Starting phenix.real_space_refine on Wed Sep 17 07:45:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j98_61255/09_2025/9j98_61255.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j98_61255/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9j98_61255/09_2025/9j98_61255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j98_61255/09_2025/9j98_61255.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j98_61255/09_2025/9j98_61255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j98_61255/09_2025/9j98_61255.map" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.56, per 1000 atoms: 0.23 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: 0.61 Conformation dependent library (CDL) restraints added in 322.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.14 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: 0.93 Time building geometry restraints manager: 0.75 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: 0.01 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: 1.120 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.980 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.410 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 624 TYR 0.011 0.001 TYR B 553 PHE 0.046 0.002 PHE A 571 TRP 0.046 0.002 TRP B 573 HIS 0.007 0.001 HIS B 587 Details of bonding type rmsd covalent geometry : bond 0.01005 ( 6976) covalent geometry : angle 1.10194 ( 9480) hydrogen bonds : bond 0.19017 ( 382) hydrogen bonds : angle 7.40109 ( 1134) *********************** 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 : 0.283 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: 0.0747 time to fit residues: 17.5585 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 : 0.279 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 499 HIS A 576 GLN A 587 HIS B 294 GLN B 298 ASN B 315 HIS B 587 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.140543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106898 restraints weight = 10544.039| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.05 r_work: 0.3120 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6976 Z= 0.163 Angle : 0.609 6.761 9480 Z= 0.320 Chirality : 0.043 0.134 1034 Planarity : 0.005 0.050 1134 Dihedral : 15.843 175.008 1175 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.14 % Favored : 91.60 % Rotamer: Outliers : 7.39 % Allowed : 18.89 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.30), residues: 786 helix: 0.48 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -2.98 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 273 TYR 0.022 0.002 TYR A 553 PHE 0.025 0.002 PHE A 546 TRP 0.006 0.001 TRP B 514 HIS 0.012 0.001 HIS B 504 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 6976) covalent geometry : angle 0.60920 ( 9480) hydrogen bonds : bond 0.05962 ( 382) hydrogen bonds : angle 4.52686 ( 1134) *********************** 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 168 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 116 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 ASN cc_start: 0.8158 (t0) cc_final: 0.7890 (t0) REVERT: A 413 MET cc_start: 0.8948 (ttp) cc_final: 0.8627 (ttp) REVERT: A 419 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8628 (pp) REVERT: A 452 GLN cc_start: 0.9286 (tm-30) cc_final: 0.8964 (tp-100) REVERT: A 467 TYR cc_start: 0.8905 (t80) cc_final: 0.8595 (t80) REVERT: A 517 PHE cc_start: 0.8314 (m-10) cc_final: 0.7980 (m-10) REVERT: A 519 ILE cc_start: 0.8920 (mm) cc_final: 0.8592 (mm) REVERT: A 523 CYS cc_start: 0.9298 (m) cc_final: 0.9086 (m) REVERT: A 548 ARG cc_start: 0.8855 (mtm110) cc_final: 0.8524 (mtm110) REVERT: A 573 TRP cc_start: 0.8115 (p-90) cc_final: 0.7597 (p-90) REVERT: B 318 GLU cc_start: 0.8373 (tt0) cc_final: 0.7964 (tt0) REVERT: B 413 MET cc_start: 0.8946 (ttp) cc_final: 0.8617 (ttp) REVERT: B 419 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8657 (pp) REVERT: B 452 GLN cc_start: 0.9304 (tm-30) cc_final: 0.8968 (tp-100) REVERT: B 467 TYR cc_start: 0.8896 (t80) cc_final: 0.8587 (t80) REVERT: B 517 PHE cc_start: 0.8344 (m-10) cc_final: 0.7862 (m-10) REVERT: B 519 ILE cc_start: 0.8874 (mm) cc_final: 0.8564 (mm) REVERT: B 523 CYS cc_start: 0.9278 (m) cc_final: 0.9071 (m) REVERT: B 548 ARG cc_start: 0.8863 (mtm110) cc_final: 0.8518 (mtm110) outliers start: 52 outliers final: 38 residues processed: 149 average time/residue: 0.0725 time to fit residues: 15.1992 Evaluate side-chains 146 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 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 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 0 optimal weight: 3.9990 chunk 8 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.141658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.109361 restraints weight = 10306.749| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.96 r_work: 0.3141 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6976 Z= 0.138 Angle : 0.552 5.807 9480 Z= 0.287 Chirality : 0.041 0.133 1034 Planarity : 0.004 0.039 1134 Dihedral : 13.305 155.979 1148 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.89 % Favored : 91.86 % Rotamer: Outliers : 6.39 % Allowed : 20.