Starting phenix.real_space_refine on Sat May 2 17:30:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jlp_61592/05_2026/9jlp_61592.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jlp_61592/05_2026/9jlp_61592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jlp_61592/05_2026/9jlp_61592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jlp_61592/05_2026/9jlp_61592.map" model { file = "/net/cci-nas-00/data/ceres_data/9jlp_61592/05_2026/9jlp_61592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jlp_61592/05_2026/9jlp_61592.cif" } resolution = 3.9 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= 0.005 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 4800 2.51 5 N 1339 2.21 5 O 1415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 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: 7593 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 5887 Classifications: {'peptide': 770} Link IDs: {'PTRANS': 36, 'TRANS': 733} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 423 Classifications: {'peptide': 52} Link IDs: {'TRANS': 51} Chain: "D" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 391 Classifications: {'peptide': 48} Link IDs: {'TRANS': 47} Chain: "E" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 446 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "F" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 446 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Time building chain proxies: 1.80, per 1000 atoms: 0.24 Number of scatterers: 7593 At special positions: 0 Unit cell: (152.32, 145.52, 76.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1415 8.00 N 1339 7.00 C 4800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 402.4 milliseconds 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1858 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 5 sheets defined 62.0% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 removed outlier: 3.717A pdb=" N ILE A 9 " --> pdb=" O LEU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 16 Processing helix chain 'A' and resid 17 through 23 removed outlier: 3.898A pdb=" N LEU A 21 " --> pdb=" O THR A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 77 Processing helix chain 'A' and resid 82 through 100 removed outlier: 3.580A pdb=" N ASN A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 129 through 134 removed outlier: 3.985A pdb=" N ILE A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 129 through 134' Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 138 through 144 removed outlier: 3.756A pdb=" N LYS A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 168 removed outlier: 4.437A pdb=" N GLN A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 211 Processing helix chain 'A' and resid 215 through 223 removed outlier: 3.933A pdb=" N THR A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 247 Processing helix chain 'A' and resid 255 through 270 Processing helix chain 'A' and resid 288 through 294 removed outlier: 3.635A pdb=" N VAL A 294 " --> pdb=" O SER A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 321 through 338 Proline residue: A 328 - end of helix Processing helix chain 'A' and resid 345 through 349 removed outlier: 3.641A pdb=" N VAL A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 345 through 349' Processing helix chain 'A' and resid 399 through 418 removed outlier: 3.727A pdb=" N SER A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) Proline residue: A 412 - end of helix removed outlier: 3.815A pdb=" N SER A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 433 Processing helix chain 'A' and resid 464 through 474 removed outlier: 3.524A pdb=" N LEU A 469 " --> pdb=" O THR A 465 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 491 Processing helix chain 'A' and resid 492 through 515 Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.520A pdb=" N ALA A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 647 Processing helix chain 'A' and resid 661 through 690 removed outlier: 4.206A pdb=" N ARG A 665 " --> pdb=" O PRO A 661 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS A 690 " --> pdb=" O LYS A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 718 removed outlier: 3.776A pdb=" N VAL A 716 " --> pdb=" O ARG A 712 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 742 removed outlier: 3.951A pdb=" N ASN A 724 " --> pdb=" O PRO A 720 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 739 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 740 " --> pdb=" O SER A 736 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA A 741 " --> pdb=" O LEU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 750 removed outlier: 3.683A pdb=" N LYS A 747 " --> pdb=" O ASP A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 770 removed outlier: 3.571A pdb=" N ILE A 756 " --> pdb=" O VAL A 752 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 757 " --> pdb=" O PRO A 753 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 788 removed outlier: 3.726A pdb=" N THR A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 796 Processing helix chain 