1.422 -0.087 1.09e-02 8.42e+03 6.34e+01 bond pdb=" C LEU B 599 " pdb=" O LEU B 599 " ideal model delta sigma weight residual 1.236 1.149 0.087 1.28e-02 6.10e+03 4.59e+01 bond pdb=" C ASP A 409 " pdb=" O ASP A 409 " ideal model delta sigma weight residual 1.236 1.147 0.089 1.33e-02 5.65e+03 4.48e+01 ... (remaining 6971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 9155 2.75 - 5.50: 261 5.50 - 8.26: 45 8.26 - 11.01: 13 11.01 - 13.76: 6 Bond angle restraints: 9480 Sorted by residual: angle pdb=" CA THR B 574 " pdb=" CB THR B 574 " pdb=" OG1 THR B 574 " ideal model delta sigma weight residual 109.60 97.57 12.03 1.50e+00 4.44e-01 6.44e+01 angle pdb=" CA THR A 574 " pdb=" CB THR A 574 " pdb=" OG1 THR A 574 " ideal model delta sigma weight residual 109.60 97.59 12.01 1.50e+00 4.44e-01 6.42e+01 angle pdb=" CA PHE B 571 " pdb=" CB PHE B 571 " pdb=" CG PHE B 571 " ideal model delta sigma weight residual 113.80 106.66 7.14 1.00e+00 1.00e+00 5.10e+01 angle pdb=" CA PHE A 571 " pdb=" CB PHE A 571 " pdb=" CG PHE A 571 " ideal model delta sigma weight residual 113.80 106.71 7.09 1.00e+00 1.00e+00 5.03e+01 angle pdb=" C SER B 578 " pdb=" N ILE B 579 " pdb=" CA ILE B 579 " ideal model delta sigma weight residual 120.64 109.78 10.86 1.66e+00 3.63e-01 4.28e+01 ... (remaining 9475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 3901 35.79 - 71.58: 164 71.58 - 107.38: 17 107.38 - 143.17: 0 143.17 - 178.96: 2 Dihedral angle restraints: 4084 sinusoidal: 1744 harmonic: 2340 Sorted by residual: dihedral pdb=" CD ARG A 273 " pdb=" NE ARG A 273 " pdb=" CZ ARG A 273 " pdb=" NH1 ARG A 273 " ideal model delta sinusoidal sigma weight residual 0.00 -87.77 87.77 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" N GLN A 576 " pdb=" C GLN A 576 " pdb=" CA GLN A 576 " pdb=" CB GLN A 576 " ideal model delta harmonic sigma weight residual 122.80 142.69 -19.89 0 2.50e+00 1.60e-01 6.33e+01 dihedral pdb=" C GLN A 576 " pdb=" N GLN A 576 " pdb=" CA GLN A 576 " pdb=" CB GLN A 576 " ideal model delta harmonic sigma weight residual -122.60 -141.50 18.90 0 2.50e+00 1.60e-01 5.71e+01 ... (remaining 4081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 994 0.155 - 0.310: 30 0.310 - 0.465: 7 0.465 - 0.621: 2 0.621 - 0.776: 1 Chirality restraints: 1034 Sorted by residual: chirality pdb=" CA GLN A 576 " pdb=" N GLN A 576 " pdb=" C GLN A 576 " pdb=" CB GLN A 576 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" CA ASP A 409 " pdb=" N ASP A 409 " pdb=" C ASP A 409 " pdb=" CB ASP A 409 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" CA ASP B 409 " pdb=" N ASP B 409 " pdb=" C ASP B 409 " pdb=" CB ASP B 409 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.09e+00 ... (remaining 1031 not shown) Planarity restraints: 1134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 273 " -1.098 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG A 273 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 273 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 273 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 273 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 273 " 0.927 9.50e-02 1.11e+02 4.16e-01 1.05e+02 pdb=" NE ARG B 273 " -0.055 2.00e-02 2.50e+03 pdb=" CZ ARG B 273 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 273 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 273 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 572 " 0.021 2.00e-02 2.50e+03 4.53e-02 2.05e+01 pdb=" C ALA B 572 " -0.078 2.00e-02 2.50e+03 pdb=" O ALA B 572 " 0.030 2.00e-02 2.50e+03 pdb=" N TRP B 573 " 0.027 2.00e-02 2.50e+03 ... (remaining 1131 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1558 2.77 - 3.30: 6749 3.30 - 3.83: 10830 3.83 - 4.37: 