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.31), residues: 786 helix: 1.20 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -2.91 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.016 0.001 TYR A 553 PHE 0.020 0.001 PHE A 511 TRP 0.011 0.001 TRP A 266 HIS 0.011 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6976) covalent geometry : angle 0.55194 ( 9480) hydrogen bonds : bond 0.05203 ( 382) hydrogen bonds : angle 4.18158 ( 1134) *********************** 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 156 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 111 time to evaluate : 0.255 Fit side-chains REVERT: A 306 ASN cc_start: 0.8056 (t0) cc_final: 0.7739 (t0) REVERT: A 314 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7798 (mt0) REVERT: A 419 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8666 (pp) REVERT: A 452 GLN cc_start: 0.9257 (tm-30) cc_final: 0.8958 (tp-100) REVERT: A 504 HIS cc_start: 0.5976 (OUTLIER) cc_final: 0.5133 (p-80) REVERT: A 517 PHE cc_start: 0.8391 (m-10) cc_final: 0.7920 (m-80) REVERT: A 519 ILE cc_start: 0.8911 (mm) cc_final: 0.8682 (mm) REVERT: A 548 ARG cc_start: 0.8869 (mtm110) cc_final: 0.8479 (mtm110) REVERT: A 622 GLU cc_start: 0.8718 (mp0) cc_final: 0.8511 (mp0) REVERT: B 314 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7825 (mp10) REVERT: B 419 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8702 (pp) REVERT: B 452 GLN cc_start: 0.9253 (tm-30) cc_final: 0.8950 (tp-100) REVERT: B 517 PHE cc_start: 0.8327 (m-10) cc_final: 0.8071 (m-80) REVERT: B 519 ILE cc_start: 0.8919 (mm) cc_final: 0.8695 (mm) REVERT: B 548 ARG cc_start: 0.8873 (mtm110) cc_final: 0.8472 (mtm110) REVERT: B 622 GLU cc_start: 0.8691 (mp0) cc_final: 0.8460 (mp0) outliers start: 45 outliers final: 29 residues processed: 138 average time/residue: 0.0790 time to fit residues: 15.0619 Evaluate side-chains 137 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 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 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 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 50 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 B 399 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.143020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.109802 restraints weight = 10383.540| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.01 r_work: 0.3140 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6976 Z= 0.138 Angle : 0.534 5.856 9480 Z= 0.276 Chirality : 0.041 0.235 1034 Planarity : 0.004 0.039 1134 Dihedral : 12.098 136.762 1131 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.14 % Favored : 91.60 % Rotamer: Outliers : 7.24 % Allowed : 19.74 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.31), residues: 786 helix: 1.44 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -2.84 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 273 TYR 0.016 0.001 TYR B 368 PHE 0.018 0.001 PHE A 386 TRP 0.010 0.001 TRP A 266 HIS 0.004 0.001 HIS B 504 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6976) covalent geometry : angle 0.53437 ( 9480) hydrogen bonds : bond 0.04872 ( 382) hydrogen bonds : angle 4.07825 ( 1134) *********************** 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 183 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 132 time to evaluate : 0.262 Fit side-chains REVERT: A 306 ASN cc_start: 0.8096 (t0) cc_final: 0.7722 (t0) REVERT: A 314 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7816 (mt0) REVERT: A 364 LYS cc_start: 0.9199 (mppt) cc_final: 0.8949 (mmtp) REVERT: A 419 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8668 (pp) REVERT: A 452 GLN cc_start: 0.9231 (tm-30) cc_final: 0.8895 (tp-100) REVERT: A 467 TYR cc_start: 0.8872 (t80) cc_final: 0.8597 (t80) REVERT: A 504 HIS cc_start: 0.5948 (OUTLIER) cc_final: 0.5206 (p-80) REVERT: A 517 PHE cc_start: 0.8310 (m-10) cc_final: 0.7973 (m-80) REVERT: A 519 ILE cc_start: 0.8963 (mm) cc_final: 0.8644 (mm) REVERT: A 523 CYS cc_start: 0.9381 (m) cc_final: 0.9149 (m) REVERT: A 548 ARG cc_start: 0.8951 (mtm110) cc_final: 0.8560 (mtm110) REVERT: B 314 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7834 (mp10) REVERT: B 419 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8684 (pp) REVERT: B 452 GLN cc_start: 0.9233 (tm-30) cc_final: 0.8890 (tp-100) REVERT: B 467 TYR cc_start: 0.8876 (t80) cc_final: 0.8597 (t80) REVERT: B 517 PHE cc_start: 