Starting phenix.real_space_refine on Sat May 2 16:51:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ine_60704/05_2026/9ine_60704.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ine_60704/05_2026/9ine_60704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ine_60704/05_2026/9ine_60704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ine_60704/05_2026/9ine_60704.map" model { file = "/net/cci-nas-00/data/ceres_data/9ine_60704/05_2026/9ine_60704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ine_60704/05_2026/9ine_60704.cif" } resolution = 3.32 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= -0.000 sd= 0.016 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 8 5.49 5 S 32 5.16 5 C 5214 2.51 5 N 1078 2.21 5 O 1188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7520 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3333 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 385} Chain: "A" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3333 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 385} Chain: "B" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 474 Unusual residues: {'3PE': 4, 'ACD': 1, 'CLR': 7, 'LPE': 1, 'PLM': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "A" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 372 Unusual residues: {'3PE': 2, 'ACD': 1, 'CLR': 7, 'LPE': 1, 'PLM': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 1.90, per 1000 atoms: 0.25 Number of scatterers: 7520 At special positions: 0 Unit cell: (86.205, 114.119, 75.532, 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 8 15.00 O 1188 8.00 N 1078 7.00 C 5214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " distance=2.03 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 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: 0.67 Conformation dependent library (CDL) restraints added in 190.6 milliseconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1524 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 75.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 230 through 258 Processing helix chain 'B' and resid 265 through 296 removed outlier: 4.476A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 312 through 336 removed outlier: 3.524A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 360 removed outlier: 4.057A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 382 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 390 through 403 Processing helix chain 'B' and resid 403 through 419 removed outlier: 3.784A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 471 removed outlier: 3.580A pdb=" N ILE B 450 " --> pdb=" O GLY B 446 " (cutoff:3.500A) Proline residue: B 455 - end of helix removed outlier: 3.651A pdb=" N ARG B 459 " --> pdb=" O PRO B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 502 removed outlier: 4.333A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL B 478 " --> pdb=" O PHE B 474 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 488 " --> pdb=" O SER B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 4.098A pdb=" N ILE B 519 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE B 520 " --> pdb=" O VAL B 516 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N SER B 522 " --> pdb=" O TYR B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 4.380A pdb=" N GLY B 542 " --> pdb=" O LYS B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 578 removed outlier: 3.803A pdb=" N TYR B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 564 " --> pdb=" O TYR B 560 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 618 Proline residue: B 598 - end of helix removed outlier: 3.567A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 258 Processing helix chain 'A' and resid 265 through 296 removed outlier: 4.457A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 312 through 336 removed outlier: 3.527A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 360 removed outlier: 3.946A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 384 through 387 Processing helix chain 'A' and resid 390 through 403 Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.754A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 471 removed outlier: 3.768A pdb=" N ILE A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) Proline residue: A 455 - end of helix removed outlier: 3.999A pdb=" N ARG A 459 " --> pdb=" O PRO A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 502 removed outlier: 4.348A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 removed outlier: 4.091A pdb=" N ILE A 519 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE A 520 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N SER A 522 " --> pdb=" O TYR A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 4.438A pdb=" N GLY A 542 " --> pdb=" O LYS A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 578 removed outlier: 3.786A pdb=" N TYR A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 564 " --> pdb=" O TYR A 560 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 618 Proline residue: A 598 - end of helix removed outlier: 3.569A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1095 1.32 - 1.45: 2173 1.45 - 1.57: 4434 1.57 - 1.69: 18 1.69 - 1.81: 44 Bond restraints: 7764 Sorted by residual: bond pdb=" CA THR A 491 " pdb=" C THR A 491 " ideal model delta sigma weight residual 1.524 1.494 0.030 1.24e-02 6.50e+03 6.03e+00 bond pdb=" CA THR B 491 " pdb=" C THR B 491 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.24e-02 6.50e+03 5.25e+00 bond pdb=" O32 LPE B 810 " pdb=" P LPE B 810 " ideal model delta sigma weight residual 1.507 1.461 0.046 2.00e-02 2.50e+03 5.21e+00 bond pdb=" O32 LPE A 809 " pdb=" P LPE A 809 " ideal model delta sigma weight residual 1.507 1.462 0.045 2.00e-02 2.50e+03 5.08e+00 bond pdb=" C2 LPE A 809 " pdb=" O2H LPE A 809 " ideal model delta sigma weight residual 1.435 1.392 0.043 2.00e-02 2.50e+03 4.62e+00 ... (remaining 7759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.32: 10489 4.32 - 8.63: 36 8.63 - 12.95: 5 12.95 - 17.26: 0 17.26 - 21.58: 2 Bond angle restraints: 10532 Sorted by residual: angle pdb=" O31 LPE A 809 " pdb=" P LPE A 809 " pdb=" O32 LPE A 809 " ideal model delta sigma weight residual 122.76 101.18 21.58 3.00e+00 1.11e-01 5.17e+01 angle pdb=" O31 LPE B 810 " pdb=" P LPE B 810 " pdb=" O32 LPE B 810 " ideal model delta sigma weight residual 122.76 101.23 21.53 3.00e+00 1.11e-01 5.15e+01 angle pdb=" C TYR A 347 " pdb=" N PRO A 348 " pdb=" CA PRO A 348 " ideal model delta sigma weight residual 119.28 115.46 3.82 1.10e+00 8.26e-01 1.20e+01 angle pdb=" C THR A 491 " pdb=" CA THR A 491 " pdb=" CB THR A 491 " ideal model delta sigma weight residual 110.96 105.78 5.18 1.54e+00 4.22e-01 1.13e+01 angle pdb=" C1N LPE A 809 " pdb=" N LPE A 809 " pdb=" C2N LPE A 809 " ideal model delta sigma weight residual 109.60 118.98 -9.38 3.00e+00 1.11e-01 9.78e+00 ... (remaining 10527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.47: 4669 24.47 - 48.94: 510 48.94 - 73.41: 61 73.41 - 97.89: 0 97.89 - 122.36: 2 Dihedral angle restraints: 5242 sinusoidal: 2876 harmonic: 2366 Sorted by residual: dihedral pdb=" CB CYS B 415 " pdb=" SG CYS B 415 " pdb=" SG CYS B 440 " pdb=" CB CYS B 440 " ideal model delta sinusoidal sigma weight residual 93.00 154.50 -61.50 1 1.00e+01 1.00e-02 5.02e+01 dihedral pdb=" CB CYS A 415 " pdb=" SG CYS A 415 " pdb=" SG CYS A 440 " pdb=" CB CYS A 440 " ideal model delta sinusoidal sigma weight residual 93.00 154.01 -61.01 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CA PHE B 517 " pdb=" C PHE B 517 " pdb=" N TYR B 518 " pdb=" CA TYR B 518 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 5239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 923 0.050 - 0.100: 193 0.100 - 0.150: 25 0.150 - 0.201: 2 0.201 - 0.251: 1 Chirality restraints: 1144 Sorted by residual: chirality pdb=" CA TYR A 347 " pdb=" N TYR A 347 " pdb=" C TYR A 347 " pdb=" CB TYR A 347 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB ILE A 520 " pdb=" CA ILE A 520 " pdb=" CG1 ILE A 520 " pdb=" CG2 ILE A 520 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CB ILE B 520 " pdb=" CA ILE B 520 " pdb=" CG1 ILE B 520 " pdb=" CG2 ILE B 520 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.32e-01 ... (remaining 1141 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 574 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.08e+00 pdb=" C THR B 574 " 0.030 2.00e-02 2.50e+03 pdb=" O THR B 574 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE B 575 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 599 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.47e+00 pdb=" C LEU B 599 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU B 599 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU B 600 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 574 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C THR A 574 " -0.024 2.00e-02 2.50e+03 pdb=" O THR A 574 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE A 575 " 0.008 2.00e-02 2.50e+03 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1628 2.78 - 3.31: 7267 3.31 - 3.84: 12864 3.84 - 4.37: 15136 4.37 - 4.90: 25814 Nonbonded interactions: 62709 Sorted by model distance: nonbonded pdb=" OH TYR B 272 " pdb=" OG SER B 330 " model vdw 2.249 3.040 nonbonded pdb=" OD1 ASP B 533 " pdb=" NH2 ARG B 611 " model vdw 2.254 3.120 nonbonded pdb=" OD1 ASP A 533 " pdb=" NH2 ARG A 611 " model vdw 2.255 3.120 nonbonded pdb=" OH TYR A 272 " pdb=" OG SER A 330 " model vdw 2.260 3.040 nonbonded pdb=" O ILE B 271 " pdb=" OH TYR B 352 " model vdw 2.281 3.040 ... (remaining 62704 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 226 through 802 or resid 804 through 805 or resid 808)) selection = (chain 'B' and (resid 226 through 802 or resid 804 through 805 or resid 808)) } 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: 8.