12478 4.37 - 4.90: 21205 Nonbonded interactions: 52820 Sorted by model distance: nonbonded pdb=" O PHE A 571 " pdb=" CD1 TRP A 573 " model vdw 2.236 3.260 nonbonded pdb=" O PHE B 571 " pdb=" CD1 TRP B 573 " model vdw 2.237 3.260 nonbonded pdb=" O ARG A 270 " pdb=" OD2 ASP A 409 " model vdw 2.248 3.040 nonbonded pdb=" O ARG B 270 " pdb=" OD2 ASP B 409 " model vdw 2.258 3.040 nonbonded pdb=" OG1 THR A 363 " pdb=" OG1 THR A 365 " model vdw 2.262 3.040 ... (remaining 52815 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.260 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 : 0.010 0.110 6976 Z= 0.608 Angle : 1.102 13.761 9480 Z= 0.691 Chirality : 0.072 0.776 1034 Planarity : 0.020 0.492 1134 Dihedral : 19.127 178.959 2576 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.31 % Favored : 89.44 % Rotamer: Outliers : 8.66 % Allowed : 17.61 % Favored : 73.72 % Cbeta Deviations : 1.59 % 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: -3.04 (0.27), residues: 786 helix: -1.38 (0.19), residues: 556 sheet: None (None), residues: 0 loop : -3.36 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 573 HIS 0.007 0.001 HIS B 587 PHE 0.046 0.002 PHE A 571 TYR 0.011 0.001 TYR B 553 ARG 0.004 0.000 ARG A 624 Details of bonding type rmsd hydrogen bonds : bond 0.19017 ( 382) hydrogen bonds : angle 7.40109 ( 1134) covalent geometry : bond 0.01005 ( 6976) covalent geometry : angle 1.10194 ( 9480) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 123 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7678 (mp10) REVERT: A 413 MET cc_start: 0.8842 (ttp) cc_final: 0.8517 (ttp) REVERT: A 419 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8486 (pp) REVERT: A 452 GLN cc_start: 0.9248 (tm-30) cc_final: 0.8967 (tp-100) REVERT: B 314 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7771 (mp10) REVERT: B 318 GLU cc_start: 0.8202 (tt0) cc_final: 0.7906 (tt0) REVERT: B 413 MET cc_start: 0.8846 (ttp) cc_final: 0.8521 (ttp) REVERT: B 419 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8496 (pp) REVERT: B 452 GLN cc_start: 0.9251 (tm-30) cc_final: 0.8986 (tp-100) outliers start: 61 outliers final: 38 residues processed: 171 average time/residue: 0.1679 time to fit residues: 39.0127 Evaluate side-chains 158 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 116 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 506 ASP Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 626 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 298 ASN A 306 ASN A 315 HIS ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS A 576 GLN A 587 HIS B 294 GLN B 298 ASN B 306 ASN B 315 HIS ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.139208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105337 restraints weight = 10407.486| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.02 r_work: 0.3122 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6976 Z= 0.195 Angle : 0.627 6.706 9480 Z= 0.328 Chirality : 0.043 0.140 1034 Planarity : 0.005 0.041 1134 Dihedral : 15.876 173.871 1175 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.40 % Favored : 91.35 % Rotamer: Outliers : 7.81 % Allowed : 18.18 % Favored : 74.01 % 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: -0.78 (0.30), residues: 786 helix: 0.46 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -2.87 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 266 HIS 0.014 0.001 HIS B 504 PHE 0.027 0.002 PHE A 546 TYR 0.023 0.002 TYR A 553 ARG 0.006 0.001 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.06103 ( 382) hydrogen bonds : angle 4.54869 ( 1134) covalent geometry : bond 0.00439 ( 6976) covalent geometry : angle 0.62724 ( 9480) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 