'C' and resid 93 through 111 Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 115 through 125 removed outlier: 3.638A pdb=" N MET C 125 " --> pdb=" O ARG C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 143 Processing helix chain 'D' and resid 94 through 110 removed outlier: 3.747A pdb=" N VAL D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 125 Processing helix chain 'D' and resid 130 through 140 Processing helix chain 'E' and resid 90 through 111 Processing helix chain 'E' and resid 112 through 124 removed outlier: 3.528A pdb=" N LEU E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 143 Processing helix chain 'F' and resid 90 through 110 Processing helix chain 'F' and resid 115 through 126 Processing helix chain 'F' and resid 128 through 143 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 56 removed outlier: 3.503A pdb=" N TYR A 54 " --> pdb=" O TYR A 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 355 Processing sheet with id=AA4, first strand: chain 'A' and resid 380 through 382 removed outlier: 3.944A pdb=" N VAL A 380 " --> pdb=" O MET A 659 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A 659 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 620 " --> pdb=" O PHE A 658 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 625 through 629 removed outlier: 3.747A pdb=" N ASP A 626 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 639 " --> pdb=" O PHE A 628 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1197 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: 1.08 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2552 1.34 - 1.46: 1630 1.46 - 1.58: 3461 1.58 - 1.70: 1 1.70 - 1.82: 76 Bond restraints: 7720 Sorted by residual: bond pdb=" CB PRO A 452 " pdb=" CG PRO A 452 " ideal model delta sigma weight residual 1.492 1.677 -0.185 5.00e-02 4.00e+02 1.36e+01 bond pdb=" N PRO A 452 " pdb=" CD PRO A 452 " ideal model delta sigma weight residual 1.473 1.502 -0.029 1.40e-02 5.10e+03 4.29e+00 bond pdb=" N PRO A 452 " pdb=" CA PRO A 452 " ideal model delta sigma weight residual 1.468 1.452 0.015 7.90e-03 1.60e+04 3.66e+00 bond pdb=" CG LEU F 136 " pdb=" CD1 LEU F 136 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.85e+00 bond pdb=" CB GLU A 513 " pdb=" CG GLU A 513 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.18e+00 ... (remaining 7715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 10351 3.42 - 6.83: 89 6.83 - 10.25: 15 10.25 - 13.66: 0 13.66 - 17.08: 1 Bond angle restraints: 10456 Sorted by residual: angle pdb=" CA PRO A 452 " pdb=" N PRO A 452 " pdb=" CD PRO A 452 " ideal model delta sigma weight residual 112.00 94.92 17.08 1.40e+00 5.10e-01 1.49e+02 angle pdb=" N PRO A 452 " pdb=" CD PRO A 452 " pdb=" CG PRO A 452 " ideal model delta sigma weight residual 103.20 94.42 8.78 1.50e+00 4.44e-01 3.43e+01 angle pdb=" N ALA A 693 " pdb=" CA ALA A 693 " pdb=" C ALA A 693 " ideal model delta sigma weight residual 114.56 108.47 6.09 1.27e+00 6.20e-01 2.30e+01 angle pdb=" C LEU A 171 " pdb=" N VAL A 172 " pdb=" CA VAL A 172 " ideal model delta sigma weight residual 121.97 129.50 -7.53 1.80e+00 3.09e-01 1.75e+01 angle pdb=" N HIS C 129 " pdb=" CA HIS C 129 " pdb=" C HIS C 129 " ideal model delta sigma weight residual 113.28 108.20 5.08 1.22e+00 6.72e-01 1.73e+01 ... (remaining 10451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3895 17.84 - 35.69: 618 35.69 - 53.53: 163 53.53 - 71.38: 27 71.38 - 89.22: 14 Dihedral angle restraints: 4717 sinusoidal: 1858 harmonic: 2859 Sorted by residual: dihedral pdb=" CA LEU D 116 " pdb=" C LEU D 116 " pdb=" N LEU D 117 " pdb=" CA LEU D 117 " ideal model delta harmonic sigma weight residual 180.00 154.89 25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA GLU A 399 " pdb=" C GLU A 399 " pdb=" N VAL A 400 " pdb=" CA VAL A 400 " ideal model delta harmonic sigma weight residual 180.00 -158.51 -21.49 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA MET A 397 " pdb=" C MET A 397 " pdb=" N GLU A 398 " pdb=" CA GLU A 398 " ideal model delta harmonic sigma weight residual -180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 4714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 974 0.049 - 0.098: 223 0.098 - 0.147: 26 0.147 - 0.197: 1 0.197 - 0.246: 2 Chirality restraints: 1226 Sorted by residual: chirality pdb=" CG LEU D 123 " pdb=" CB LEU D 123 " pdb=" CD1 LEU D 123 " pdb=" CD2 LEU D 123 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB VAL A 172 " pdb=" CA VAL A 172 " pdb=" CG1 VAL A 172 " pdb=" CG2 VAL A 172 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA LEU F 136 " pdb=" N LEU F 136 " pdb=" C LEU F 136 " pdb=" CB LEU F 136 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 1223 not shown) Planarity restraints: 1340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 451 " 0.077 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO A 452 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 452 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 452 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 579 " 0.064 5.00e-02 4.00e+02 9.87e-02 1.56e+01 pdb=" N PRO A 580 