Starting phenix.real_space_refine on Thu Jul 2 03:32:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rav_24387/07_2026/7rav_24387.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rav_24387/07_2026/7rav_24387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rav_24387/07_2026/7rav_24387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rav_24387/07_2026/7rav_24387.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7rav_24387/07_2026/7rav_24387.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rav_24387/07_2026/7rav_24387.cif" model { file = "/net/cci-nas-00/data/ceres_data/7rav_24387/07_2026/7rav_24387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rav_24387/07_2026/7rav_24387.cif" } resolution = 3.3 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 40 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 39 5.16 5 C 3976 2.51 5 N 1046 2.21 5 O 1151 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6215 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6184 Classifications: {'peptide': 773} Link IDs: {'PTRANS': 26, 'TRANS': 746} Chain breaks: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.49, per 1000 atoms: 0.24 Number of scatterers: 6215 At special positions: 0 Unit cell: (74.858, 78.0662, 133.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 3 15.00 O 1151 8.00 N 1046 7.00 C 3976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 124 " distance=2.03 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 224 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 397.0 milliseconds 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1460 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 46.6% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 64 through 70 removed outlier: 4.092A pdb=" N THR A 69 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 84 Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 177 through 183 Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.511A pdb=" N ALA A 218 " --> pdb=" O TRP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 231 Processing helix chain 'A' and resid 234 through 240 removed outlier: 3.782A pdb=" N GLN A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 280 removed outlier: 4.022A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.668A pdb=" N ARG A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 339 Processing helix chain 'A' and resid 343 through 350 removed outlier: 3.639A pdb=" N THR A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 418 Processing helix chain 'A' and resid 454 through 459 removed outlier: 3.711A pdb=" N PHE A 459 " --> pdb=" O ILE A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'A' and resid 492 through 498 removed outlier: 3.668A pdb=" N LEU A 495 " --> pdb=" O CYS A 492 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG A 497 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 521 Processing helix chain 'A' and resid 531 through 542 Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 560 through 569 Processing helix chain 'A' and resid 603 through 615 removed outlier: 3.541A pdb=" N THR A 607 " --> pdb=" O PRO A 603 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 630 removed outlier: 3.506A pdb=" N ILE A 630 " --> pdb=" O ILE A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 651 Processing helix chain 'A' and resid 652 through 654 No H-bonds generated for 'chain 'A' and resid 652 through 654' Processing helix chain 'A' and resid 662 through 679 removed outlier: 3.764A pdb=" N THR A 666 " --> pdb=" O PHE A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 704 removed outlier: 4.203A pdb=" N LEU A 686 " --> pdb=" O THR A 682 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 696 " --> pdb=" O SER A 692 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 697 " --> pdb=" O CYS A 693 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A 702 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER A 703 " --> pdb=" O THR A 699 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 704 " --> pdb=" O GLY A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 717 removed outlier: 3.809A pdb=" N LEU A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A 714 " --> pdb=" O SER A 710 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 715 " --> pdb=" O ASP A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 removed outlier: 3.636A pdb=" N THR A 726 " --> pdb=" O LYS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 763 Processing helix chain 'A' and resid 765 through 778 removed outlier: 4.432A pdb=" N LEU A 771 " --> pdb=" O GLU A 767 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY A 772 " --> pdb=" O ASP A 768 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN A 778 " --> pdb=" O TYR A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 788 removed outlier: 3.607A pdb=" N SER A 788 " --> pdb=" O LYS A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 797 removed outlier: 3.945A pdb=" N VAL A 796 " --> pdb=" O PHE A 792 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 792 through 797' Processing helix chain 'A' and resid 803 through 814 removed outlier: 4.569A pdb=" N THR A 807 " --> pdb=" O LYS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 878 removed outlier: 3.993A pdb=" N THR A 877 " --> pdb=" O TYR A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 887 Processing helix chain 'A' and resid 910 through 914 removed outlier: 3.553A pdb=" N LEU A 914 " --> pdb=" O LEU A 911 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 188 Processing sheet with id=AA3, first strand: chain 'A' and resid 305 through 306 Processing sheet with id=AA4, first strand: chain 'A' and resid 440 through 441 Processing sheet with id=AA5, first strand: chain 'A' and resid 466 through 468 removed outlier: 6.714A pdb=" N MET A 466 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL A 546 " --> pdb=" O CYS A 576 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU A 578 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE A 548 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ALA A 580 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU A 550 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 500 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU A 549 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE A 502 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ASP A 551 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A 504 " --> pdb=" O ASP A 551 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 199 hydrogen bonds defined for protein. 