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.130 Find NCS groups from input model: 0.140 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 : 0.004 0.046 7766 Z= 0.198 Angle : 0.737 21.580 10536 Z= 0.351 Chirality : 0.040 0.251 1144 Planarity : 0.004 0.042 1172 Dihedral : 17.183 122.357 3712 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.56 % Allowed : 24.23 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.20 (0.30), residues: 798 helix: 1.62 (0.22), residues: 564 sheet: None (None), residues: 0 loop : -1.27 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 293 TYR 0.022 0.002 TYR A 496 PHE 0.018 0.002 PHE A 492 TRP 0.018 0.002 TRP B 514 HIS 0.003 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 7764) covalent geometry : angle 0.73701 (10532) SS BOND : bond 0.00091 ( 2) SS BOND : angle 0.69564 ( 4) hydrogen bonds : bond 0.10581 ( 434) hydrogen bonds : angle 4.57118 ( 1287) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.272 Fit side-chains REVERT: B 538 ASP cc_start: 0.8865 (t70) cc_final: 0.8628 (t70) outliers start: 4 outliers final: 1 residues processed: 98 average time/residue: 0.0932 time to fit residues: 12.1365 Evaluate side-chains 90 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 387 HIS B 614 ASN B 618 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN A 614 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.173277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.135843 restraints weight = 8827.586| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.13 r_work: 0.3382 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7766 Z= 0.172 Angle : 0.574 6.388 10536 Z= 0.294 Chirality : 0.040 0.145 1144 Planarity : 0.004 0.039 1172 Dihedral : 13.867 115.155 2214 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.35 % Allowed : 20.56 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.23 (0.30), residues: 798 helix: 1.68 (0.22), residues: 564 sheet: None (None), residues: 0 loop : -1.37 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 293 TYR 0.016 0.001 TYR B 443 PHE 0.016 0.002 PHE A 610 TRP 0.012 0.002 TRP A 423 HIS 0.005 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 7764) covalent geometry : angle 0.57347 (10532) SS BOND : bond 0.00163 ( 2) SS BOND : angle 0.68651 ( 4) hydrogen bonds : bond 0.04623 ( 434) hydrogen bonds : angle 4.28938 ( 1287) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 0.294 Fit side-chains REVERT: B 260 GLU cc_start: 0.7035 (pm20) cc_final: 0.6798 (pm20) REVERT: B 374 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7846 (tm) REVERT: B 398 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8062 (m-30) REVERT: B 570 ARG cc_start: 0.8336 (tpt170) cc_final: 0.8090 (mmt180) REVERT: A 374 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7829 (tm) REVERT: A 453 CYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7812 (m) REVERT: A 469 ASP cc_start: 0.7887 (t0) cc_final: 0.7305 (m-30) REVERT: A 495 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8342 (mm) REVERT: A 514 TRP cc_start: 0.7999 (t60) cc_final: 0.7660 (t60) outliers start: 38 outliers final: 21 residues processed: 128 average time/residue: 0.0901 time to fit residues: 15.3226 Evaluate side-chains 122 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 440 CYS Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 620 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 11 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.173267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.136182 restraints weight = 8815.352| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.10 r_work: 0.3285 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7766 Z= 0.175 Angle : 0.565 5.862 10536 Z= 0.289 Chirality : 0.040 0.157 1144 Planarity : 0.004 0.031 1172 Dihedral : 13.610 109.856 2214 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.76 % Allowed : 19.86 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.20 (0.29), residues: 798 helix: 1.67 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -1.41 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 293 TYR 0.015 0.001 TYR B 443 PHE 0.019 0.002 PHE B 517 TRP 0.017 0.001 TRP B 514 HIS 0.004 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 7764) covalent geometry : angle 0.56473 (10532) SS BOND : bond 0.00120 ( 2) SS BOND : angle 0.70343 ( 4) hydrogen bonds : bond 0.04595 ( 434) hydrogen bonds : angle 4.27981 ( 1287) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 99 time to evaluate : 0.187 Fit side-chains REVERT: B 260 GLU cc_start: 0.7066 (pm20) cc_final: 0.6805 (pm20) REVERT: B 331 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8426 (tp) REVERT: B 374 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7897 (tm) REVERT: B 398 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8042 (m-30) REVERT: B 555 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.6752 (mp10) REVERT: B 570 ARG cc_start: 0.8416 (tpt170) cc_final: 0.8142 (mmt180) REVERT: A 331 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8452 (tp) REVERT: A 398 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8093 (m-30) REVERT: A 453 CYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7809 (m) REVERT: A 469 ASP cc_start: 0.7879 (t0) cc_final: 0.7293 (m-30) REVERT: A 495 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8382 (mm) REVERT: A 514 TRP cc_start: 0.8001 (t60) cc_final: 0.7687 (t60) REVERT: A 555 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.6773 (mp10) outliers start: 48 outliers final: 20 residues processed: 136 average time/residue: 0.0818 time to fit residues: 15.1984 Evaluate side-chains 124 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 440 CYS Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 620 