Starting phenix.real_space_refine on Thu Jul 2 06:25:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zqb_60381/07_2026/8zqb_60381.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zqb_60381/07_2026/8zqb_60381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zqb_60381/07_2026/8zqb_60381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zqb_60381/07_2026/8zqb_60381.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zqb_60381/07_2026/8zqb_60381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zqb_60381/07_2026/8zqb_60381.map" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 38 5.49 5 S 24 5.16 5 C 4390 2.51 5 N 1333 2.21 5 O 1437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s 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: 7222 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6412 Classifications: {'peptide': 787} Link IDs: {'PTRANS': 28, 'TRANS': 758} Chain breaks: 8 Chain: "B" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 810 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 17, 'rna3p_pyr': 17} Link IDs: {'rna2p': 3, 'rna3p': 34} Time building chain proxies: 1.13, per 1000 atoms: 0.16 Number of scatterers: 7222 At special positions: 0 Unit cell: (95.04, 96.36, 100.98, 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 24 16.00 P 38 15.00 O 1437 8.00 N 1333 7.00 C 4390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 311.1 milliseconds 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1484 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 7 sheets defined 48.0% alpha, 17.8% beta 14 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 15 through 39 removed outlier: 4.548A pdb=" N HIS A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 Processing helix chain 'A' and resid 76 through 88 removed outlier: 3.584A pdb=" N LEU A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 211 through 252 Processing helix chain 'A' and resid 255 through 270 removed outlier: 3.525A pdb=" N GLU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 298 through 303 removed outlier: 4.373A pdb=" N LEU A 303 " --> pdb=" O GLY A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 330 removed outlier: 3.862A pdb=" N VAL A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.606A pdb=" N LYS A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 553 removed outlier: 4.069A pdb=" N ARG A 541 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.926A pdb=" N ALA A 560 " --> pdb=" O ASN A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 572 Processing helix chain 'A' and resid 579 through 606 Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 620 through 641 removed outlier: 4.252A pdb=" N PHE A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN A 635 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 688 removed outlier: 3.730A pdb=" N GLU A 688 " --> pdb=" O ARG A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 720 removed outlier: 3.801A pdb=" N LEU A 719 " --> pdb=" O SER A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 736 Processing helix chain 'A' and resid 782 through 797 Processing helix chain 'A' and resid 820 through 831 removed outlier: 3.524A pdb=" N LEU A 827 " --> pdb=" O GLU A 823 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 885 Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 899 through 903 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 11 removed outlier: 3.583A pdb=" N LYS A 5 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 439 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR A 433 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU A 423 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASN A 440 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL A 421 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 11 removed outlier: 3.583A pdb=" N LYS A 5 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 439 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR A 433 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU A 423 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASN A 440 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL A 421 " --> pdb=" O ASN A 440 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A 415 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 419 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 360 through 365 Processing sheet with id=AA4, first strand: chain 'A' and resid 513 through 517 removed outlier: 4.048A pdb=" N SER A 513 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 517 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 486 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 488 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU A 697 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU A 479 " --> pdb=" O GLU A 697 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL A 743 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N MET A 696 " --> pdb=" O VAL A 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 499 through 503 removed outlier: 4.444A pdb=" N VAL A 503 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLU A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 760 through 761 removed outlier: 3.579A pdb=" N TYR A 760 " --> pdb=" O TYR A 770 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 845 through 848 removed outlier: 3.793A pdb=" N SER A 845 " --> pdb=" O THR A 841 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR A 814 " --> pdb=" O LEU A 838 " (cutoff:3.500A) 333 hydrogen bonds defined for protein. 