555 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1961 1.34 - 1.46: 1377 1.46 - 1.58: 2962 1.58 - 1.70: 5 1.70 - 1.83: 52 Bond restraints: 6357 Sorted by residual: bond pdb=" C4 ATP A1501 " pdb=" C5 ATP A1501 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.24e+01 bond pdb=" C5 ATP A1501 " pdb=" C6 ATP A1501 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.79e+01 bond pdb=" C8 ATP A1501 " pdb=" N7 ATP A1501 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.11e+01 bond pdb=" C5 ATP A1501 " pdb=" N7 ATP A1501 " ideal model delta sigma weight residual 1.387 1.342 0.045 1.00e-02 1.00e+04 2.01e+01 bond pdb=" C4 ATP A1501 " pdb=" N9 ATP A1501 " ideal model delta sigma weight residual 1.374 1.331 0.043 1.00e-02 1.00e+04 1.89e+01 ... (remaining 6352 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.13: 8527 4.13 - 8.25: 60 8.25 - 12.38: 4 12.38 - 16.50: 0 16.50 - 20.63: 2 Bond angle restraints: 8593 Sorted by residual: angle pdb=" PB ATP A1501 " pdb=" O3B ATP A1501 " pdb=" PG ATP A1501 " ideal model delta sigma weight residual 139.87 119.24 20.63 1.00e+00 1.00e+00 4.26e+02 angle pdb=" PA ATP A1501 " pdb=" O3A ATP A1501 " pdb=" PB ATP A1501 " ideal model delta sigma weight residual 136.83 118.98 17.85 1.00e+00 1.00e+00 3.19e+02 angle pdb=" N GLY A 175 " pdb=" CA GLY A 175 " pdb=" C GLY A 175 " ideal model delta sigma weight residual 112.73 100.90 11.83 1.20e+00 6.94e-01 9.72e+01 angle pdb=" C5 ATP A1501 " pdb=" C4 ATP A1501 " pdb=" N3 ATP A1501 " ideal model delta sigma weight residual 126.80 118.66 8.14 1.00e+00 1.00e+00 6.62e+01 angle pdb=" N3 ATP A1501 " pdb=" C4 ATP A1501 " pdb=" N9 ATP A1501 " ideal model delta sigma weight residual 127.04 134.79 -7.75 1.15e+00 7.59e-01 4.56e+01 ... (remaining 8588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3323 17.97 - 35.93: 366 35.93 - 53.90: 71 53.90 - 71.86: 15 71.86 - 89.83: 10 Dihedral angle restraints: 3785 sinusoidal: 1528 harmonic: 2257 Sorted by residual: dihedral pdb=" CB CYS A 100 " pdb=" SG CYS A 100 " pdb=" SG CYS A 124 " pdb=" CB CYS A 124 " ideal model delta sinusoidal sigma weight residual 93.00 48.56 44.44 1 1.00e+01 1.00e-02 2.75e+01 dihedral pdb=" CA HIS A 157 " pdb=" C HIS A 157 " pdb=" N GLU A 158 " pdb=" CA GLU A 158 " ideal model delta harmonic sigma weight residual -180.00 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ILE A 135 " pdb=" C ILE A 135 " pdb=" N GLY A 136 " pdb=" CA GLY A 136 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 3782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 756 0.058 - 0.117: 170 0.117 - 0.175: 18 0.175 - 0.233: 2 0.233 - 0.292: 1 Chirality restraints: 947 Sorted by residual: chirality pdb=" CA PRO A 340 " pdb=" N PRO A 340 " pdb=" C PRO A 340 " pdb=" CB PRO A 340 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA HIS A 174 " pdb=" N HIS A 174 " pdb=" C HIS A 174 " pdb=" CB HIS A 174 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" CA GLN A 766 " pdb=" N GLN A 766 " pdb=" C GLN A 766 " pdb=" CB GLN A 766 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.68e-01 ... (remaining 944 not shown) Planarity restraints: 1089 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 339 " 0.061 5.00e-02 4.00e+02 9.20e-02 1.36e+01 pdb=" N PRO A 340 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 340 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 340 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 492 " -0.038 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO A 493 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 493 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 493 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 330 " 0.037 5.00e-02 4.00e+02 5.58e-02 4.97e+00 pdb=" N PRO A 331 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 331 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 331 " 0.032 5.00e-02 4.00e+02 ... (remaining 1086 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1067 2.76 - 3.29: 6528 3.29 - 3.83: 9907 3.83 - 4.36: 11611 4.36 - 4.90: 18876 Nonbonded interactions: 47989 Sorted by model distance: nonbonded pdb=" OH TYR A 172 " pdb=" NH2 ARG A 261 " model vdw 2.224 3.120 nonbonded pdb=" NZ LYS A 723 " pdb=" OG1 THR A 725 " model vdw 2.224 3.120 nonbonded pdb=" NH1 ARG A 314 " pdb=" O THR A 430 " model vdw 2.242 3.120 nonbonded pdb=" OG SER A 554 " pdb=" OG SER A 558 " model vdw 2.247 3.040 nonbonded pdb=" O ASN A 900 " pdb=" ND2 ASN A 900 " model vdw 2.248 3.120 ... (remaining 47984 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.370 Find NCS groups from input model: 0.160 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 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 0.079 6359 Z= 0.260 Angle : 0.930 20.628 8597 Z= 0.590 Chirality : 0.049 0.292 947 Planarity : 0.005 0.092 1089 Dihedral : 15.842 89.826 2319 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.39 % Allowed : 16.73 % Favored : 82.88 % Rotamer: Outliers : 1.17 % Allowed : 0.44 % Favored : 98.39 % 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: -3.36 (0.29), residues: 765 helix: -0.98 (0.29), residues: 313 sheet: -1.74 (0.75), residues: 37 loop : -3.46 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 74 TYR 0.037 0.002 TYR A 496 PHE 0.027 0.002 PHE A 859 TRP 0.009 0.001 TRP A 220 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.26 ( 6357) covalent geometry : angle 0.93007 / 0.59 ( 8593) SS BOND : bond 0.00360 / 0.18 ( 2) SS BOND : angle 0.96772 / 0.46 ( 4) hydrogen bonds : bond 0.18112 / 11.28 ( 199) hydrogen bonds : angle 7.18963 / 4.88 ( 555) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 225 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7514 (tpp) cc_final: 0.7266 (tpp) REVERT: A 57 MET cc_start: 