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 48 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 19 optimal weight: 0.0670 chunk 25 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.173682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.136538 restraints weight = 8933.312| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.11 r_work: 0.3372 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7766 Z= 0.155 Angle : 0.543 5.689 10536 Z= 0.278 Chirality : 0.040 0.139 1144 Planarity : 0.004 0.034 1172 Dihedral : 13.191 104.529 2214 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 6.20 % Allowed : 19.72 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.25 (0.30), residues: 798 helix: 1.68 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -1.37 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 448 TYR 0.027 0.002 TYR A 443 PHE 0.015 0.002 PHE A 610 TRP 0.014 0.001 TRP B 423 HIS 0.005 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7764) covalent geometry : angle 0.54328 (10532) SS BOND : bond 0.00118 ( 2) SS BOND : angle 0.59368 ( 4) hydrogen bonds : bond 0.04425 ( 434) hydrogen bonds : angle 4.20059 ( 1287) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 95 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: B 331 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8423 (tp) REVERT: B 374 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7853 (tm) REVERT: B 398 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8094 (m-30) REVERT: B 459 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.7728 (mmm160) REVERT: B 555 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.6700 (mp10) REVERT: B 570 ARG cc_start: 0.8319 (tpt170) cc_final: 0.8064 (mmt180) REVERT: A 331 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8423 (tp) REVERT: A 453 CYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7775 (m) REVERT: A 469 ASP cc_start: 0.7881 (t0) cc_final: 0.7263 (m-30) REVERT: A 495 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8354 (mm) REVERT: A 514 TRP cc_start: 0.7898 (t60) cc_final: 0.7634 (t60) REVERT: A 555 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.6698 (mp10) outliers start: 44 outliers final: 24 residues processed: 126 average time/residue: 0.0863 time to fit residues: 14.7491 Evaluate side-chains 127 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 459 ARG Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 620 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 13 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 64 optimal weight: 0.0870 chunk 39 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS B 618 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.173570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.136263 restraints weight = 8789.247| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.11 r_work: 0.3400 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7766 Z= 0.146 Angle : 0.533 5.574 10536 Z= 0.273 Chirality : 0.039 0.135 1144 Planarity : 0.004 0.036 1172 Dihedral : 13.008 99.789 2212 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 6.34 % Allowed : 20.00 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.35 (0.30), residues: 798 helix: 1.75 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -1.30 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 548 TYR 0.020 0.002 TYR A 443 PHE 0.018 0.002 PHE A 492 TRP 0.013 0.001 TRP A 423 HIS 0.005 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7764) covalent geometry : angle 0.53270 (10532) SS BOND : bond 0.00123 ( 2) SS BOND : angle 0.52784 ( 4) hydrogen bonds : bond 0.04361 ( 434) hydrogen bonds : angle 4.15929 ( 1287) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 99 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 331 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8401 (tp) REVERT: B 398 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8087 (m-30) REVERT: B 459 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.7722 (mmm160) REVERT: B 549 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8183 (pt0) REVERT: B 555 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.6711 (mp10) REVERT: B 570 ARG cc_start: 0.8277 (tpt170) cc_final: 0.7965 (mmt180) REVERT: A 331 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8414 (tp) REVERT: A 398 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8180 (m-30) REVERT: A 453 CYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7766 (m) REVERT: A 459 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.7757 (mmm160) REVERT: A 469 ASP cc_start: 0.7848 (t0) cc_final: 0.7261 (m-30) REVERT: A 495 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8350 (mm) REVERT: A 514 TRP cc_start: 0.7860 (t60) cc_final: 0.7609 (t60) REVERT: A 555 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.6655 (mp10) REVERT: A 622 GLU cc_start: 0.8428 (mp0) cc_final: 0.7989 (mp0) outliers start: 45 outliers final: 26 residues processed: 133 average time/residue: 0.0789 time to fit residues: 14.3586 Evaluate side-chains 130 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 459 ARG Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 620 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 