117 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 ASN cc_start: 0.8235 (t0) cc_final: 0.7987 (t0) REVERT: A 413 MET cc_start: 0.8969 (ttp) cc_final: 0.8661 (ttp) REVERT: A 419 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8623 (pp) REVERT: A 452 GLN cc_start: 0.9287 (tm-30) cc_final: 0.8911 (tp-100) REVERT: A 467 TYR cc_start: 0.8880 (t80) cc_final: 0.8597 (t80) REVERT: A 517 PHE cc_start: 0.8370 (m-10) cc_final: 0.7988 (m-10) REVERT: A 519 ILE cc_start: 0.8907 (mm) cc_final: 0.8572 (mm) REVERT: A 523 CYS cc_start: 0.9294 (m) cc_final: 0.9042 (m) REVERT: A 548 ARG cc_start: 0.8905 (mtm110) cc_final: 0.8540 (mtm110) REVERT: A 600 GLU cc_start: 0.8640 (tp30) cc_final: 0.8401 (tp30) REVERT: B 306 ASN cc_start: 0.8257 (t0) cc_final: 0.8018 (t0) REVERT: B 318 GLU cc_start: 0.8527 (tt0) cc_final: 0.8155 (tt0) REVERT: B 413 MET cc_start: 0.8957 (ttp) cc_final: 0.8641 (ttp) REVERT: B 419 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8647 (pp) REVERT: B 452 GLN cc_start: 0.9297 (tm-30) cc_final: 0.8915 (tp-100) REVERT: B 467 TYR cc_start: 0.8882 (t80) cc_final: 0.8597 (t80) REVERT: B 517 PHE cc_start: 0.8377 (m-10) cc_final: 0.7989 (m-10) REVERT: B 519 ILE cc_start: 0.8889 (mm) cc_final: 0.8569 (mm) REVERT: B 523 CYS cc_start: 0.9287 (m) cc_final: 0.9041 (m) REVERT: B 548 ARG cc_start: 0.8909 (mtm110) cc_final: 0.8533 (mtm110) outliers start: 55 outliers final: 42 residues processed: 152 average time/residue: 0.1606 time to fit residues: 33.8155 Evaluate side-chains 156 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 112 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 626 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 22 optimal weight: 0.0370 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.140821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108419 restraints weight = 10417.437| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.96 r_work: 0.3135 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6976 Z= 0.143 Angle : 0.557 5.673 9480 Z= 0.290 Chirality : 0.041 0.132 1034 Planarity : 0.004 0.039 1134 Dihedral : 13.357 153.682 1148 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.27 % Favored : 91.48 % Rotamer: Outliers : 6.82 % Allowed : 20.03 % Favored : 73.15 % 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: -0.02 (0.31), residues: 786 helix: 1.15 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -2.89 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 266 HIS 0.009 0.001 HIS A 499 PHE 0.020 0.001 PHE B 511 TYR 0.016 0.001 TYR A 553 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.05348 ( 382) hydrogen bonds : angle 4.21358 ( 1134) covalent geometry : bond 0.00321 ( 6976) covalent geometry : angle 0.55741 ( 9480) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 115 time to evaluate : 0.699 Fit side-chains REVERT: A 306 ASN cc_start: 0.8070 (t0) cc_final: 0.7765 (t0) REVERT: A 314 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7835 (mt0) REVERT: A 413 MET cc_start: 0.8916 (ttp) cc_final: 0.8614 (ttp) REVERT: A 419 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8670 (pp) REVERT: A 452 GLN cc_start: 0.9287 (tm-30) cc_final: 0.8894 (tp-100) REVERT: A 504 HIS cc_start: 0.6010 (OUTLIER) cc_final: 0.5158 (p-80) REVERT: A 517 PHE cc_start: 0.8401 (m-10) cc_final: 0.7947 (m-80) REVERT: A 519 ILE cc_start: 0.8925 (mm) cc_final: 0.8702 (mm) REVERT: A 548 ARG cc_start: 0.8906 (mtm110) cc_final: 0.8487 (mtm110) REVERT: A 622 GLU cc_start: 0.8727 (mp0) cc_final: 0.8521 (mp0) REVERT: B 306 ASN cc_start: 0.8124 (t0) cc_final: 0.7834 (t0) REVERT: B 314 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7823 (mt0) REVERT: B 413 MET cc_start: 