0.7615 (ptp) cc_final: 0.7406 (ptp) REVERT: A 148 MET cc_start: 0.6317 (tmm) cc_final: 0.6110 (tmm) REVERT: A 160 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7252 (tm-30) REVERT: A 164 GLU cc_start: 0.7523 (pp20) cc_final: 0.7231 (pp20) REVERT: A 167 GLU cc_start: 0.7299 (mp0) cc_final: 0.6992 (mp0) REVERT: A 332 MET cc_start: 0.5342 (pmm) cc_final: 0.5045 (pmm) REVERT: A 408 ARG cc_start: 0.7768 (tmm-80) cc_final: 0.7233 (tmm-80) REVERT: A 443 LYS cc_start: 0.8249 (mtmm) cc_final: 0.7908 (mtmm) REVERT: A 535 LEU cc_start: 0.8698 (tp) cc_final: 0.8469 (tp) REVERT: A 551 ASP cc_start: 0.7115 (t70) cc_final: 0.6681 (t0) REVERT: A 598 GLU cc_start: 0.6899 (tt0) cc_final: 0.6650 (tt0) REVERT: A 630 ILE cc_start: 0.8585 (tp) cc_final: 0.8332 (tp) REVERT: A 651 ASP cc_start: 0.7321 (t0) cc_final: 0.7086 (t0) REVERT: A 812 LEU cc_start: 0.8393 (mt) cc_final: 0.8094 (mt) REVERT: A 814 GLN cc_start: 0.7762 (pp30) cc_final: 0.7405 (pp30) REVERT: A 865 LEU cc_start: 0.8483 (mm) cc_final: 0.8281 (mm) REVERT: A 867 LEU cc_start: 0.8955 (pp) cc_final: 0.8365 (pp) REVERT: A 869 LEU cc_start: 0.8422 (mm) cc_final: 0.8213 (mm) REVERT: A 871 PHE cc_start: 0.7230 (m-80) cc_final: 0.6856 (m-80) outliers start: 8 outliers final: 0 residues processed: 228 average time/residue: 0.0849 time to fit residues: 24.8020 Evaluate side-chains 198 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.0010 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 overall best weight: 0.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 ASN A 570 ASN A 900 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.156507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.138926 restraints weight = 10495.417| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 3.68 r_work: 0.3738 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6359 Z= 0.154 Angle : 0.759 9.119 8597 Z= 0.396 Chirality : 0.046 0.168 947 Planarity : 0.005 0.050 1089 Dihedral : 6.796 83.767 840 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 15.56 % Favored : 84.18 % Rotamer: Outliers : 1.90 % Allowed : 13.18 % Favored : 84.92 % 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: -3.04 (0.30), residues: 765 helix: -0.49 (0.30), residues: 324 sheet: -1.76 (0.76), residues: 37 loop : -3.53 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 585 TYR 0.043 0.003 TYR A 496 PHE 0.051 0.002 PHE A 792 TRP 0.010 0.001 TRP A 220 HIS 0.004 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 6357) covalent geometry : angle 0.75835 / 0.40 ( 8593) SS BOND : bond 0.00352 / 0.17 ( 2) SS BOND : angle 1.14301 / 0.51 ( 4) hydrogen bonds : bond 0.04356 / 2.79 ( 199) hydrogen bonds : angle 5.07708 / 3.40 ( 555) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 211 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7643 (tpp) cc_final: 0.7331 (tpp) REVERT: A 57 MET cc_start: 0.8499 (ptp) cc_final: 0.8284 (ptp) REVERT: A 62 LYS cc_start: 0.8595 (ttmm) cc_final: 0.8255 (mtmm) REVERT: A 138 TYR cc_start: 0.6923 (t80) cc_final: 0.6638 (t80) REVERT: A 148 MET cc_start: 0.6919 (tmm) cc_final: 0.6587 (tmm) REVERT: A 160 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7670 (tm-30) REVERT: A 164 GLU cc_start: 0.8026 (pp20) cc_final: 0.7753 (pp20) REVERT: A 167 GLU cc_start: 0.7900 (mp0) cc_final: 0.7411 (mp0) REVERT: A 223 LYS cc_start: 0.8571 (mtmm) cc_final: 0.8368 (mtmm) REVERT: A 226 PHE cc_start: 0.8783 (t80) cc_final: 0.8160 (t80) REVERT: A 230 LYS cc_start: 0.8892 (mmmm) cc_final: 0.8645 (mmmm) REVERT: A 332 MET cc_start: 0.5979 (pmm) cc_final: 0.5426 (pmm) REVERT: A 408 ARG cc_start: 0.8174 (tmm-80) cc_final: 0.7665 (tmm-80) REVERT: A 443 LYS cc_start: 0.8587 (mtmm) cc_final: 0.8003 (mtmm) REVERT: A 454 THR cc_start: 0.8342 (p) cc_final: 0.7943 (t) REVERT: A 455 ILE cc_start: 0.8428 (mm) cc_final: 0.7953 (tp) REVERT: A 457 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8048 (tm-30) REVERT: A 551 ASP cc_start: 0.7478 (t70) cc_final: 0.6821 (t0) REVERT: A 570 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.7501 (t0) REVERT: A 615 PHE cc_start: 0.7460 (m-80) cc_final: 0.7225 (m-80) REVERT: A 630 ILE cc_start: 0.8718 (tp) cc_final: 0.8400 (tp) REVERT: A 652 TRP cc_start: 0.6278 (t60) cc_final: 0.6000 (t60) REVERT: A 709 ASN cc_start: 0.7727 (p0) cc_final: 0.7464 (p0) REVERT: A 712 ASP cc_start: 0.8363 (m-30) cc_final: 0.8079 (m-30) REVERT: A 766 GLN cc_start: 0.8422 (tm-30) cc_final: 0.7830 (pp30) REVERT: A 812 LEU cc_start: 0.8696 (mt) cc_final: 0.8397 (mt) REVERT: A 814 GLN cc_start: 0.8142 (pp30) cc_final: 0.7727 (pp30) REVERT: A 863 HIS cc_start: 0.7988 (m90) cc_final: 0.7196 (m90) REVERT: A 865 LEU cc_start: 0.8603 (mm) cc_final: 0.8370 (mm) REVERT: A 867 LEU cc_start: 0.9036 (pp) cc_final: 0.8548 (pp) REVERT: A 871 PHE cc_start: 0.7770 (m-80) cc_final: 0.7290 (m-80) REVERT: A 873 TYR cc_start: 0.7715 (t80) cc_final: 0.7308 (t80) outliers start: 13 outliers final: 6 residues processed: 215 average time/residue: 0.0885 time to fit residues: 24.3671 Evaluate side-chains 204 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 197 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 731 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 900 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.153119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.136022 restraints weight = 10297.564| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 3.52 r_work: 0.3687 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6359 Z= 0.239 Angle : 0.767 10.711 8597 Z= 0.405 Chirality : 0.049 0.165 947 Planarity : 0.005 0.052 1089 Dihedral : 6.712 72.265 840 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 16.99 % Favored : 82.75 % Rotamer: Outliers : 2.64 % Allowed : 18.16 % Favored : 79.21 % 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: -3.02 (0.30), residues: 765 helix: -0.49 (0.30), residues: 329 sheet: -1.51 (0.89), residues: 30 loop : -3.54 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 417 TYR 0.050 0.003 TYR A 496 PHE 0.035 0.002 PHE A 792 TRP 0.012 0.001 TRP A 220 HIS 0.006 0.001 HIS A 811 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.24 ( 