41 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 310 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS B 616 HIS B 618 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.172848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.135544 restraints weight = 8821.586| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.11 r_work: 0.3296 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7766 Z= 0.177 Angle : 0.562 5.594 10536 Z= 0.287 Chirality : 0.041 0.145 1144 Planarity : 0.004 0.035 1172 Dihedral : 13.068 95.134 2212 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 6.62 % Allowed : 20.28 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.24 (0.30), residues: 798 helix: 1.66 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -1.32 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 448 TYR 0.020 0.002 TYR A 496 PHE 0.019 0.002 PHE B 492 TRP 0.018 0.001 TRP B 423 HIS 0.005 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 7764) covalent geometry : angle 0.56168 (10532) SS BOND : bond 0.00077 ( 2) SS BOND : angle 0.58828 ( 4) hydrogen bonds : bond 0.04466 ( 434) hydrogen bonds : angle 4.22287 ( 1287) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 98 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 331 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8439 (tp) REVERT: B 336 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6170 (p90) REVERT: B 398 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8158 (m-30) REVERT: B 459 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.7772 (mmm160) REVERT: B 555 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.6755 (mp10) REVERT: B 570 ARG cc_start: 0.8362 (tpt170) cc_final: 0.8018 (mmt180) REVERT: A 331 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8444 (tp) REVERT: A 398 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8190 (m-30) REVERT: A 453 CYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7785 (m) REVERT: A 459 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.7823 (mmm160) REVERT: A 469 ASP cc_start: 0.7860 (t0) cc_final: 0.7291 (m-30) REVERT: A 495 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8293 (mm) REVERT: A 514 TRP cc_start: 0.7879 (t60) cc_final: 0.7609 (t60) REVERT: A 555 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.6672 (mp10) REVERT: A 622 GLU cc_start: 0.8421 (mp0) cc_final: 0.8001 (mp0) outliers start: 47 outliers final: 29 residues processed: 134 average time/residue: 0.0810 time to fit residues: 14.8788 Evaluate side-chains 134 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 94 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 459 ARG Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 620 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 1 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 77 optimal weight: 0.0970 chunk 31 optimal weight: 0.0470 chunk 67 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 310 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS B 618 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.175014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137623 restraints weight = 8830.544| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.13 r_work: 0.3383 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7766 Z= 0.141 Angle : 0.543 5.794 10536 Z= 0.278 Chirality : 0.040 0.170 1144 Planarity : 0.004 0.047 1172 Dihedral : 12.897 92.184 2212 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 6.76 % Allowed : 20.70 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.33 (0.30), residues: 798 helix: 1.73 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -1.30 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 293 TYR 0.020 0.002 TYR A 496 PHE 0.020 0.002 PHE A 492 TRP 0.017 0.001 TRP B 423 HIS 0.005 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7764) covalent geometry : angle 0.54323 (10532) SS BOND : bond 0.00111 ( 2) SS BOND : angle 0.46004 ( 4) hydrogen bonds : bond 0.04362 ( 434) hydrogen bonds : angle 4.16596 ( 1287) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 95 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 331 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8406 (tp) REVERT: B 336 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.6092 (p90) REVERT: B 398 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8105 (m-30) REVERT: B 454 ILE cc_start: 0.8528 (mt) cc_final: 0.8308 (mt) REVERT: B 459 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.7764 (mmm160) REVERT: B 555 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.6703 (mp10) REVERT: B 570 ARG cc_start: 0.8269 (tpt170) cc_final: 0.7964 (mmt180) REVERT: A 331 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8402 (tp) REVERT: A 398 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8158 (m-30) REVERT: A 453 CYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7734 (m) REVERT: A 459 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.7838 (mmm160) REVERT: A 469 ASP cc_start: 0.7855 (t0) cc_final: 0.7271 (m-30) REVERT: A 495 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8282 (mm) REVERT: A 514 TRP cc_start: 0.7827 (t60) cc_final: 0.7562 (t60) REVERT: A 555 