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 580 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 580 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 128 " -0.044 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO A 129 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " -0.037 5.00e-02 4.00e+02 ... (remaining 1337 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 467 2.73 - 3.27: 8099 3.27 - 3.81: 11966 3.81 - 4.36: 12865 4.36 - 4.90: 22380 Nonbonded interactions: 55777 Sorted by model distance: nonbonded pdb=" O SER A 578 " pdb=" OG SER A 578 " model vdw 2.183 3.040 nonbonded pdb=" O GLU F 128 " pdb=" OG1 THR F 131 " model vdw 2.207 3.040 nonbonded pdb=" O VAL A 108 " pdb=" OG1 THR A 112 " model vdw 2.226 3.040 nonbonded pdb=" O SER A 518 " pdb=" OG SER A 518 " model vdw 2.253 3.040 nonbonded pdb=" OG1 THR A 17 " pdb=" OE1 GLU A 579 " model vdw 2.273 3.040 ... (remaining 55772 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 'C' and resid 93 through 140) selection = chain 'D' selection = (chain 'E' and resid 93 through 140) selection = (chain 'F' and resid 93 through 140) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.970 Find NCS groups from input model: 0.060 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 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 0.185 7720 Z= 0.167 Angle : 0.840 17.076 10456 Z= 0.459 Chirality : 0.041 0.246 1226 Planarity : 0.006 0.105 1340 Dihedral : 18.740 89.222 2859 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.72 % Allowed : 15.29 % Favored : 83.99 % Rotamer: Outliers : 0.86 % Allowed : 37.10 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.28), residues: 968 helix: 1.01 (0.23), residues: 526 sheet: -3.21 (0.71), residues: 51 loop : -3.44 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 135 TYR 0.018 0.001 TYR A 73 PHE 0.012 0.001 PHE A 628 TRP 0.029 0.002 TRP A 671 HIS 0.016 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 7720) covalent geometry : angle 0.83955 (10456) hydrogen bonds : bond 0.14175 ( 409) hydrogen bonds : angle 5.65597 ( 1197) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 165 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR A 796 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 670 MET cc_start: 0.7965 (ttm) cc_final: 0.7675 (ttm) REVERT: C 132 MET cc_start: 0.6398 (mmp) cc_final: 0.3562 (tmm) REVERT: F 132 MET cc_start: 0.5310 (tmm) cc_final: 0.5052 (tpt) outliers start: 7 outliers final: 5 residues processed: 167 average time/residue: 0.0999 time to fit residues: 21.5916 Evaluate side-chains 164 residues out of total 814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 159 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain E residue 130 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.165302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.132625 restraints weight = 12461.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.132065 restraints weight = 13491.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.133893 restraints weight = 9621.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.134136 restraints weight = 6426.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.134148 restraints weight = 5591.637| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7720 Z= 0.188 Angle : 0.725 9.649 10456 Z= 0.374 Chirality : 0.042 0.221 1226 Planarity : 0.005 0.063 1340 Dihedral : 5.650 57.198 1081 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.62 % Allowed : 15.29 % Favored : 84.09 % Rotamer: Outliers : 7.00 % Allowed : 32.68 % Favored : 60.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.28), residues: 968 helix: 0.96 (0.23), residues: 545 sheet: -3.33 (0.63), residues: 61 loop : -3.60 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 135 TYR 0.021 0.002 TYR C 133 PHE 0.012 0.002 PHE A 658 TRP 0.017 0.001 TRP A 671 HIS 0.008 0.002 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 7720) covalent geometry : angle 0.72542 (10456) hydrogen bonds : bond 0.05118 ( 409) hydrogen bonds : angle 5.13504 ( 1197) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 169 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR A 796 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 171 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6437 (tt) REVERT: A 214 ASP cc_start: 0.7958 (p0) cc_final: 0.7604 (p0) REVERT: A 366 HIS cc_start: 0.7989 (OUTLIER) cc_final: 0.7716 (m-70) REVERT: A 470 SER cc_start: 0.8977 (m) cc_final: 0.8713 (t) REVERT: A 590 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8334 (pt0) REVERT: F 129 HIS cc_start: 0.4714 (OUTLIER) cc_final: 0.4427 (t-170) outliers start: 57 outliers final: 35 residues processed: 205 average time/residue: 0.0913 time to fit residues: 24.5176 Evaluate side-chains 199 residues out of total 814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 129 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 38 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 86 optimal weight: 30.0000 chunk 30 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.165435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.132584 restraints weight = 12471.