6357) covalent geometry : angle 0.76707 / 0.40 ( 8593) SS BOND : bond 0.00223 / 0.11 ( 2) SS BOND : angle 1.29305 / 0.50 ( 4) hydrogen bonds : bond 0.04296 / 2.74 ( 199) hydrogen bonds : angle 5.03803 / 3.38 ( 555) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 0.231 Fit side-chains REVERT: A 47 MET cc_start: 0.7637 (tpp) cc_final: 0.7287 (tpp) REVERT: A 148 MET cc_start: 0.6976 (tmm) cc_final: 0.6608 (tmm) REVERT: A 160 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7662 (tm-30) REVERT: A 164 GLU cc_start: 0.8071 (pp20) cc_final: 0.7532 (pp20) REVERT: A 167 GLU cc_start: 0.8012 (mp0) cc_final: 0.7353 (mp0) REVERT: A 172 TYR cc_start: 0.7401 (m-80) cc_final: 0.7136 (m-80) REVERT: A 226 PHE cc_start: 0.8783 (t80) cc_final: 0.8134 (t80) REVERT: A 282 MET cc_start: 0.7057 (tpt) cc_final: 0.6756 (tpt) REVERT: A 332 MET cc_start: 0.5959 (pmm) cc_final: 0.5458 (pmm) REVERT: A 408 ARG cc_start: 0.8197 (tmm-80) cc_final: 0.7763 (tmm-80) REVERT: A 443 LYS cc_start: 0.8722 (mtmm) cc_final: 0.8129 (mtmm) REVERT: A 454 THR cc_start: 0.8406 (p) cc_final: 0.8110 (t) REVERT: A 457 GLU cc_start: 0.8430 (tm-30) cc_final: 0.7831 (tm-30) REVERT: A 542 LEU cc_start: 0.8645 (mt) cc_final: 0.8418 (mp) REVERT: A 551 ASP cc_start: 0.7655 (t70) cc_final: 0.7188 (t70) REVERT: A 590 ARG cc_start: 0.8297 (tpp-160) cc_final: 0.7940 (tpp80) REVERT: A 624 LYS cc_start: 0.8166 (tptm) cc_final: 0.7816 (tttm) REVERT: A 630 ILE cc_start: 0.8760 (tp) cc_final: 0.8470 (tp) REVERT: A 652 TRP cc_start: 0.6060 (t60) cc_final: 0.5831 (t60) REVERT: A 695 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7879 (tm-30) REVERT: A 723 LYS cc_start: 0.8150 (tmtt) cc_final: 0.7638 (tmtt) REVERT: A 766 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8047 (pp30) REVERT: A 778 GLN cc_start: 0.8157 (mp10) cc_final: 0.7954 (mp10) REVERT: A 812 LEU cc_start: 0.8642 (mt) cc_final: 0.8363 (mt) REVERT: A 814 GLN cc_start: 0.8205 (pp30) cc_final: 0.7778 (pp30) REVERT: A 863 HIS cc_start: 0.7993 (m90) cc_final: 0.7276 (m90) REVERT: A 865 LEU cc_start: 0.8647 (mm) cc_final: 0.8439 (mm) REVERT: A 867 LEU cc_start: 0.9042 (pp) cc_final: 0.8553 (pp) REVERT: A 871 PHE cc_start: 0.7759 (m-80) cc_final: 0.7264 (m-80) REVERT: A 873 TYR cc_start: 0.7721 (t80) cc_final: 0.7323 (t80) outliers start: 18 outliers final: 10 residues processed: 211 average time/residue: 0.0861 time to fit residues: 23.0949 Evaluate side-chains 209 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 199 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 771 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 21 optimal weight: 0.0000 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 0.0170 overall best weight: 0.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN A 206 ASN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.156109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.138851 restraints weight = 10366.629| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 3.63 r_work: 0.3722 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6359 Z= 0.149 Angle : 0.717 8.855 8597 Z= 0.372 Chirality : 0.046 0.183 947 Planarity : 0.005 0.046 1089 Dihedral : 6.422 71.789 840 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.56 % Favored : 84.31 % Rotamer: Outliers : 2.93 % Allowed : 21.38 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -2.92 (0.30), residues: 765 helix: -0.30 (0.30), residues: 324 sheet: -1.97 (0.72), residues: 37 loop : -3.51 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 417 TYR 0.032 0.002 TYR A 496 PHE 0.026 0.001 PHE A 792 TRP 0.009 0.001 TRP A 220 HIS 0.005 0.001 HIS A 811 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 6357) covalent geometry : angle 0.71657 / 0.37 ( 8593) SS BOND : bond 0.00273 / 0.13 ( 2) SS BOND : angle 0.93655 / 0.38 ( 4) hydrogen bonds : bond 0.03715 / 2.40 ( 199) hydrogen bonds : angle 4.79840 / 3.18 ( 555) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7661 (tpp) cc_final: 0.7350 (tpp) REVERT: A 58 ARG cc_start: 0.7099 (tpp-160) cc_final: 0.6737 (tpp-160) REVERT: A 148 MET cc_start: 0.6957 (tmm) cc_final: 0.6566 (tmm) REVERT: A 160 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7673 (tm-30) REVERT: A 172 TYR cc_start: 0.7307 (m-80) cc_final: 0.7013 (m-80) REVERT: A 208 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7219 (mm-30) REVERT: A 226 PHE cc_start: 0.8719 (t80) cc_final: 0.8345 (t80) REVERT: A 260 ARG cc_start: 0.7149 (mpp-170) cc_final: 0.6784 (mpp-170) REVERT: A 282 MET cc_start: 0.7084 (tpt) cc_final: 0.6762 (tpt) REVERT: A 332 MET cc_start: 0.5761 (pmm) cc_final: 0.5241 (pmm) REVERT: A 408 ARG cc_start: 0.8153 (tmm-80) cc_final: 0.7772 (tmm-80) REVERT: A 443 LYS cc_start: 0.8458 (mtmm) cc_final: 0.8143 (mtmm) REVERT: A 455 ILE cc_start: 0.8543 (mm) cc_final: 0.8099 (tp) REVERT: A 457 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7873 (tm-30) REVERT: A 532 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7685 (mm-30) REVERT: A 551 ASP cc_start: 0.7604 (t70) cc_final: 0.6981 (t0) REVERT: A 598 GLU cc_start: 0.7601 (tt0) cc_final: 0.7362 (tt0) REVERT: A 624 LYS cc_start: 0.8107 (tptm) cc_final: 0.7738 (tttm) REVERT: A 630 ILE cc_start: 0.8697 (tp) cc_final: 0.8412 (tp) REVERT: A 674 TYR cc_start: 0.8521 (t80) cc_final: 0.8306 (t80) REVERT: A 695 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7795 (tm-30) REVERT: A 699 THR cc_start: 0.7746 (m) cc_final: 0.7448 (p) REVERT: A 723 LYS cc_start: 0.8098 (tmtt) cc_final: 0.7556 (tmtt) REVERT: A 747 LEU cc_start: 0.8395 (mm) cc_final: 0.8163 (mm) REVERT: A 766 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8114 (pp30) REVERT: A 812 LEU cc_start: 0.8588 (mt) cc_final: 0.8289 (mt) REVERT: A 814 GLN cc_start: 0.8198 (pp30) cc_final: 0.7760 (pp30) REVERT: A 863 HIS cc_start: 0.8029 (m90) cc_final: 0.7276 (m90) REVERT: A 865 LEU cc_start: 0.8654 (mm) cc_final: 0.8327 (mt) REVERT: A 867 LEU cc_start: 0.9028 (pp) cc_final: 0.8550 (pp) REVERT: A 871 PHE cc_start: 0.7729 (m-80) cc_final: 0.7287 (m-80) REVERT: A 873 TYR cc_start: 0.7604 (t80) cc_final: 0.7166 (t80) outliers start: 20 outliers final: 14 residues processed: 216 average time/residue: 