0.8900 (ttp) cc_final: 0.8626 (ttp) REVERT: B 419 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8694 (pp) REVERT: B 452 GLN cc_start: 0.9281 (tm-30) cc_final: 0.8882 (tp-100) REVERT: B 517 PHE cc_start: 0.8400 (m-10) cc_final: 0.8124 (m-80) REVERT: B 519 ILE cc_start: 0.8896 (mm) cc_final: 0.8666 (mm) REVERT: B 548 ARG cc_start: 0.8891 (mtm110) cc_final: 0.8469 (mtm110) REVERT: B 622 GLU cc_start: 0.8700 (mp0) cc_final: 0.8478 (mp0) outliers start: 48 outliers final: 33 residues processed: 144 average time/residue: 0.1646 time to fit residues: 32.4514 Evaluate side-chains 143 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 35 optimal weight: 0.0170 chunk 31 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.142676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.109668 restraints weight = 10431.886| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.00 r_work: 0.3140 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6976 Z= 0.136 Angle : 0.532 5.603 9480 Z= 0.276 Chirality : 0.041 0.236 1034 Planarity : 0.004 0.039 1134 Dihedral : 12.221 136.433 1135 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.02 % Favored : 91.73 % Rotamer: Outliers : 7.10 % Allowed : 20.60 % Favored : 72.30 % 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: 0.32 (0.31), residues: 786 helix: 1.43 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -2.84 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 266 HIS 0.003 0.001 HIS B 476 PHE 0.017 0.001 PHE A 386 TYR 0.015 0.001 TYR B 368 ARG 0.003 0.000 ARG B 273 Details of bonding type rmsd hydrogen bonds : bond 0.04882 ( 382) hydrogen bonds : angle 4.08751 ( 1134) covalent geometry : bond 0.00307 ( 6976) covalent geometry : angle 0.53243 ( 9480) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 132 time to evaluate : 0.736 Fit side-chains REVERT: A 306 ASN cc_start: 0.8101 (t0) cc_final: 0.7738 (t0) REVERT: A 314 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7850 (mt0) REVERT: A 413 MET cc_start: 0.8929 (ttp) cc_final: 0.8656 (ttp) REVERT: A 419 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8704 (pp) REVERT: A 452 GLN cc_start: 0.9242 (tm-30) cc_final: 0.8907 (tp-100) REVERT: A 467 TYR cc_start: 0.8851 (t80) cc_final: 0.8607 (t80) REVERT: A 504 HIS cc_start: 0.5921 (OUTLIER) cc_final: 0.5156 (p-80) REVERT: A 517 PHE cc_start: 0.8321 (m-10) cc_final: 0.8058 (m-80) REVERT: A 519 ILE cc_start: 0.8953 (mm) cc_final: 0.8619 (mm) REVERT: A 523 CYS cc_start: 0.9372 (m) cc_final: 0.9151 (m) REVERT: A 548 ARG cc_start: 0.8958 (mtm110) cc_final: 0.8545 (mtm110) REVERT: B 314 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7826 (mt0) REVERT: B 419 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8718 (pp) REVERT: B 452 GLN cc_start: 0.9236 (tm-30) cc_final: 0.8900 (tp-100) REVERT: B 467 TYR cc_start: 0.8855 (t80) cc_final: 0.8607 (t80) REVERT: B 517 PHE cc_start: 0.8347 (m-10) cc_final: 0.8085 (m-80) REVERT: B 519 ILE cc_start: 0.8903 (mm) cc_final: 0.8679 (mm) outliers start: 50 outliers final: 30 residues processed: 165 average time/residue: 0.1559 time to fit residues: 35.4897 Evaluate side-chains 141 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 3 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 0.0050 chunk 50 optimal weight: 0.0670 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.4534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.143927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.110455 restraints weight = 10277.418| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.06 r_work: 0.3172 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6976 Z= 0.125 Angle : 0.536 7.124 9480 Z= 0.277 Chirality : 0.041 0.228 1034 