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.131486 restraints weight = 13214.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.133594 restraints weight = 9608.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.133870 restraints weight = 6584.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.133869 restraints weight = 6088.724| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7720 Z= 0.161 Angle : 0.699 8.989 10456 Z= 0.357 Chirality : 0.041 0.218 1226 Planarity : 0.005 0.050 1340 Dihedral : 5.653 57.274 1078 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.88 % Favored : 84.61 % Rotamer: Outliers : 7.25 % Allowed : 34.28 % Favored : 58.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.28), residues: 968 helix: 1.06 (0.23), residues: 542 sheet: -3.50 (0.65), residues: 51 loop : -3.58 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 324 TYR 0.016 0.001 TYR C 133 PHE 0.014 0.002 PHE C 130 TRP 0.020 0.001 TRP A 671 HIS 0.007 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 7720) covalent geometry : angle 0.69874 (10456) hydrogen bonds : bond 0.04717 ( 409) hydrogen bonds : angle 5.02866 ( 1197) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 167 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR A 796 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 1 MET cc_start: 0.7543 (mmt) cc_final: 0.6380 (mmp) REVERT: A 127 ARG cc_start: 0.3882 (mtm180) cc_final: 0.3217 (mtm180) REVERT: A 171 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6369 (tt) REVERT: A 366 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.7786 (m-70) REVERT: A 417 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.5256 (m-80) REVERT: A 470 SER cc_start: 0.8935 (m) cc_final: 0.8681 (t) REVERT: A 670 MET cc_start: 0.8498 (ttm) cc_final: 0.7628 (ttm) REVERT: A 680 LYS cc_start: 0.8297 (tppt) cc_final: 0.7940 (mtmm) REVERT: C 132 MET cc_start: 0.5951 (mmm) cc_final: 0.5737 (mmp) REVERT: F 113 LEU cc_start: 0.7511 (tt) cc_final: 0.6839 (mp) REVERT: F 125 MET cc_start: 0.6085 (tmm) cc_final: 0.5885 (tmm) REVERT: F 129 HIS cc_start: 0.4433 (OUTLIER) cc_final: 0.4029 (t-170) outliers start: 59 outliers final: 41 residues processed: 199 average time/residue: 0.0899 time to fit residues: 23.4442 Evaluate side-chains 209 residues out of total 814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain F residue 132 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 87 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 86 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 93 optimal weight: 40.0000 chunk 39 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.169173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.136553 restraints weight = 12230.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.135286 restraints weight = 9103.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.137145 restraints weight = 6748.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.137332 restraints weight = 5214.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.137512 restraints weight = 4883.475| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7720 Z= 0.202 Angle : 0.712 9.306 10456 Z= 0.369 Chirality : 0.042 0.221 1226 Planarity : 0.005 0.050 1340 Dihedral : 5.798 57.223 1078 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.52 % Allowed : 16.01 % Favored : 83.47 % Rotamer: Outliers : 8.72 % Allowed : 32.80 % Favored : 58.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.28), residues: 968 helix: 1.01 (0.23), residues: 542 sheet: -3.53 (0.59), residues: 61 loop : -3.59 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 665 TYR 0.020 0.002 TYR C 133 PHE 0.028 0.002 PHE A 232 TRP 0.021 0.002 TRP A 671 HIS 0.007 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 7720) covalent geometry : angle 0.71229 (10456) hydrogen bonds : bond 0.05104 ( 409) hydrogen bonds : angle 5.09623 ( 1197) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 162 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR A 796 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9031 (tp) REVERT: A 127 ARG cc_start: 0.4075 (mtm180) cc_final: 0.3102 (mtm180) REVERT: A 171 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6462 (tt) REVERT: A 366 HIS cc_start: 0.8065 (OUTLIER) cc_final: 0.7846 (m-70) REVERT: A 389 ARG cc_start: 0.6151 (mmt180) cc_final: 0.5641 (mmt180) REVERT: A 417 PHE cc_start: 0.6560 (OUTLIER) cc_final: 0.5138 (m-80) REVERT: A 470 SER cc_start: 0.9015 (m) cc_final: 0.8763 (t) REVERT: A 500 MET cc_start: 0.7561 (mmt) cc_final: 0.7315 (mmt) REVERT: A 670 MET cc_start: 0.8612 (ttm) cc_final: 0.7709 (ttm) REVERT: A 680 LYS cc_start: 0.8289 (tppt) cc_final: 0.8051 (tppt) REVERT: A 767 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8669 (mp) REVERT: C 132 MET cc_start: 0.5669 (mmm) cc_final: 0.5465 (mmp) REVERT: F 113 LEU cc_start: 0.7122 (tt) cc_final: 0.6565 (mp) REVERT: F 129 HIS cc_start: 0.4167 (OUTLIER) cc_final: 0.3866 (t-170) outliers start: 71 outliers final: 53 residues processed: 205 average time/residue: 0.0957 time to fit residues: 25.9347 Evaluate side-chains 214 residues out of total 814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 155 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain F residue 132 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 16 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 32 optimal weight: 0.0870 chunk 70 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 HIS A 748 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.171991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.139562 restraints weight = 12014.