0.0783 time to fit residues: 21.4321 Evaluate side-chains 215 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 779 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 62 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.152847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.135418 restraints weight = 10382.481| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 3.57 r_work: 0.3663 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6359 Z= 0.241 Angle : 0.772 10.744 8597 Z= 0.402 Chirality : 0.050 0.233 947 Planarity : 0.005 0.044 1089 Dihedral : 6.560 63.906 840 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.99 % Favored : 82.88 % Rotamer: Outliers : 3.22 % Allowed : 23.57 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -2.99 (0.29), residues: 765 helix: -0.38 (0.29), residues: 324 sheet: -1.33 (1.03), residues: 25 loop : -3.56 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 92 TYR 0.030 0.002 TYR A 496 PHE 0.024 0.002 PHE A 792 TRP 0.010 0.001 TRP A 220 HIS 0.004 0.001 HIS A 811 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.24 ( 6357) covalent geometry : angle 0.77150 / 0.40 ( 8593) SS BOND : bond 0.00111 / 0.05 ( 2) SS BOND : angle 1.09999 / 0.41 ( 4) hydrogen bonds : bond 0.03987 / 2.53 ( 199) hydrogen bonds : angle 4.92538 / 3.29 ( 555) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.310 Fit side-chains REVERT: A 47 MET cc_start: 0.7687 (tpp) cc_final: 0.7317 (tpp) REVERT: A 148 MET cc_start: 0.7064 (tmm) cc_final: 0.6655 (tmm) REVERT: A 160 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7687 (tm-30) REVERT: A 164 GLU cc_start: 0.8333 (pp20) cc_final: 0.7946 (pp20) REVERT: A 167 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7976 (mm-30) REVERT: A 172 TYR cc_start: 0.7596 (m-80) cc_final: 0.7249 (m-80) REVERT: A 208 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7188 (mm-30) REVERT: A 226 PHE cc_start: 0.8773 (t80) cc_final: 0.8051 (t80) REVERT: A 260 ARG cc_start: 0.7052 (mpp-170) cc_final: 0.6764 (mpp-170) REVERT: A 262 GLU cc_start: 0.7558 (pm20) cc_final: 0.7358 (pm20) REVERT: A 282 MET cc_start: 0.7101 (tpt) cc_final: 0.6758 (tpt) REVERT: A 332 MET cc_start: 0.5946 (pmm) cc_final: 0.5428 (pmm) REVERT: A 408 ARG cc_start: 0.8213 (tmm-80) cc_final: 0.7855 (tmm-80) REVERT: A 441 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8177 (mm) REVERT: A 443 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8055 (mtmm) REVERT: A 457 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7862 (tm-30) REVERT: A 532 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7749 (mm-30) REVERT: A 551 ASP cc_start: 0.7659 (t70) cc_final: 0.7062 (t0) REVERT: A 630 ILE cc_start: 0.8752 (tp) cc_final: 0.8487 (tp) REVERT: A 674 TYR cc_start: 0.8555 (t80) cc_final: 0.7822 (t80) REVERT: A 695 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7811 (tm-30) REVERT: A 712 ASP cc_start: 0.8413 (m-30) cc_final: 0.8007 (m-30) REVERT: A 766 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8157 (tm-30) REVERT: A 814 GLN cc_start: 0.8232 (pp30) cc_final: 0.7784 (pp30) REVERT: A 865 LEU cc_start: 0.8713 (mm) cc_final: 0.8391 (mt) REVERT: A 867 LEU cc_start: 0.9073 (pp) cc_final: 0.8630 (pp) REVERT: A 871 PHE cc_start: 0.7756 (m-80) cc_final: 0.7332 (m-80) REVERT: A 873 TYR cc_start: 0.7558 (t80) cc_final: 0.7115 (t80) outliers start: 22 outliers final: 17 residues processed: 214 average time/residue: 0.0780 time to fit residues: 21.3868 Evaluate side-chains 218 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 779 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 54 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 0.0000 chunk 48 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 0.0270 chunk 66 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 49 optimal weight: 0.2980 chunk 61 optimal weight: 0.0770 overall best weight: 0.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 ASN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 HIS A 900 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.158214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.140719 restraints weight = 10409.752| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 3.62 r_work: 0.3748 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6359 Z= 0.127 Angle : 0.720 12.315 8597 Z= 0.366 Chirality : 0.046 0.346 947 Planarity : 0.005 0.044 1089 Dihedral : 6.064 63.479 840 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.99 % Favored : 85.88 % Rotamer: Outliers : 3.81 % Allowed : 25.33 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -2.78 (0.30), residues: 765 helix: -0.08 (0.30), residues: 309 sheet: -1.85 (0.73), residues: 37 loop : -3.44 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 92 TYR 0.026 0.002 TYR A 639 PHE 0.020 0.001 PHE A 792 TRP 0.006 0.001 TRP A 652 HIS 0.003 0.001 HIS A 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 6357) covalent geometry : angle 0.71953 / 0.37 ( 8593) SS BOND : bond 0.00236 / 0.11 ( 2) SS BOND : angle 0.76077 / 0.33 ( 4) hydrogen bonds : bond 0.03464 / 2.25 ( 199) hydrogen bonds : angle 4.68654 / 3.09 ( 555) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7688 (tpp) cc_final: 0.7445 (tpp) REVERT: A 119 LYS cc_start: 0.8786 (tppp) cc_final: 0.8394 (tppp) REVERT: A 148 MET cc_start: 0.6924 (tmm) cc_final: 0.6526 (tmm) REVERT: A 160 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7672 (tm-30) REVERT: A 172 TYR cc_start: 0.7368 (m-80) cc_final: 0.7012 (m-80) REVERT: A 208 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7363 (mm-30) REVERT: A 226 PHE cc_start: 0.8671 (t80) cc_final: 0.8231 (t80) REVERT: A 282 MET cc_start: 0.7276 (tpt) cc_final: 0.6932 (tpt) REVERT: A 332 MET cc_start: 0.5648 (pmm) cc_final: 0.5141 (pmm) REVERT: A 408 ARG cc_start: 0.8108 (tmm-80) cc_final: 0.7750 (tmm-80) REVERT: A 455 ILE cc_start: 0.8477 (mm) cc_final: 0.8127 (tp) REVERT: A 457 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7774 (tm-30) REVERT: A 532 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7656 (mm-30) REVERT: A 551 ASP cc_start: 0.7512 (t70) cc_final: 0.6929 (t0) REVERT: A 624 LYS cc_start: 0.8010 (tptm) cc_final: 0.7770 (tmtt) REVERT: A 628 TYR cc_start: 0.7462 (t80) cc_final: 0.6977 (t80) REVERT: A 630 ILE cc_start: 0.8589 (tp) cc_final: 0.8315 (tp) REVERT: A 669 GLN cc_start: 0.8266 (tp40) cc_final: 0.8045 (tp40) REVERT: A 674 TYR cc_start: 0.8399 (t80) cc_final: 0.7622 (t80) REVERT: A 695 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7575 (tm-30) REVERT: A 741 TYR cc_start: 0.8142 (m-80) cc_final: 0.7715 (m-80) REVERT: A 747 LEU cc_start: 0.8310 (mm) cc_final: 0.8101 (mm) REVERT: A 766 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8199 (tm-30) REVERT: A 812 LEU cc_start: 0.8556 (mt) cc_final: 0.8256 (mt) REVERT: A 814 GLN cc_start: 0.8169 (pp30) cc_final: 0.7720 (pp30) REVERT: A 865 LEU cc_start: 0.8684 (mm) cc_final: 0.8356 (mt) REVERT: A 867 LEU cc_start: 0.9029 (pp) cc_final: 0.8590 (pp) REVERT: A 871 PHE cc_start: 0.7683 (m-80) cc_final: 0.7271 (m-80) REVERT: A 873 TYR cc_start: 0.7504 (t80) cc_final: 0.7083 (t80) outliers start: 26 outliers final: 15 residues processed: 223 average time/residue: 0.0746 time to fit residues: 21.2481 Evaluate side-chains 231 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 216 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 911 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 35 optimal weight: 0.0570 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 0.1980 chunk 3 optimal weight: 0.5980 chunk 75 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.157030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.139818 restraints weight = 10263.374| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 3.51 r_work: 0.3741 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6359 Z= 0.136 Angle : 0.724 13.211 8597 Z= 0.368 Chirality : 0.046 0.391 947 Planarity : 0.005 0.043 1089 Dihedral : 5.879 57.250 840 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.29 % Favored : 84.58 % Rotamer: Outliers : 2.93 % Allowed : 25.77 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.30), residues: 765 helix: 0.02 (0.30), residues: 309 sheet: -1.77 (0.73), residues: 37 loop : -3.36 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 92 TYR 0.022 0.002 TYR A 903 PHE 0.019 0.001 PHE A 629 TRP 0.007 0.001 TRP A 220 HIS 0.002 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 6357) covalent geometry : angle 0.72408 / 0.37 ( 8593) SS BOND : bond 0.00195 / 0.09 ( 2) SS BOND : angle 0.70819 / 0.26 ( 4) hydrogen bonds : bond 0.03409 / 2.18 ( 199) hydrogen bonds : angle 4.63826 / 3.07 ( 555) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7656 (tpp) cc_final: 0.7405 (tpp) REVERT: A 119 LYS cc_start: 0.8784 (tppp) cc_final: 0.8387 (tppp) REVERT: A 148 MET cc_start: 0.6855 (tmm) cc_final: 0.6456 (tmm) REVERT: A 159 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7731 (tm-30) REVERT: A 168 ASP cc_start: 0.7884 (p0) cc_final: 0.7302 (p0) REVERT: A 172 TYR cc_start: 0.7424 (m-80) cc_final: 0.7067 (m-80) REVERT: A 208 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7339 (mm-30) REVERT: A 226 PHE cc_start: 0.8686 (t80) cc_final: 0.8381 (t80) REVERT: A 252 GLU cc_start: 0.8769 (pt0) cc_final: 0.7825 (mt-10) REVERT: A 279 GLU cc_start: 0.7623 (tp30) cc_final: 0.6934 (mm-30) REVERT: A 282 MET cc_start: 0.7291 (tpt) cc_final: 0.6914 (tpt) REVERT: A 332 MET cc_start: 0.5533 (pmm) cc_final: 0.5053 (pmm) REVERT: A 408 ARG cc_start: 0.8128 (tmm-80) cc_final: 0.7768 (tmm-80) REVERT: A 409 ASP cc_start: 0.7759 (t0) cc_final: 0.7394 (t0) REVERT: A 441 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8155 (mm) REVERT: A 443 LYS cc_start: 0.8425 (mtmm) cc_final: 0.7899 (mtmm) REVERT: A 457 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7809 (tm-30) REVERT: A 532 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7603 (mm-30) REVERT: A 551 ASP cc_start: 0.7468 (t70) cc_final: 0.7010 (t70) REVERT: A 565 THR cc_start: 0.8376 (m) cc_final: 0.7916 (p) REVERT: A 624 LYS cc_start: 0.8055 (tptm) cc_final: 0.7720 (tttm) REVERT: A 628 TYR cc_start: 0.7646 (t80) cc_final: 0.6996 (t80) REVERT: A 630 ILE cc_start: 0.8631 (tp) cc_final: 0.8369 (tp) REVERT: A 634 ASP cc_start: 0.7860 (p0) cc_final: 0.7527 (p0) REVERT: A 669 GLN cc_start: 0.8302 (tp40) cc_final: 0.8083 (tp40) REVERT: A 674 TYR cc_start: 0.8378 (t80) cc_final: 0.7602 (t80) REVERT: A 695 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7589 (tm-30) REVERT: A 715 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8082 (tm-30) REVERT: A 766 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8318 (tm-30) REVERT: A 812 LEU cc_start: 0.8556 (mt) cc_final: 0.8267 (mt) REVERT: A 814 GLN cc_start: 0.8206 (pp30) cc_final: 0.7718 (pp30) REVERT: A 865 LEU cc_start: 0.8673 (mm) cc_final: 0.8339 (mt) REVERT: A 867 LEU cc_start: 0.9033 (pp) cc_final: 0.8603 (pp) REVERT: A 871 PHE cc_start: 0.7736 (m-80) cc_final: 0.7327 (m-80) REVERT: A 873 TYR cc_start: 0.7397 (t80) cc_final: 0.7011 (t80) outliers start: 20 outliers final: 14 residues processed: 222 average time/residue: 0.0846 time to fit residues: 23.8898 Evaluate side-chains 228 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 779 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 0.0270 chunk 68 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 GLN A 900 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.155367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.137950 restraints weight = 10424.290| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 3.58 r_work: 0.3712 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6359 Z= 0.161 Angle : 0.741 13.618 8597 Z= 0.378 Chirality : 0.048 0.400 947 Planarity : 0.005 0.043 1089 Dihedral : 5.986 56.522 840 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.42 % Favored : 84.44 % Rotamer: Outliers : 3.22 % Allowed : 26.50 % Favored : 70.28 % 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: -2.73 (0.30), residues: 765 helix: -0.12 (0.30), residues: 321 sheet: -1.68 (0.75), residues: 37 loop : -3.43 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 92 TYR 0.020 0.002 TYR A 605 PHE 0.019 0.001 PHE A 629 TRP 0.008 0.001 TRP A 258 HIS 0.003 0.001 HIS A 811 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 