0.8361 (m-10) cc_final: 0.8061 (m-80) REVERT: B 519 ILE cc_start: 0.8931 (mm) cc_final: 0.8679 (mm) REVERT: B 548 ARG cc_start: 0.8946 (mtm110) cc_final: 0.8548 (mtm110) REVERT: B 622 GLU cc_start: 0.8722 (mp0) cc_final: 0.8512 (mp0) outliers start: 51 outliers final: 29 residues processed: 166 average time/residue: 0.0770 time to fit residues: 17.7980 Evaluate side-chains 135 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 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 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 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 6 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 B 399 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.141732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.108050 restraints weight = 10352.129| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.04 r_work: 0.3132 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6976 Z= 0.158 Angle : 0.556 7.278 9480 Z= 0.285 Chirality : 0.042 0.250 1034 Planarity : 0.004 0.039 1134 Dihedral : 11.826 131.490 1129 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.76 % Favored : 91.98 % Rotamer: Outliers : 6.68 % Allowed : 21.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.31), residues: 786 helix: 1.51 (0.23), residues: 550 sheet: None (None), residues: 0 loop : -2.75 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.017 0.001 TYR B 368 PHE 0.015 0.001 PHE B 610 TRP 0.009 0.001 TRP A 266 HIS 0.008 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 6976) covalent geometry : angle 0.55601 ( 9480) hydrogen bonds : bond 0.04902 ( 382) hydrogen bonds : angle 4.00978 ( 1134) *********************** 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 163 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 116 time to evaluate : 0.265 Fit side-chains REVERT: A 314 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7845 (mp10) REVERT: A 364 LYS cc_start: 0.9217 (mppt) cc_final: 0.8958 (mmtp) REVERT: A 419 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8692 (pp) REVERT: A 452 GLN cc_start: 0.9245 (tm-30) cc_final: 0.8898 (tp-100) REVERT: A 467 TYR cc_start: 0.8873 (t80) cc_final: 0.8611 (t80) REVERT: A 504 HIS cc_start: 0.5907 (OUTLIER) cc_final: 0.4944 (p-80) REVERT: A 517 PHE cc_start: 0.8344 (m-10) cc_final: 0.7972 (m-80) REVERT: A 519 ILE cc_start: 0.8966 (mm) cc_final: 0.8738 (mm) REVERT: B 314 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7864 (mp10) REVERT: B 364 LYS cc_start: 0.9219 (mppt) cc_final: 0.8960 (mmtp) REVERT: B 409 ASP cc_start: 0.7875 (m-30) cc_final: 0.7669 (m-30) REVERT: B 419 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8698 (pp) REVERT: B 452 GLN cc_start: 0.9220 (tm-30) cc_final: 0.8868 (tp-100) REVERT: B 467 TYR cc_start: 0.8887 (t80) cc_final: 0.8625 (t80) REVERT: B 517 PHE cc_start: 0.8409 (m-10) cc_final: 0.8114 (m-80) REVERT: B 519 ILE cc_start: 0.8926 (mm) cc_final: 0.8694 (mm) REVERT: B 523 CYS cc_start: 0.9457 (m) cc_final: 0.9195 (m) outliers start: 47 outliers final: 35 residues processed: 149 average time/residue: 0.0719 time to fit residues: 15.0739 Evaluate side-chains 144 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 104 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 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 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 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 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 530 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 B 306 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.142509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.108970 restraints weight = 10357.758| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.05 r_work: 0.3149 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6976 Z= 0.139 Angle : 0.540 6.279 9480 Z= 0.279 Chirality : 0.042 0.222 1034 Planarity : 0.004 0.039 1134 Dihedral : 11.451 125.300 1128 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.89 % Favored : 91.86 % Rotamer: Outliers : 7.39 % Allowed : 21.45 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.32), residues: 786 helix: 1.59 (0.23), residues: 550 sheet: None (None), residues: 0 loop : -2.73 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 570 TYR 0.017 0.001 TYR B 368 PHE 0.016 0.001 PHE A 386 TRP 0.009 0.001 TRP A 266 HIS 0.009 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6976) covalent geometry : angle 0.54047 ( 9480) hydrogen bonds : bond 0.04665 ( 382) hydrogen bonds : angle 3.95024 ( 1134) *********************** 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 157 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 105 time to evaluate : 0.240 Fit side-chains REVERT: A 314 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7808 (mt0) REVERT: A 364 LYS cc_start: 0.9211 (mppt) cc_final: 0.8950 (mmtp) REVERT: A 419 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8692 (pp) REVERT: A 467 TYR cc_start: 0.8864 (t80) cc_final: 0.8595 (t80) REVERT: A 477 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8831 (mm) REVERT: A 504 HIS cc_start: 0.5852 (OUTLIER) cc_final: 0.4876 (p-80) REVERT: A 517 PHE cc_start: 0.8394 (m-10) cc_final: 0.8012 (m-80) REVERT: A 519 ILE cc_start: 0.8979 (mm) cc_final: 0.8659 (mm) REVERT: A 523 CYS cc_start: 0.9372 (m) cc_final: 0.9166 (m) REVERT: A 548 ARG cc_start: 0.8956 (mtm110) cc_final: 0.8718 (mtm110) REVERT: B 306 ASN cc_start: 0.8246 (t0) cc_final: 0.7960 (t0) REVERT: B 314 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7807 (mt0) REVERT: B 364 LYS cc_start: 0.9211 (mppt) cc_final: 0.8949 (mmtp) REVERT: B 419 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8704 (pp) REVERT: B 467 TYR cc_start: 0.8872 (t80) cc_final: 0.8595 (t80) REVERT: B 517 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.8057 (m-80) REVERT: B 519 ILE cc_start: 0.8971 (mm) cc_final: 0.8741 (mm) REVERT: B 523 CYS cc_start: 0.9459 (m) cc_final: 0.9189 (m) REVERT: B 548 ARG cc_start: 0.8957 (mtm110) cc_final: 0.8720 (mtm110) outliers start: 52 outliers final: 36 residues processed: 143 average time/residue: 0.0692 time to fit residues: 13.9050 Evaluate side-chains 154 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 111 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 314 GLN 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 477 LEU 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 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 311 LEU Chi-restraints excluded: chain B residue 314 GLN 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 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 508 MET Chi-restraints excluded: chain B residue 517 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 11 optimal weight: 0.0970 chunk 7 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.143746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.110277 restraints weight = 10175.298| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.01 r_work: 0.3188 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2508 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= 0.131 Angle : 0.539 6.139 9480 Z= 0.281 Chirality : 0.042 0.256 1034 Planarity : 0.004 0.039 1134 Dihedral : 10.959 117.228 1128 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.38 % Favored : 92.37 % Rotamer: Outliers : 7.24 % Allowed : 21.73 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.32), residues: 786 helix: 1.69 (0.23), residues: 546 sheet: None (None), residues: 0 loop : -2.72 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 570 TYR 0.019 0.001 TYR A 368 PHE 0.015 0.001 PHE B 610 TRP 0.009 0.001 TRP A 266 HIS 0.013 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6976) covalent geometry : angle 0.53930 ( 9480) hydrogen bonds : bond 0.04485 ( 382) hydrogen bonds : angle 3.91654 ( 1134) *********************** 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 170 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 119 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7859 (mp10) REVERT: A 364 LYS cc_start: 0.9170 (mppt) cc_final: 0.8900 (mmtp) REVERT: A 424 ASP cc_start: 0.7888 (p0) cc_final: 0.7672 (p0) REVERT: A 517 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8007 (m-80) REVERT: A 519 ILE cc_start: 0.9003 (mm) cc_final: 0.8645 (mm) REVERT: A 523 CYS cc_start: 0.9398 (m) cc_final: 0.9164 (m) REVERT: A 548 ARG cc_start: 0.8951 (mtm110) cc_final: 0.8696 (mtm110) REVERT: B 306 ASN cc_start: 0.8170 (t0) cc_final: 0.7854 (t0) REVERT: B 314 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7821 (mt0) REVERT: B 364 LYS cc_start: 0.9199 (mppt) cc_final: 0.8931 (mmtp) REVERT: B 419 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8686 (pp) REVERT: B 467 TYR cc_start: 0.8795 (t80) cc_final: 0.8583 (t80) REVERT: B 517 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8027 (m-80) REVERT: B 519 ILE cc_start: 0.9056 (mm) cc_final: 0.8839 (mm) REVERT: B 523 CYS cc_start: 0.9449 (m) cc_final: 0.9163 (m) REVERT: B 548 ARG cc_start: 0.8943 (mtm110) cc_final: 0.8683 (mtm110) outliers start: 51 outliers final: 37 residues processed: 153 average time/residue: 0.0651 time to fit residues: 13.9418 Evaluate side-chains 154 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 112 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 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 311 LEU 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 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 517 PHE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 547 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 