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.138163 restraints weight = 8565.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.140102 restraints weight = 6796.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.140562 restraints weight = 5112.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.140853 restraints weight = 4624.575| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7720 Z= 0.139 Angle : 0.682 10.051 10456 Z= 0.346 Chirality : 0.041 0.208 1226 Planarity : 0.004 0.052 1340 Dihedral : 5.728 58.578 1078 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.88 % Favored : 84.61 % Rotamer: Outliers : 8.11 % Allowed : 34.03 % Favored : 57.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.28), residues: 968 helix: 1.17 (0.23), residues: 542 sheet: -3.42 (0.61), residues: 60 loop : -3.50 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 665 TYR 0.017 0.001 TYR C 133 PHE 0.015 0.002 PHE C 130 TRP 0.022 0.001 TRP A 671 HIS 0.007 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7720) covalent geometry : angle 0.68204 (10456) hydrogen bonds : bond 0.04340 ( 409) hydrogen bonds : angle 4.89326 ( 1197) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 167 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR A 796 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 44 HIS cc_start: 0.8401 (OUTLIER) cc_final: 0.8106 (m170) REVERT: A 127 ARG cc_start: 0.3808 (mtm180) cc_final: 0.3217 (mtm180) REVERT: A 171 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6184 (tt) REVERT: A 235 HIS cc_start: 0.7455 (OUTLIER) cc_final: 0.6975 (t-90) REVERT: A 389 ARG cc_start: 0.5973 (mmt180) cc_final: 0.5549 (mmt180) REVERT: A 417 PHE cc_start: 0.6670 (OUTLIER) cc_final: 0.5355 (m-80) REVERT: A 470 SER cc_start: 0.8966 (m) cc_final: 0.8690 (t) REVERT: A 670 MET cc_start: 0.8566 (ttm) cc_final: 0.7593 (ttm) REVERT: A 797 MET cc_start: 0.7590 (ppp) cc_final: 0.7120 (ppp) REVERT: F 113 LEU cc_start: 0.7411 (tt) cc_final: 0.6817 (mp) REVERT: F 129 HIS cc_start: 0.4332 (OUTLIER) cc_final: 0.3991 (t-170) outliers start: 66 outliers final: 51 residues processed: 207 average time/residue: 0.0945 time to fit residues: 25.7055 Evaluate side-chains 217 residues out of total 814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 161 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain F residue 132 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 94 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.162899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.129913 restraints weight = 12656.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.129550 restraints weight = 14201.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.131144 restraints weight = 9868.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.131589 restraints weight = 6902.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.131854 restraints weight = 5945.825| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7720 Z= 0.191 Angle : 0.722 9.380 10456 Z= 0.369 Chirality : 0.042 0.216 1226 Planarity : 0.005 0.048 1340 Dihedral : 5.767 58.177 1078 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.52 % Allowed : 15.60 % Favored : 83.88 % Rotamer: Outliers : 9.71 % Allowed : 32.92 % Favored : 57.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.28), residues: 968 helix: 1.07 (0.23), residues: 542 sheet: -3.48 (0.61), residues: 61 loop : -3.55 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 665 TYR 0.021 0.002 TYR C 133 PHE 0.016 0.002 PHE A 232 TRP 0.021 0.002 TRP A 671 HIS 0.006 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 7720) covalent geometry : angle 0.72185 (10456) hydrogen bonds : bond 0.04933 ( 409) hydrogen bonds : angle 4.99946 ( 1197) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 156 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR A 796 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8998 (tp) REVERT: A 62 ASP cc_start: 0.7938 (m-30) cc_final: 0.7629 (m-30) REVERT: A 94 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.8911 (tm-30) REVERT: A 140 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7339 (tm-30) REVERT: A 171 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6493 (tt) REVERT: A 235 HIS cc_start: 0.7540 (OUTLIER) cc_final: 0.7066 (t-90) REVERT: A 389 ARG cc_start: 0.6156 (mmt180) cc_final: 0.5770 (mmt180) REVERT: A 417 PHE cc_start: 0.6552 (OUTLIER) cc_final: 0.5112 (m-80) REVERT: A 470 SER cc_start: 0.9016 (m) cc_final: 0.8750 (t) REVERT: A 500 MET cc_start: 0.7470 (mmt) cc_final: 0.7204 (mmt) REVERT: A 680 LYS cc_start: 