Planarity : 0.004 0.039 1134 Dihedral : 11.585 127.951 1129 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 7.39 % Allowed : 20.31 % Favored : 72.30 % 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: 0.52 (0.31), residues: 786 helix: 1.58 (0.23), residues: 548 sheet: None (None), residues: 0 loop : -2.76 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 266 HIS 0.016 0.001 HIS A 499 PHE 0.016 0.001 PHE B 386 TYR 0.016 0.001 TYR B 368 ARG 0.006 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 382) hydrogen bonds : angle 3.98098 ( 1134) covalent geometry : bond 0.00276 ( 6976) covalent geometry : angle 0.53577 ( 9480) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 109 time to evaluate : 0.669 Fit side-chains REVERT: A 314 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7817 (mt0) REVERT: A 364 LYS cc_start: 0.9212 (mppt) cc_final: 0.8952 (mmtp) REVERT: A 413 MET cc_start: 0.8916 (ttp) cc_final: 0.8652 (ttp) REVERT: A 419 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8676 (pp) REVERT: A 467 TYR cc_start: 0.8850 (t80) cc_final: 0.8471 (t80) REVERT: A 504 HIS cc_start: 0.5867 (OUTLIER) cc_final: 0.4995 (p-80) REVERT: A 517 PHE cc_start: 0.8318 (m-10) cc_final: 0.7942 (m-80) REVERT: A 519 ILE cc_start: 0.8937 (mm) cc_final: 0.8696 (mm) REVERT: B 314 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7804 (mt0) REVERT: B 364 LYS cc_start: 0.9211 (mppt) cc_final: 0.8951 (mmtp) REVERT: B 409 ASP cc_start: 0.7909 (m-30) cc_final: 0.7685 (m-30) REVERT: B 419 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8689 (pp) REVERT: B 467 TYR cc_start: 0.8857 (t80) cc_final: 0.8469 (t80) REVERT: B 517 PHE cc_start: 0.8354 (m-10) cc_final: 0.7970 (m-80) REVERT: B 519 ILE cc_start: 0.8923 (mm) cc_final: 0.8597 (mm) REVERT: B 523 CYS cc_start: 0.9357 (m) cc_final: 0.9153 (m) REVERT: B 548 ARG cc_start: 0.8930 (mtm110) cc_final: 0.8693 (mtm110) outliers start: 52 outliers final: 34 residues processed: 146 average time/residue: 0.1565 time to fit residues: 31.5862 Evaluate side-chains 148 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.143787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.110435 restraints weight = 10212.141| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.02 r_work: 0.3164 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6976 Z= 0.133 Angle : 0.536 6.629 9480 Z= 0.279 Chirality : 0.042 0.225 1034 Planarity : 0.004 0.039 1134 Dihedral : 11.162 120.295 1128 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.38 % Favored : 92.37 % Rotamer: Outliers : 7.53 % Allowed : 20.17 % Favored : 72.30 % 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: 0.55 (0.31), residues: 786 helix: 1.59 (0.23), residues: 548 sheet: None (None), residues: 0 loop : -2.70 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 266 HIS 0.011 0.001 HIS A 499 PHE 0.016 0.001 PHE A 386 TYR 0.018 0.001 TYR A 368 ARG 0.003 0.000 ARG A 570 Details of bonding type rmsd hydrogen bonds : bond 0.04473 ( 382) hydrogen bonds : angle 3.94334 ( 1134) covalent geometry : bond 0.00311 ( 6976) covalent geometry : angle 0.53643 ( 9480) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 116 time to evaluate : 0.737 Fit side-chains REVERT: A 314 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7807 (mt0) REVERT: A 364 LYS cc_start: 0.9209 (mppt) cc_final: 0.8950 (mmtp) REVERT: A 419 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8685 (pp) REVERT: A 467 TYR cc_start: 0.8846 (t80) cc_final: 0.8546 (t80) REVERT: A 504 HIS cc_start: 0.5778 (OUTLIER) cc_final: 0.4821 (p-80) REVERT: A 517 PHE cc_start: 0.8332 (m-10) cc_final: 0.7967 (m-80) REVERT: A 519 ILE cc_start: 0.8937 (mm) cc_final: 0.8610 (mm) REVERT: A 