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.6627 (mp10) REVERT: A 600 GLU cc_start: 0.7871 (tt0) cc_final: 0.7669 (mt-10) REVERT: A 622 GLU cc_start: 0.8367 (mp0) cc_final: 0.7926 (mp0) outliers start: 48 outliers final: 31 residues processed: 131 average time/residue: 0.0905 time to fit residues: 16.0799 Evaluate side-chains 133 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 91 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 459 ARG Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 620 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 3 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS B 618 ASN ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.175275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.138420 restraints weight = 8827.640| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.08 r_work: 0.3369 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7766 Z= 0.172 Angle : 0.566 5.577 10536 Z= 0.289 Chirality : 0.041 0.159 1144 Planarity : 0.004 0.046 1172 Dihedral : 12.916 89.703 2212 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 6.62 % Allowed : 21.97 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.23 (0.30), residues: 798 helix: 1.65 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -1.32 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 293 TYR 0.022 0.002 TYR A 496 PHE 0.023 0.002 PHE A 492 TRP 0.018 0.002 TRP A 423 HIS 0.005 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 7764) covalent geometry : angle 0.56598 (10532) SS BOND : bond 0.00070 ( 2) SS BOND : angle 0.55073 ( 4) hydrogen bonds : bond 0.04449 ( 434) hydrogen bonds : angle 4.20300 ( 1287) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 93 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 331 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8463 (tp) REVERT: B 336 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.6244 (p90) REVERT: B 398 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8134 (m-30) REVERT: B 454 ILE cc_start: 0.8581 (mt) cc_final: 0.8375 (mt) REVERT: B 459 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.7765 (mmm160) REVERT: B 555 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.6764 (mp10) REVERT: B 570 ARG cc_start: 0.8381 (tpt170) cc_final: 0.8049 (mmt180) REVERT: A 331 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8475 (tp) REVERT: A 374 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7913 (tm) REVERT: A 398 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8175 (m-30) REVERT: A 453 CYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7783 (m) REVERT: A 459 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.7827 (mmm160) REVERT: A 469 ASP cc_start: 0.7834 (t0) cc_final: 0.7277 (m-30) REVERT: A 495 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8312 (mm) REVERT: A 514 TRP cc_start: 0.7902 (t60) cc_final: 0.7640 (t60) REVERT: A 555 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.6672 (mp10) REVERT: A 622 GLU cc_start: 0.8339 (mp0) cc_final: 0.7930 (mp0) outliers start: 47 outliers final: 31 residues processed: 128 average time/residue: 0.0845 time to fit residues: 14.7293 Evaluate side-chains 134 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 91 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 459 ARG Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 620 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 61 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 63 optimal weight: 0.1980 chunk 7 optimal weight: 0.0020 chunk 40 optimal weight: 0.3980 chunk 55 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 35 optimal weight: 0.2980 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 310 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS B 462 GLN B 618 ASN ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.178635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.141951 restraints weight = 8768.420| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.10 r_work: 0.3410 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7766 Z= 0.129 Angle : 0.535 5.798 10536 Z= 0.275 Chirality : 0.039 0.142 1144 Planarity : 0.004 0.040 1172 Dihedral : 12.671 87.693 2212 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.77 % Allowed : 22.25 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.37 (0.30), residues: 798 helix: 1.75 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -1.26 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 293 TYR 0.032 0.002 TYR B 443 PHE 0.020 0.001 PHE A 492 TRP 0.019 0.001 TRP A 423 HIS 0.005 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7764) covalent geometry : angle 0.53527 (10532) SS BOND : bond 0.00158 ( 2) SS BOND : angle 0.42619 ( 4) hydrogen bonds : bond 0.04257 ( 434) hydrogen bonds : angle 4.11676 ( 1287) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8456 (tp) REVERT: B 454 ILE cc_start: 0.8560 (mt) cc_final: 0.8339 (mt) REVERT: B 459 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.7905 (mmm160) REVERT: B 555 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.6687 (mp10) REVERT: B 570 ARG cc_start: 0.8260 (tpt170) cc_final: 0.8012 (mmt180) REVERT: B 622 GLU cc_start: 0.8331 (mp0) cc_final: 0.7887 (mp0) REVERT: A 331 