0.8325 (tppt) cc_final: 0.8040 (mtmm) REVERT: A 767 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8547 (mp) REVERT: A 797 MET cc_start: 0.7587 (ppp) cc_final: 0.7076 (ppp) REVERT: E 131 THR cc_start: 0.7774 (m) cc_final: 0.7331 (p) REVERT: F 105 VAL cc_start: 0.2642 (OUTLIER) cc_final: 0.2345 (p) REVERT: F 113 LEU cc_start: 0.7258 (tt) cc_final: 0.6758 (mp) REVERT: F 129 HIS cc_start: 0.4247 (OUTLIER) cc_final: 0.3923 (t-170) outliers start: 79 outliers final: 62 residues processed: 212 average time/residue: 0.0921 time to fit residues: 25.7012 Evaluate side-chains 220 residues out of total 814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 150 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain F residue 132 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 56 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 58 optimal weight: 0.0980 chunk 57 optimal weight: 20.0000 chunk 19 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.166266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.133290 restraints weight = 12502.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.133201 restraints weight = 11843.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.134579 restraints weight = 8692.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.135189 restraints weight = 6559.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.135433 restraints weight = 5699.469| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 7720 Z= 0.136 Angle : 0.691 10.221 10456 Z= 0.349 Chirality : 0.041 0.293 1226 Planarity : 0.004 0.050 1340 Dihedral : 5.624 57.421 1078 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.67 % Favored : 84.81 % Rotamer: Outliers : 9.34 % Allowed : 33.29 % Favored : 57.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.28), residues: 968 helix: 1.23 (0.23), residues: 543 sheet: -3.44 (0.61), residues: 60 loop : -3.48 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 665 TYR 0.014 0.001 TYR C 133 PHE 0.014 0.002 PHE C 130 TRP 0.022 0.001 TRP A 671 HIS 0.007 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7720) covalent geometry : angle 0.69058 (10456) hydrogen bonds : bond 0.04247 ( 409) hydrogen bonds : angle 4.82981 ( 1197) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 166 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR A 796 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 1 MET cc_start: 0.7298 (mmt) cc_final: 0.6197 (mmp) REVERT: A 62 ASP cc_start: 0.7766 (m-30) cc_final: 0.7475 (m-30) REVERT: A 140 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7227 (tm-30) REVERT: A 171 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6389 (tt) REVERT: A 235 HIS cc_start: 0.7475 (OUTLIER) cc_final: 0.7020 (t-90) REVERT: A 389 ARG cc_start: 0.6067 (mmt180) cc_final: 0.5717 (mmt180) REVERT: A 417 PHE cc_start: 0.6683 (OUTLIER) cc_final: 0.5358 (m-80) REVERT: A 470 SER cc_start: 0.8965 (m) cc_final: 0.8674 (t) REVERT: A 670 MET cc_start: 0.8867 (ttm) cc_final: 0.7753 (ttm) REVERT: A 680 LYS cc_start: 0.8293 (tppt) cc_final: 0.8011 (mtmm) REVERT: A 767 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8435 (mp) REVERT: A 797 MET cc_start: 0.7458 (ppp) cc_final: 0.7103 (ppp) REVERT: C 132 MET cc_start: 0.5894 (mmm) cc_final: 0.5432 (mmm) REVERT: F 90 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6259 (mp) REVERT: F 105 VAL cc_start: 0.2574 (OUTLIER) cc_final: 0.2270 (p) REVERT: F 113 LEU cc_start: 0.7128 (tt) cc_final: 0.6871 (mp) REVERT: F 129 HIS cc_start: 0.4920 (OUTLIER) cc_final: 0.4517 (t-170) outliers start: 76 outliers final: 57 residues processed: 218 average time/residue: 0.0919 time to fit residues: 26.2789 Evaluate side-chains 223 residues out of total 814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 159 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain F residue 132 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 61 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.0570 chunk 53 optimal weight: 6.9990 chunk 92 optimal weight: 30.0000 chunk 6 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 94 optimal weight: 20.0000 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.170405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.137208 restraints weight = 12214.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.136203 restraints weight = 9314.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.137969 restraints weight = 7120.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.138816 restraints weight = 5185.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.139000 restraints weight = 4657.183| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7720 Z= 0.164 Angle : 0.709 10.276 10456 Z= 0.361 Chirality : 0.042 0.219 1226 Planarity : 0.004 0.048 1340 Dihedral : 5.599 57.429 1078 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.52 % Allowed : 15.29 % Favored : 84.19 % Rotamer: Outliers : 10.07 % Allowed : 31.94 % Favored : 57.