24 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.144221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.110571 restraints weight = 10180.632| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.03 r_work: 0.3171 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2574 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= 0.132 Angle : 0.535 5.852 9480 Z= 0.279 Chirality : 0.042 0.238 1034 Planarity : 0.004 0.039 1134 Dihedral : 10.317 108.245 1126 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.25 % Favored : 92.49 % Rotamer: Outliers : 6.68 % Allowed : 22.02 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.32), residues: 786 helix: 1.70 (0.23), residues: 546 sheet: None (None), residues: 0 loop : -2.66 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 570 TYR 0.034 0.001 TYR A 467 PHE 0.017 0.001 PHE B 386 TRP 0.009 0.001 TRP A 266 HIS 0.004 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6976) covalent geometry : angle 0.53541 ( 9480) hydrogen bonds : bond 0.04374 ( 382) hydrogen bonds : angle 3.86843 ( 1134) *********************** 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 163 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 116 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: A 364 LYS cc_start: 0.9177 (mppt) cc_final: 0.8900 (mmtp) REVERT: A 467 TYR cc_start: 0.8835 (t80) cc_final: 0.8524 (t80) REVERT: A 517 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7995 (m-80) REVERT: A 519 ILE cc_start: 0.9006 (mm) cc_final: 0.8779 (mm) REVERT: A 548 ARG cc_start: 0.8948 (mtm110) cc_final: 0.8689 (mtm110) REVERT: B 306 ASN cc_start: 0.8139 (t0) cc_final: 0.7802 (t0) REVERT: B 314 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7770 (mt0) REVERT: B 364 LYS cc_start: 0.9181 (mppt) cc_final: 0.8904 (mmtp) REVERT: B 517 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.8047 (m-80) REVERT: B 519 ILE cc_start: 0.9040 (mm) cc_final: 0.8813 (mm) REVERT: B 523 CYS cc_start: 0.9448 (m) cc_final: 0.9156 (m) REVERT: B 548 ARG cc_start: 0.8940 (mtm110) cc_final: 0.8679 (mtm110) REVERT: B 555 GLN cc_start: 0.8517 (tp40) cc_final: 0.8234 (mm110) outliers start: 47 outliers final: 39 residues processed: 148 average time/residue: 0.0705 time to fit residues: 14.6762 Evaluate side-chains 150 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 107 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 311 LEU 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 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 517 PHE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 547 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 76 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 59 optimal weight: 0.0070 chunk 74 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.144757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.111067 restraints weight = 10233.682| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.05 r_work: 0.3180 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6976 Z= 0.129 Angle : 0.533 5.772 9480 Z= 0.278 Chirality : 0.042 0.225 1034 Planarity : 0.004 0.039 1134 Dihedral : 10.009 99.860 1126 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 6.39 % Allowed : 22.87 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.31), residues: 786 helix: 1.70 (0.23), residues: 554 sheet: None (None), residues: 0 loop : -2.53 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 502 TYR 0.027 0.002 TYR A 467 PHE 0.015 0.001 PHE B 610 TRP 0.011 0.001 TRP B 573 HIS 0.003 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6976) covalent geometry : angle 0.53255 ( 9480) hydrogen bonds : bond 0.04274 ( 382) hydrogen bonds : angle 3.84705 ( 1134) *********************** 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 160 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 115 time to evaluate : 0.277 Fit side-chains REVERT: A 314 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7811 (mt0) REVERT: A 364 LYS cc_start: 0.9172 (mppt) cc_final: 0.8895 (mmtp) REVERT: A 467 TYR cc_start: 0.8831 (t80) cc_final: 0.8543 (t80) REVERT: A 504 HIS cc_start: 0.5847 (OUTLIER) cc_final: 0.4922 (p-80) REVERT: A 517 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.8048 (m-80) REVERT: A 519 ILE cc_start: 0.8974 (mm) cc_final: 0.8627 (mm) REVERT: A 548 ARG cc_start: 0.8958 (mtm110) cc_final: 0.8720 (mtm110) REVERT: B 306 ASN cc_start: 0.8115 (t0) cc_final: 0.7777 (t0) REVERT: B 314 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7860 (mt0) REVERT: B 364 LYS cc_start: 0.9179 (mppt) cc_final: 0.8902 (mmtp) REVERT: B 467 TYR cc_start: 0.8847 (t80) cc_final: 0.8549 (t80) REVERT: B 517 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7952 (m-80) REVERT: B 519 ILE cc_start: 0.9035 (mm) cc_final: 0.8807 (mm) REVERT: B 523 CYS