538 ASP cc_start: 0.8887 (t0) cc_final: 0.8450 (t0) REVERT: A 548 ARG cc_start: 0.8951 (mtm110) cc_final: 0.8729 (mtm110) REVERT: A 575 ILE cc_start: 0.8639 (mm) cc_final: 0.8414 (tt) REVERT: B 314 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7784 (mt0) REVERT: B 364 LYS cc_start: 0.9207 (mppt) cc_final: 0.8948 (mmtp) REVERT: B 419 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8717 (pp) REVERT: B 467 TYR cc_start: 0.8852 (t80) cc_final: 0.8552 (t80) REVERT: B 517 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: B 519 ILE cc_start: 0.8948 (mm) cc_final: 0.8723 (mm) REVERT: B 548 ARG cc_start: 0.8934 (mtm110) cc_final: 0.8667 (mtm110) outliers start: 53 outliers final: 39 residues processed: 152 average time/residue: 0.1593 time to fit residues: 33.8154 Evaluate side-chains 164 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 119 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.143224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.109612 restraints weight = 10242.975| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.06 r_work: 0.3153 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6976 Z= 0.149 Angle : 0.541 6.463 9480 Z= 0.282 Chirality : 0.042 0.255 1034 Planarity : 0.004 0.039 1134 Dihedral : 10.857 112.780 1128 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.51 % Favored : 92.24 % Rotamer: Outliers : 7.67 % Allowed : 20.60 % Favored : 71.73 % 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: 0.60 (0.31), residues: 786 helix: 1.61 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -2.67 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 266 HIS 0.004 0.001 HIS B 476 PHE 0.016 0.001 PHE B 386 TYR 0.018 0.001 TYR A 368 ARG 0.003 0.000 ARG A 570 Details of bonding type rmsd hydrogen bonds : bond 0.04547 ( 382) hydrogen bonds : angle 3.90621 ( 1134) covalent geometry : bond 0.00354 ( 6976) covalent geometry : angle 0.54120 ( 9480) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 117 time to evaluate : 0.740 Fit side-chains REVERT: A 314 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7792 (mt0) REVERT: A 364 LYS cc_start: 0.9184 (mppt) cc_final: 0.8908 (mmtp) REVERT: A 467 TYR cc_start: 0.8860 (t80) cc_final: 0.8608 (t80) REVERT: A 504 HIS cc_start: 0.5859 (OUTLIER) cc_final: 0.4828 (p-80) REVERT: A 517 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7987 (m-80) REVERT: A 523 CYS cc_start: 0.9463 (m) cc_final: 0.8954 (m) REVERT: A 548 ARG cc_start: 0.8982 (mtm110) cc_final: 0.8714 (mtm110) REVERT: B 314 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7790 (mt0) REVERT: B 364 LYS cc_start: 0.9214 (mppt) cc_final: 0.8950 (mmtp) REVERT: B 419 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8714 (pp) REVERT: B 467 TYR cc_start: 0.8860 (t80) cc_final: 0.8616 (t80) REVERT: B 517 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: B 519 ILE cc_start: 0.8961 (mm) cc_final: 0.8642 (mm) REVERT: B 538 ASP cc_start: 0.8877 (t0) cc_final: 0.8437 (t0) REVERT: B 548 ARG cc_start: 0.8958 (mtm110) cc_final: 0.8662 (mtm110) outliers start: 54 outliers final: 41 residues processed: 153 average time/residue: 0.1545 time to fit residues: 32.9072 Evaluate side-chains 158 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 111 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 0.0060 chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN A 499 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.144651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.111179 restraints weight = 10126.760| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.03 r_work: 0.3176 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6976 Z= 0.129 Angle : 0.530 6.342 9480 Z= 0.277 