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.28), residues: 968 helix: 1.21 (0.23), residues: 542 sheet: -3.51 (0.59), residues: 60 loop : -3.51 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 665 TYR 0.018 0.001 TYR C 133 PHE 0.014 0.002 PHE C 130 TRP 0.023 0.001 TRP A 671 HIS 0.007 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 7720) covalent geometry : angle 0.70897 (10456) hydrogen bonds : bond 0.04552 ( 409) hydrogen bonds : angle 4.85059 ( 1197) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 160 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR A 796 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 1 MET cc_start: 0.7457 (mmt) cc_final: 0.7096 (mpp) REVERT: A 16 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8951 (tp) REVERT: A 62 ASP cc_start: 0.8043 (m-30) cc_final: 0.7810 (m-30) REVERT: A 171 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6391 (tt) REVERT: A 235 HIS cc_start: 0.7572 (OUTLIER) cc_final: 0.7102 (t-90) REVERT: A 389 ARG cc_start: 0.6166 (mmt180) cc_final: 0.5812 (mmt180) REVERT: A 417 PHE cc_start: 0.6574 (OUTLIER) cc_final: 0.5244 (m-80) REVERT: A 470 SER cc_start: 0.8993 (m) cc_final: 0.8715 (t) REVERT: A 500 MET cc_start: 0.7447 (mmt) cc_final: 0.7158 (mmt) REVERT: A 659 MET cc_start: 0.8142 (tpt) cc_final: 0.7687 (tpt) REVERT: A 670 MET cc_start: 0.8863 (ttm) cc_final: 0.7577 (ttm) REVERT: A 680 LYS cc_start: 0.8218 (tppt) cc_final: 0.7806 (mtmm) REVERT: A 767 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8492 (mp) REVERT: A 797 MET cc_start: 0.7543 (ppp) cc_final: 0.7283 (ppp) REVERT: C 132 MET cc_start: 0.5763 (mmm) cc_final: 0.5557 (mmp) REVERT: E 131 THR cc_start: 0.7699 (m) cc_final: 0.7282 (p) REVERT: F 90 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6341 (mp) REVERT: F 105 VAL cc_start: 0.2161 (OUTLIER) cc_final: 0.1893 (p) REVERT: F 113 LEU cc_start: 0.7123 (tt) cc_final: 0.6870 (mp) REVERT: F 129 HIS cc_start: 0.4874 (OUTLIER) cc_final: 0.4491 (t-170) outliers start: 82 outliers final: 62 residues processed: 219 average time/residue: 0.0907 time to fit residues: 26.4047 Evaluate side-chains 226 residues out of total 814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 156 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain F residue 132 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 75 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 0.0870 chunk 55 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 56 optimal weight: 0.0050 chunk 47 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.0178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 HIS E 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.174320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.142440 restraints weight = 12011.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.141157 restraints weight = 9265.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.143016 restraints weight = 7286.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.144238 restraints weight = 5043.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.144353 restraints weight = 4116.088| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7720 Z= 0.124 Angle : 0.687 10.452 10456 Z= 0.344 Chirality : 0.040 0.235 1226 Planarity : 0.004 0.053 1340 Dihedral : 5.388 57.966 1078 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.52 % Allowed : 13.84 % Favored : 85.64 % Rotamer: Outliers : 7.74 % Allowed : 34.15 % Favored : 58.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.28), residues: 968 helix: 1.33 (0.23), residues: 544 sheet: -2.69 (0.76), residues: 42 loop : -3.48 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 665 TYR 0.013 0.001 TYR C 133 PHE 0.013 0.001 PHE C 130 TRP 0.026 0.002 TRP A 671 HIS 0.007 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7720) covalent geometry : angle 0.68695 (10456) hydrogen bonds : bond 0.03617 ( 409) hydrogen bonds : angle 4.62498 ( 1197) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 172 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR A 796 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 1 MET cc_start: 0.7207 (mmt) cc_final: 0.6720 (mpp) REVERT: A 16 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8907 (tp) REVERT: A 140 GLU cc_start: 0.7402 (tm-30) cc_final: 0.7021 (tm-30) REVERT: A 171 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6023 (tt) REVERT: A 235 HIS cc_start: 0.7489 (OUTLIER) cc_final: 0.7019 (t-90) REVERT: A 389 ARG cc_start: 0.5767 (mmt180) cc_final: 0.5547 (mmt180) REVERT: A 406 MET cc_start: 0.9069 (mtp) cc_final: 0.8693 (mtp) REVERT: A 417 PHE cc_start: 0.6657 (OUTLIER) cc_final: 0.5433 (m-80) REVERT: A 470 SER cc_start: 0.8939 (m) cc_final: 0.8645 (t) REVERT: A 627 ARG cc_start: 0.8555 (mtp85) cc_final: 0.8164 (mtm-85) REVERT: A 670 MET cc_start: 0.8696 (ttm) cc_final: 0.7604 (ttm) REVERT: A 712 ARG cc_start: 0.8087 (tpp80) cc_final: 0.7850 (tpp80) REVERT: A 797 MET cc_start: 0.7530 (ppp) cc_final: 0.7125 (ppp) REVERT: C 132 MET cc_start: 0.5713 (mmm) cc_final: 0.5496 (mmp) REVERT: D 128 GLU cc_start: 0.4885 (OUTLIER) cc_final: 0.4386 (mt-10) REVERT: F 129 HIS cc_start: 0.4766 (OUTLIER) cc_final: 0.4390 (t-170) outliers start: 63 outliers final: 51 residues processed: 220 average time/residue: 0.0870 time to fit residues: 25.5391 Evaluate side-chains 220 residues out of total 814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 163 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain F residue 132 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 75 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 41 optimal weight: 0.0470 chunk 93 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 HIS E 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.171384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.140079 restraints weight = 12099.