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8483 (tp) REVERT: A 398 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8133 (m-30) REVERT: A 453 CYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7719 (m) REVERT: A 459 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.7894 (mmm160) REVERT: A 469 ASP cc_start: 0.7824 (t0) cc_final: 0.7264 (m-30) REVERT: A 495 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8311 (mm) REVERT: A 514 TRP cc_start: 0.7844 (t60) cc_final: 0.7616 (t60) REVERT: A 555 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.6654 (mp10) REVERT: A 622 GLU cc_start: 0.8255 (mp0) cc_final: 0.7854 (mp0) outliers start: 41 outliers final: 30 residues processed: 127 average time/residue: 0.0881 time to fit residues: 15.1323 Evaluate side-chains 130 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 459 ARG Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 620 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.2980 chunk 36 optimal weight: 0.0670 chunk 64 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 35 optimal weight: 0.1980 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS B 618 ASN ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.174536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.137296 restraints weight = 8748.223| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.09 r_work: 0.3345 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7766 Z= 0.133 Angle : 0.545 5.915 10536 Z= 0.279 Chirality : 0.040 0.137 1144 Planarity : 0.004 0.040 1172 Dihedral : 12.593 86.413 2212 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.92 % Allowed : 22.96 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.41 (0.30), residues: 798 helix: 1.78 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -1.22 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 293 TYR 0.027 0.002 TYR B 443 PHE 0.020 0.001 PHE A 492 TRP 0.018 0.001 TRP A 423 HIS 0.005 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7764) covalent geometry : angle 0.54545 (10532) SS BOND : bond 0.00129 ( 2) SS BOND : angle 0.36740 ( 4) hydrogen bonds : bond 0.04266 ( 434) hydrogen bonds : angle 4.11139 ( 1287) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 92 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: B 331 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8406 (tp) REVERT: B 448 ARG cc_start: 0.7854 (tpp80) cc_final: 0.7444 (ttt90) REVERT: B 454 ILE cc_start: 0.8542 (mt) cc_final: 0.8305 (mt) REVERT: B 459 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.7898 (mmm160) REVERT: B 555 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.6668 (mp10) REVERT: B 570 ARG cc_start: 0.8247 (tpt170) cc_final: 0.8004 (mmt180) REVERT: B 622 GLU cc_start: 0.8306 (mp0) cc_final: 0.7855 (mp0) REVERT: A 331 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8431 (tp) REVERT: A 398 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8153 (m-30) REVERT: A 432 ASN cc_start: 0.6928 (OUTLIER) cc_final: 0.6652 (m110) REVERT: A 453 CYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7650 (m) REVERT: A 459 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.7873 (mmm160) REVERT: A 469 ASP cc_start: 0.7866 (t0) cc_final: 0.7288 (m-30) REVERT: A 495 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8318 (mm) REVERT: A 514 TRP cc_start: 0.7839 (t60) cc_final: 0.7630 (t60) REVERT: A 555 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.6633 (mp10) REVERT: A 622 GLU cc_start: 0.8224 (mp0) cc_final: 0.7826 (mp0) outliers start: 42 outliers final: 28 residues processed: 123 average time/residue: 0.0850 time to fit residues: 14.1646 Evaluate side-chains 129 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 91 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 459 ARG Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 620 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 18 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 8 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: B 310 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS B 618 ASN ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.173932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.136645 restraints weight = 8755.314| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.10 r_work: 0.3332 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7766 Z= 0.188 Angle : 0.584 5.578 10536 Z= 0.298 Chirality : 0.042 0.181 1144 Planarity : 0.004 0.032 1172 Dihedral : 12.761 85.104 2212 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.92 % Allowed : 23.24 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.19 (0.30), residues: 798 helix: 1.61 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -1.31 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 293 TYR 0.026 0.002 TYR B 443 PHE 0.021 0.002 PHE A 492 TRP 0.033 0.002 TRP B 514 HIS 0.005 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 7764) covalent geometry : angle 0.58379 (10532) SS BOND : bond 0.00050 ( 2) SS BOND : angle 0.51094 ( 4) hydrogen bonds : bond 0.04482 ( 434) hydrogen bonds : angle 4.21543 ( 1287) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1734.33 seconds wall clock time: 30 minutes 39.75 seconds (1839.75 seconds total)