Chirality : 0.042 0.245 1034 Planarity : 0.004 0.039 1134 Dihedral : 10.458 103.847 1128 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.25 % Favored : 92.49 % Rotamer: Outliers : 7.10 % Allowed : 21.31 % Favored : 71.59 % 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: 0.73 (0.31), residues: 786 helix: 1.64 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -2.55 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 573 HIS 0.004 0.001 HIS A 499 PHE 0.017 0.001 PHE A 386 TYR 0.017 0.001 TYR A 368 ARG 0.003 0.000 ARG B 570 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 382) hydrogen bonds : angle 3.87738 ( 1134) covalent geometry : bond 0.00295 ( 6976) covalent geometry : angle 0.53032 ( 9480) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 121 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7775 (mt0) REVERT: A 364 LYS cc_start: 0.9176 (mppt) cc_final: 0.8900 (mmtp) REVERT: A 517 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7920 (m-80) REVERT: A 523 CYS cc_start: 0.9449 (m) cc_final: 0.8945 (m) REVERT: A 538 ASP cc_start: 0.8841 (t0) cc_final: 0.8408 (t0) REVERT: A 548 ARG cc_start: 0.8957 (mtm110) cc_final: 0.8701 (mtm110) REVERT: B 314 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7797 (mt0) REVERT: B 364 LYS cc_start: 0.9207 (mppt) cc_final: 0.8941 (mmtp) REVERT: B 517 PHE cc_start: 0.8353 (m-10) cc_final: 0.7969 (m-80) REVERT: B 523 CYS cc_start: 0.9455 (m) cc_final: 0.8947 (m) REVERT: B 548 ARG cc_start: 0.8956 (mtm110) cc_final: 0.8688 (mtm110) outliers start: 50 outliers final: 38 residues processed: 153 average time/residue: 0.1521 time to fit residues: 32.4196 Evaluate side-chains 161 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 73 optimal weight: 0.1980 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 499 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.145246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.111681 restraints weight = 10172.520| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.04 r_work: 0.3182 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6976 Z= 0.130 Angle : 0.535 8.087 9480 Z= 0.280 Chirality : 0.042 0.233 1034 Planarity : 0.004 0.039 1134 Dihedral : 10.114 96.667 1126 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.51 % Favored : 92.24 % Rotamer: Outliers : 6.53 % Allowed : 21.88 % Favored : 71.59 % 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 (0.31), residues: 786 helix: 1.65 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -2.48 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 573 HIS 0.004 0.001 HIS A 499 PHE 0.017 0.001 PHE B 386 TYR 0.035 0.002 TYR A 467 ARG 0.003 0.000 ARG B 570 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 382) hydrogen bonds : angle 3.85843 ( 1134) covalent geometry : bond 0.00300 ( 6976) covalent geometry : angle 0.53544 ( 9480) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7772 (mt0) REVERT: A 364 LYS cc_start: 0.9176 (mppt) cc_final: 0.8898 (mmtp) REVERT: A 467 TYR cc_start: 0.8837 (t80) cc_final: 0.8585 (t80) REVERT: A 517 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7970 (m-80) REVERT: A 538 ASP cc_start: 0.8829 (t0) cc_final: 0.8398 (t0) REVERT: A 548 ARG cc_start: 0.8966 (mtm110) cc_final: 0.8727 (mtm110) REVERT: B 314 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7782 (mt0) REVERT: B 364 LYS cc_start: 0.9205 (mppt) cc_final: 0.8932 (mmtp) REVERT: B 467 TYR cc_start: 0.8853 (t80) cc_final: 0.8572 (t80) REVERT: B 517 PHE cc_start: 0.8314 (m-10) cc_final: 0.7963 (m-80) REVERT: B 523 CYS cc_start: 0.9446 (m) cc_final: 0.8956 (m) REVERT: B 548 ARG cc_start: 0.8960 (mtm110) cc_final: 0.8699 (mtm110) outliers start: 46 outliers final: 36 residues