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.138180 restraints weight = 8573.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.139607 restraints weight = 6831.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.140754 restraints weight = 5276.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.140994 restraints weight = 4384.115| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7720 Z= 0.139 Angle : 0.696 10.291 10456 Z= 0.351 Chirality : 0.041 0.232 1226 Planarity : 0.004 0.050 1340 Dihedral : 5.323 59.055 1077 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.52 % Allowed : 13.95 % Favored : 85.54 % Rotamer: Outliers : 7.74 % Allowed : 34.64 % Favored : 57.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.29), residues: 968 helix: 1.37 (0.23), residues: 542 sheet: -2.76 (0.76), residues: 42 loop : -3.47 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 665 TYR 0.015 0.001 TYR C 133 PHE 0.014 0.001 PHE C 130 TRP 0.024 0.001 TRP A 671 HIS 0.007 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7720) covalent geometry : angle 0.69648 (10456) hydrogen bonds : bond 0.03982 ( 409) hydrogen bonds : angle 4.64991 ( 1197) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 170 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR A 796 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 1 MET cc_start: 0.7432 (mmt) cc_final: 0.6800 (mpp) REVERT: A 16 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8939 (tp) REVERT: A 105 ARG cc_start: 0.8326 (tpm170) cc_final: 0.8073 (tpm170) REVERT: A 107 LEU cc_start: 0.8554 (tt) cc_final: 0.8351 (tp) REVERT: A 171 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6114 (tt) REVERT: A 235 HIS cc_start: 0.7501 (OUTLIER) cc_final: 0.7062 (t-90) REVERT: A 389 ARG cc_start: 0.5900 (mmt180) cc_final: 0.5594 (mmt180) REVERT: A 417 PHE cc_start: 0.6639 (OUTLIER) cc_final: 0.5337 (m-80) REVERT: A 470 SER cc_start: 0.8969 (m) cc_final: 0.8682 (t) REVERT: A 500 MET cc_start: 0.7315 (mmt) cc_final: 0.7111 (mmt) REVERT: A 627 ARG cc_start: 0.8610 (mtp85) cc_final: 0.8217 (mtm-85) REVERT: A 659 MET cc_start: 0.8215 (tpt) cc_final: 0.7819 (tpt) REVERT: A 670 MET cc_start: 0.8784 (ttm) cc_final: 0.7622 (ttm) REVERT: A 680 LYS cc_start: 0.8344 (tppt) cc_final: 0.7968 (mtmm) REVERT: A 681 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8161 (tm-30) REVERT: A 712 ARG cc_start: 0.8114 (tpp80) cc_final: 0.7882 (tpp80) REVERT: A 797 MET cc_start: 0.7541 (ppp) cc_final: 0.7198 (ppp) REVERT: C 132 MET cc_start: 0.5844 (mmm) cc_final: 0.5619 (mmp) REVERT: D 128 GLU cc_start: 0.4719 (OUTLIER) cc_final: 0.4225 (mt-10) REVERT: F 129 HIS cc_start: 0.4848 (OUTLIER) cc_final: 0.4473 (t-170) outliers start: 63 outliers final: 55 residues processed: 216 average time/residue: 0.0904 time to fit residues: 25.8617 Evaluate side-chains 227 residues out of total 814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 166 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain F residue 132 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 44 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 HIS E 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.174484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.141102 restraints weight = 12111.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.141385 restraints weight = 9291.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.142900 restraints weight = 6771.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.143083 restraints weight = 5183.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.143472 restraints weight = 4703.123| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7720 Z= 0.127 Angle : 0.708 10.329 10456 Z= 0.353 Chirality : 0.041 0.234 1226 Planarity : 0.004 0.053 1340 Dihedral : 5.380 59.372 1077 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.62 % Allowed : 13.64 % Favored : 85.74 % Rotamer: Outliers : 7.13 % Allowed : 35.38 % Favored : 57.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.28), residues: 968 helix: 1.38 (0.23), residues: 544 sheet: -2.67 (0.76), residues: 42 loop : -3.44 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 135 TYR 0.021 0.001 TYR E 133 PHE 0.014 0.001 PHE C 130 TRP 0.024 0.001 TRP A 671 HIS 0.007 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 7720) covalent geometry : angle 0.70791 (10456) hydrogen bonds : bond 0.03692 ( 409) hydrogen bonds : angle 4.58314 ( 1197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1357.76 seconds wall clock time: 24 minutes 5.46 seconds (1445.46 seconds total)