cc_start: 0.9462 (m) cc_final: 0.9189 (m) REVERT: B 548 ARG cc_start: 0.8951 (mtm110) cc_final: 0.8712 (mtm110) REVERT: B 555 GLN cc_start: 0.8541 (tp40) cc_final: 0.8250 (mm110) outliers start: 45 outliers final: 37 residues processed: 143 average time/residue: 0.0733 time to fit residues: 14.6116 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 : 0.237 ------------------------------------------------------------------------------- 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 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 311 LEU 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 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 517 PHE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 547 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 63 optimal weight: 0.4980 chunk 77 optimal weight: 0.0980 chunk 56 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 76 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.146088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.112454 restraints weight = 10171.919| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.05 r_work: 0.3194 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6976 Z= 0.123 Angle : 0.529 5.702 9480 Z= 0.278 Chirality : 0.042 0.221 1034 Planarity : 0.004 0.038 1134 Dihedral : 9.748 92.777 1126 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 5.82 % Allowed : 23.58 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.32), residues: 786 helix: 1.79 (0.23), residues: 554 sheet: None (None), residues: 0 loop : -2.48 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 502 TYR 0.025 0.001 TYR A 467 PHE 0.017 0.001 PHE B 386 TRP 0.011 0.001 TRP B 528 HIS 0.006 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6976) covalent geometry : angle 0.52919 ( 9480) hydrogen bonds : bond 0.04134 ( 382) hydrogen bonds : angle 3.79463 ( 1134) ********************** 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 158 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 0.255 Fit side-chains REVERT: A 314 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7812 (mt0) REVERT: A 364 LYS cc_start: 0.9170 (mppt) cc_final: 0.8891 (mmtp) REVERT: A 467 TYR cc_start: 0.8850 (t80) cc_final: 0.8595 (t80) REVERT: A 504 HIS cc_start: 0.5800 (OUTLIER) cc_final: 0.4846 (p-80) REVERT: A 517 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.8047 (m-80) REVERT: A 519 ILE cc_start: 0.8945 (mm) cc_final: 0.8721 (mm) REVERT: A 548 ARG cc_start: 0.8943 (mtm110) cc_final: 0.8724 (mtm110) REVERT: B 306 ASN cc_start: 0.8093 (t0) cc_final: 0.7733 (t0) REVERT: B 314 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: B 364 LYS cc_start: 0.9177 (mppt) cc_final: 0.8898 (mmtp) REVERT: B 467 TYR cc_start: 0.8861 (t80) cc_final: 0.8568 (t80) REVERT: B 513 LEU cc_start: 0.8971 (tp) cc_final: 0.8744 (tp) REVERT: B 517 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.8079 (m-80) REVERT: B 519 ILE cc_start: 0.9037 (mm) cc_final: 0.8808 (mm) REVERT: B 523 CYS cc_start: 0.9406 (m) cc_final: 0.9101 (m) REVERT: B 548 ARG cc_start: 0.8938 (mtm110) cc_final: 0.8718 (mtm110) REVERT: B 555 GLN cc_start: 0.8561 (tp40) cc_final: 0.8259 (mm110) outliers start: 41 outliers final: 34 residues processed: 142 average time/residue: 0.0736 time to fit residues: 14.5921 Evaluate side-chains 154 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 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 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 311 LEU 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 517 PHE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 547 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 53 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.145567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.111845 restraints weight = 10178.779| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.06 r_work: 0.3187 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6976 Z= 0.132 Angle : 0.542 7.174 9480 Z= 0.283 Chirality : 0.042 0.216 1034 Planarity : 0.004 0.039 1134 Dihedral : 9.671 88.414 1126 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.12 % Favored : 92.62 % Rotamer: Outliers : 5.97 % Allowed : 22.87 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.32), residues: 786 helix: 1.80 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -2.41 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 465 TYR 0.024 0.001 TYR A 467 PHE 0.016 0.001 PHE B 610 TRP 0.022 0.001 TRP A 528 HIS 0.003 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6976) covalent geometry : angle 0.54150 ( 9480) hydrogen bonds : bond 0.04161 ( 382) hydrogen bonds : angle 3.79794 ( 1134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1693.31 seconds wall clock time: 29 minutes 49.15 seconds (1789.15 seconds total)