6357) covalent geometry : angle 0.74095 / 0.38 ( 8593) SS BOND : bond 0.00206 / 0.10 ( 2) SS BOND : angle 0.81878 / 0.31 ( 4) hydrogen bonds : bond 0.03453 / 2.21 ( 199) hydrogen bonds : angle 4.67156 / 3.10 ( 555) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7677 (tpp) cc_final: 0.7439 (tpp) REVERT: A 62 LYS cc_start: 0.8573 (ttmm) cc_final: 0.7964 (mtmm) REVERT: A 119 LYS cc_start: 0.8808 (tppp) cc_final: 0.8420 (tppp) REVERT: A 148 MET cc_start: 0.6862 (tmm) cc_final: 0.6469 (tmm) REVERT: A 150 ARG cc_start: 0.7337 (ptp-110) cc_final: 0.7019 (ptp-110) REVERT: A 158 GLU cc_start: 0.7735 (tp30) cc_final: 0.7483 (tp30) REVERT: A 159 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7925 (tm-30) REVERT: A 168 ASP cc_start: 0.7940 (p0) cc_final: 0.7388 (p0) REVERT: A 172 TYR cc_start: 0.7446 (m-80) cc_final: 0.7031 (m-80) REVERT: A 208 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7093 (mm-30) REVERT: A 226 PHE cc_start: 0.8729 (t80) cc_final: 0.8341 (t80) REVERT: A 252 GLU cc_start: 0.8777 (pt0) cc_final: 0.7701 (mt-10) REVERT: A 262 GLU cc_start: 0.7602 (pm20) cc_final: 0.7391 (pm20) REVERT: A 279 GLU cc_start: 0.7704 (tp30) cc_final: 0.6950 (mm-30) REVERT: A 282 MET cc_start: 0.7261 (tpt) cc_final: 0.6876 (tpt) REVERT: A 332 MET cc_start: 0.5668 (pmm) cc_final: 0.5162 (pmm) REVERT: A 408 ARG cc_start: 0.8133 (tmm-80) cc_final: 0.7777 (tmm-80) REVERT: A 441 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8191 (mm) REVERT: A 457 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7766 (tm-30) REVERT: A 532 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7617 (mm-30) REVERT: A 551 ASP cc_start: 0.7452 (t70) cc_final: 0.6980 (t70) REVERT: A 565 THR cc_start: 0.8349 (m) cc_final: 0.7872 (p) REVERT: A 624 LYS cc_start: 0.8067 (tptm) cc_final: 0.7748 (tttm) REVERT: A 630 ILE cc_start: 0.8640 (tp) cc_final: 0.8370 (tp) REVERT: A 669 GLN cc_start: 0.8342 (tp40) cc_final: 0.8118 (tp40) REVERT: A 674 TYR cc_start: 0.8419 (t80) cc_final: 0.8206 (t80) REVERT: A 695 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7664 (tm-30) REVERT: A 766 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8247 (tm-30) REVERT: A 808 VAL cc_start: 0.8804 (p) cc_final: 0.8459 (t) REVERT: A 812 LEU cc_start: 0.8600 (mt) cc_final: 0.8328 (mt) REVERT: A 814 GLN cc_start: 0.8204 (pp30) cc_final: 0.7713 (pp30) REVERT: A 865 LEU cc_start: 0.8709 (mm) cc_final: 0.8394 (mt) REVERT: A 867 LEU cc_start: 0.9080 (pp) cc_final: 0.8661 (pp) REVERT: A 871 PHE cc_start: 0.7789 (m-80) cc_final: 0.7389 (m-80) REVERT: A 873 TYR cc_start: 0.7412 (t80) cc_final: 0.7037 (t80) outliers start: 22 outliers final: 16 residues processed: 222 average time/residue: 0.0894 time to fit residues: 25.3576 Evaluate side-chains 225 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 887 GLN Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 911 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 2 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 75 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 GLN A 900 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.155536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.138164 restraints weight = 10415.124| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 3.56 r_work: 0.3716 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6359 Z= 0.159 Angle : 0.752 14.051 8597 Z= 0.384 Chirality : 0.048 0.416 947 Planarity : 0.005 0.050 1089 Dihedral : 5.948 55.510 840 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.29 % Favored : 84.58 % Rotamer: Outliers : 2.93 % Allowed : 27.23 % Favored : 69.84 % 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: -2.73 (0.30), residues: 765 helix: -0.05 (0.30), residues: 315 sheet: -1.76 (0.75), residues: 37 loop : -3.45 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 92 TYR 0.020 0.002 TYR A 903 PHE 0.017 0.001 PHE A 629 TRP 0.007 0.001 TRP A 220 HIS 0.002 0.001 HIS A 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 6357) covalent geometry : angle 0.75224 / 0.38 ( 8593) SS BOND : bond 0.00212 / 0.10 ( 2) SS BOND : angle 0.76883 / 0.28 ( 4) hydrogen bonds : bond 0.03475 / 2.22 ( 199) hydrogen bonds : angle 4.70750 / 3.14 ( 555) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7628 (tpp) cc_final: 0.7392 (tpp) REVERT: A 62 LYS cc_start: 0.8562 (ttmm) cc_final: 0.7952 (mtmm) REVERT: A 119 LYS cc_start: 0.8781 (tppp) cc_final: 0.8398 (tppp) REVERT: A 148 MET cc_start: 0.6830 (tmm) cc_final: 0.6463 (tmm) REVERT: A 150 ARG cc_start: 0.7335 (ptp-110) cc_final: 0.7003 (ptp-110) REVERT: A 158 GLU cc_start: 0.7699 (tp30) cc_final: 0.7426 (tp30) REVERT: A 159 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7937 (tm-30) REVERT: A 168 ASP cc_start: 0.7916 (p0) cc_final: 0.7372 (p0) REVERT: A 208 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7087 (mm-30) REVERT: A 226 PHE cc_start: 0.8726 (t80) cc_final: 0.8346 (t80) REVERT: A 252 GLU cc_start: 0.8768 (pt0) cc_final: 0.7715 (mt-10) REVERT: A 279 GLU cc_start: 0.7697 (tp30) cc_final: 0.7000 (mm-30) REVERT: A 282 MET cc_start: 0.7278 (tpt) cc_final: 0.6894 (tpt) REVERT: A 332 MET cc_start: 0.5647 (pmm) cc_final: 0.5149 (pmm) REVERT: A 408 ARG cc_start: 0.8121 (tmm-80) cc_final: 0.7729 (tmm-80) REVERT: A 443 LYS cc_start: 0.8541 (mtmm) cc_final: 0.8018 (mtmm) REVERT: A 457 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7760 (tm-30) REVERT: A 532 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7504 (mm-30) REVERT: A 551 ASP cc_start: 0.7476 (t70) cc_final: 0.7008 (t70) REVERT: A 565 THR cc_start: 0.8398 (m) cc_final: 0.7917 (p) REVERT: A 630 ILE cc_start: 0.8650 (tp) cc_final: 0.8375 (tp) REVERT: A 669 GLN cc_start: 0.8346 (tp40) cc_final: 0.8121 (tp40) REVERT: A 674 TYR cc_start: 0.8405 (t80) cc_final: 0.8182 (t80) REVERT: A 695 GLN cc_start: 0.8013 (tm-30) cc_final: 0.7669 (tm-30) REVERT: A 766 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8304 (tm-30) REVERT: A 808 VAL cc_start: 0.8801 (p) cc_final: 0.8454 (t) REVERT: A 812 LEU cc_start: 0.8578 (mt) cc_final: 0.8300 (mt) REVERT: A 814 GLN cc_start: 0.8200 (pp30) cc_final: 0.7700 (pp30) REVERT: A 865 LEU