processed: 151 average time/residue: 0.1602 time to fit residues: 33.5873 Evaluate side-chains 157 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.144651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.110771 restraints weight = 10222.436| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.06 r_work: 0.3172 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6976 Z= 0.139 Angle : 0.549 10.117 9480 Z= 0.286 Chirality : 0.043 0.227 1034 Planarity : 0.004 0.039 1134 Dihedral : 9.999 91.742 1126 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.25 % Favored : 92.49 % Rotamer: Outliers : 5.82 % Allowed : 22.30 % Favored : 71.88 % 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 (0.31), residues: 786 helix: 1.65 (0.22), residues: 558 sheet: None (None), residues: 0 loop : -2.52 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 528 HIS 0.003 0.001 HIS A 616 PHE 0.016 0.001 PHE A 386 TYR 0.031 0.002 TYR A 467 ARG 0.003 0.000 ARG A 502 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 382) hydrogen bonds : angle 3.82136 ( 1134) covalent geometry : bond 0.00329 ( 6976) covalent geometry : angle 0.54932 ( 9480) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.772 Fit side-chains REVERT: A 314 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7787 (mt0) REVERT: A 364 LYS cc_start: 0.9180 (mppt) cc_final: 0.8902 (mmtp) REVERT: A 467 TYR cc_start: 0.8853 (t80) cc_final: 0.8598 (t80) REVERT: A 477 LEU cc_start: 0.8989 (mm) cc_final: 0.8720 (mm) REVERT: A 504 HIS cc_start: 0.5806 (OUTLIER) cc_final: 0.4826 (p-80) REVERT: A 517 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7977 (m-80) REVERT: A 538 ASP cc_start: 0.8830 (t0) cc_final: 0.8398 (t0) REVERT: A 548 ARG cc_start: 0.8981 (mtm110) cc_final: 0.8736 (mtm110) REVERT: A 555 GLN cc_start: 0.8530 (tp40) cc_final: 0.8293 (mm110) REVERT: B 314 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7771 (mt0) REVERT: B 364 LYS cc_start: 0.9210 (mppt) cc_final: 0.8935 (mmtp) REVERT: B 467 TYR cc_start: 0.8853 (t80) cc_final: 0.8601 (t80) REVERT: B 477 LEU cc_start: 0.8955 (mm) cc_final: 0.8676 (mm) REVERT: B 517 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: B 548 ARG cc_start: 0.8982 (mtm110) cc_final: 0.8720 (mtm110) outliers start: 41 outliers final: 36 residues processed: 148 average time/residue: 0.1583 time to fit residues: 32.5905 Evaluate side-chains 162 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.0020 chunk 11 optimal weight: 0.0770 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 overall best weight: 0.3546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.146478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.112865 restraints weight = 10150.731| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.07 r_work: 0.3198 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6976 Z= 0.120 Angle : 0.536 7.864 9480 Z= 0.281 Chirality : 0.042 0.221 1034 Planarity : 0.004 0.038 1134 Dihedral : 9.757 87.011 1126 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 5.82 % Allowed : 22.59 % Favored : 71.59 % 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 (0.32), residues: 786 helix: 1.77 (0.23), residues: 554 sheet: None (None), residues: 0 loop : -2.38 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 528 HIS 0.006 0.001 HIS A 499 PHE 0.017 0.001 PHE B 386 TYR 0.028 0.001 TYR A 467 ARG 0.004 0.000 ARG B 465 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 382) hydrogen bonds : angle 3.81244 ( 1134) covalent geometry : bond 0.00269 ( 6976) covalent geometry : angle 0.53604 ( 9480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3445.51 seconds wall clock time: 59 minutes 48.27 seconds (3588.27 seconds total)