cc_start: 0.8682 (mm) cc_final: 0.8378 (mt) REVERT: A 867 LEU cc_start: 0.9098 (pp) cc_final: 0.8692 (pp) REVERT: A 871 PHE cc_start: 0.7775 (m-80) cc_final: 0.7382 (m-80) REVERT: A 873 TYR cc_start: 0.7387 (t80) cc_final: 0.7027 (t80) outliers start: 20 outliers final: 17 residues processed: 217 average time/residue: 0.0886 time to fit residues: 24.3938 Evaluate side-chains 229 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 212 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 887 GLN Chi-restraints excluded: chain A residue 911 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 0.0470 chunk 45 optimal weight: 0.3980 chunk 46 optimal weight: 0.0970 chunk 55 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 GLN A 887 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.157317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.139883 restraints weight = 10364.794| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 3.58 r_work: 0.3735 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6359 Z= 0.139 Angle : 0.753 13.926 8597 Z= 0.383 Chirality : 0.048 0.413 947 Planarity : 0.005 0.046 1089 Dihedral : 5.842 54.184 840 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.77 % Favored : 85.10 % Rotamer: Outliers : 3.07 % Allowed : 26.65 % Favored : 70.28 % 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: -2.67 (0.30), residues: 765 helix: -0.02 (0.30), residues: 315 sheet: -1.86 (0.74), residues: 37 loop : -3.38 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 92 TYR 0.018 0.002 TYR A 903 PHE 0.017 0.001 PHE A 629 TRP 0.006 0.001 TRP A 258 HIS 0.002 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 6357) covalent geometry : angle 0.75266 / 0.38 ( 8593) SS BOND : bond 0.00233 / 0.11 ( 2) SS BOND : angle 0.65067 / 0.25 ( 4) hydrogen bonds : bond 0.03379 / 2.17 ( 199) hydrogen bonds : angle 4.65849 / 3.11 ( 555) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7615 (tpp) cc_final: 0.7387 (tpp) REVERT: A 58 ARG cc_start: 0.7074 (tpp-160) cc_final: 0.6753 (tpp-160) REVERT: A 62 LYS cc_start: 0.8565 (ttmm) cc_final: 0.7843 (mtmm) REVERT: A 119 LYS cc_start: 0.8750 (tppp) cc_final: 0.8351 (tppp) REVERT: A 138 TYR cc_start: 0.7058 (t80) cc_final: 0.6762 (t80) REVERT: A 148 MET cc_start: 0.6787 (tmm) cc_final: 0.6401 (tmm) REVERT: A 150 ARG cc_start: 0.7302 (ptp-110) cc_final: 0.6884 (ptp-110) REVERT: A 158 GLU cc_start: 0.7644 (tp30) cc_final: 0.7367 (tp30) REVERT: A 159 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7947 (tm-30) REVERT: A 166 PHE cc_start: 0.8785 (m-10) cc_final: 0.8388 (m-80) REVERT: A 168 ASP cc_start: 0.7902 (p0) cc_final: 0.7340 (p0) REVERT: A 208 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7114 (mm-30) REVERT: A 226 PHE cc_start: 0.8691 (t80) cc_final: 0.8303 (t80) REVERT: A 252 GLU cc_start: 0.8737 (pt0) cc_final: 0.7672 (mt-10) REVERT: A 279 GLU cc_start: 0.7612 (tp30) cc_final: 0.6948 (mm-30) REVERT: A 282 MET cc_start: 0.7287 (tpt) cc_final: 0.6886 (tpt) REVERT: A 332 MET cc_start: 0.5417 (pmm) cc_final: 0.4920 (pmm) REVERT: A 408 ARG cc_start: 0.8118 (tmm-80) cc_final: 0.7714 (tmm-80) REVERT: A 443 LYS cc_start: 0.8563 (mtmm) cc_final: 0.8011 (mtmm) REVERT: A 457 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7733 (tm-30) REVERT: A 532 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7484 (mm-30) REVERT: A 551 ASP cc_start: 0.7473 (t70) cc_final: 0.6988 (t70) REVERT: A 565 THR cc_start: 0.8370 (m) cc_final: 0.7905 (p) REVERT: A 585 ARG cc_start: 0.8759 (mmm-85) cc_final: 0.8492 (mmm-85) REVERT: A 630 ILE cc_start: 0.8618 (tp) cc_final: 0.8346 (tp) REVERT: A 669 GLN cc_start: 0.8311 (tp40) cc_final: 0.8090 (tp40) REVERT: A 674 TYR cc_start: 0.8396 (t80) cc_final: 0.7760 (t80) REVERT: A 695 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7631 (tm-30) REVERT: A 715 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8162 (tm-30) REVERT: A 766 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8321 (tm-30) REVERT: A 808 VAL cc_start: 0.8784 (p) cc_final: 0.8441 (t) REVERT: A 812 LEU cc_start: 0.8573 (mt) cc_final: 0.8339 (mt) REVERT: A 814 GLN cc_start: 0.8178 (pp30) cc_final: 0.7755 (pp30) REVERT: A 864 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8362 (mm) REVERT: A 865 LEU cc_start: 0.8652 (mm) cc_final: 0.8349 (mt) REVERT: A 867 LEU cc_start: 0.9089 (pp) cc_final: 0.8694 (pp) REVERT: A 871 PHE cc_start: 0.7786 (m-80) cc_final: 0.7401 (m-80) REVERT: A 873 TYR cc_start: 0.7343 (t80) cc_final: 0.6995 (t80) outliers start: 21 outliers final: 17 residues processed: 218 average time/residue: 0.0828 time to fit residues: 23.0536 Evaluate side-chains 226 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 887 GLN Chi-restraints excluded: chain A residue 911 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 53 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 0.0980 chunk 17 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.155557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.137943 restraints weight = 10336.607| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 3.63 r_work: 0.3709 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6359 Z= 0.168 Angle : 0.769 13.517 8597 Z= 0.393 Chirality : 0.049 0.409 947 Planarity : 0.005 0.043 1089 Dihedral : 5.874 51.990 840 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.29 % Favored : 84.58 % Rotamer: Outliers : 2.78 % Allowed : 27.38 % Favored : 69.84 % 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: -2.72 (0.30), residues: 765 helix: -0.07 (0.30), residues: 321 sheet: -1.79 (0.76), residues: 37 loop : -3.45 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 92 TYR 0.020 0.002 TYR A 605 PHE 0.017 0.002 PHE A 629 TRP 0.008 0.001 TRP A 258 HIS 0.002 0.001 HIS A 811 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 6357) covalent geometry : angle 0.76871 / 0.39 ( 8593) SS BOND : bond 0.00493 / 0.24 ( 2) SS BOND : angle 0.73804 / 0.35 ( 4) hydrogen bonds : bond 0.03477 / 2.22 ( 199) hydrogen bonds : angle 4.67672 / 3.12 ( 555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1406.56 seconds wall clock time: 24 minutes 53.07 seconds (1493.07 seconds total)