942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 66 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2162 1.33 - 1.45: 1280 1.45 - 1.57: 3880 1.57 - 1.69: 75 1.69 - 1.81: 37 Bond restraints: 7434 Sorted by residual: bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.13e+00 bond pdb=" C8 G B -36 " pdb=" N7 G B -36 " ideal model delta sigma weight residual 1.305 1.295 0.010 6.00e-03 2.78e+04 2.53e+00 bond pdb=" CG LEU A 670 " pdb=" CD2 LEU A 670 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.76e+00 bond pdb=" CA THR A 837 " pdb=" C THR A 837 " ideal model delta sigma weight residual 1.522 1.507 0.016 1.23e-02 6.61e+03 1.60e+00 bond pdb=" C THR A 837 " pdb=" N LEU A 838 " ideal model delta sigma weight residual 1.334 1.319 0.015 1.29e-02 6.01e+03 1.43e+00 ... (remaining 7429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 9819 1.40 - 2.81: 291 2.81 - 4.21: 66 4.21 - 5.62: 13 5.62 - 7.02: 2 Bond angle restraints: 10191 Sorted by residual: angle pdb=" N ASN A 482 " pdb=" CA ASN A 482 " pdb=" C ASN A 482 " ideal model delta sigma weight residual 112.35 107.68 4.67 1.34e+00 5.57e-01 1.22e+01 angle pdb=" N VAL A 743 " pdb=" CA VAL A 743 " pdb=" C VAL A 743 " ideal model delta sigma weight residual 108.45 113.57 -5.12 1.48e+00 4.57e-01 1.20e+01 angle pdb=" C1' G B -36 " pdb=" N9 G B -36 " pdb=" C4 G B -36 " ideal model delta sigma weight residual 126.50 130.82 -4.32 1.30e+00 5.92e-01 1.10e+01 angle pdb=" N SER A 6 " pdb=" CA SER A 6 " pdb=" C SER A 6 " ideal model delta sigma weight residual 108.55 113.87 -5.32 1.62e+00 3.81e-01 1.08e+01 angle pdb=" N9 G B -36 " pdb=" C4 G B -36 " pdb=" N3 G B -36 " ideal model delta sigma weight residual 126.00 127.94 -1.94 6.00e-01 2.78e+00 1.04e+01 ... (remaining 10186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 4359 35.87 - 71.74: 215 71.74 - 107.62: 18 107.62 - 143.49: 1 143.49 - 179.36: 1 Dihedral angle restraints: 4594 sinusoidal: 2303 harmonic: 2291 Sorted by residual: dihedral pdb=" O4' U B -32 " pdb=" C1' U B -32 " pdb=" N1 U B -32 " pdb=" C2 U B -32 " ideal model delta sinusoidal sigma weight residual 232.00 52.64 179.36 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' A B -21 " pdb=" C1' A B -21 " pdb=" N9 A B -21 " pdb=" C4 A B -21 " ideal model delta sinusoidal sigma weight residual -90.00 -18.62 -71.38 1 2.00e+01 2.50e-03 1.63e+01 dihedral pdb=" CA ARG A 873 " pdb=" C ARG A 873 " pdb=" N HIS A 874 " pdb=" CA HIS A 874 " ideal model delta harmonic sigma weight residual -180.00 -161.42 -18.58 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 4591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 791 0.033 - 0.065: 249 0.065 - 0.098: 60 0.098 - 0.131: 31 0.131 - 0.164: 3 Chirality restraints: 1134 Sorted by residual: chirality pdb=" CA PRO A 310 " pdb=" N PRO A 310 " pdb=" C PRO A 310 " pdb=" CB PRO A 310 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA ILE A 780 " pdb=" N ILE A 780 " pdb=" C ILE A 780 " pdb=" CB ILE A 780 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA VAL A 385 " pdb=" N VAL A 385 " pdb=" C VAL A 385 " pdb=" CB VAL A 385 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 1131 not shown) Planarity restraints: 1181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 903 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO A 904 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 904 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 904 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G B -36 " -0.016 2.00e-02 2.50e+03 7.84e-03 1.84e+00 pdb=" N9 G B -36 " 0.019 2.00e-02 2.50e+03 pdb=" C8 G B -36 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G B -36 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G B -36 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G B -36 " -0.000 2.00e-02 2.50e+03 pdb=" O6 G B -36 " -0.004 2.00e-02 2.50e+03 pdb=" N1 G B -36 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G B -36 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B -36 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B -36 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G B -36 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 734 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C LYS A 734 " -0.023 2.00e-02 2.50e+03 pdb=" O LYS A 734 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN A 735 " 0.008 2.00e-02 2.50e+03 ... (remaining 1178 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1030 2.75 - 3.29: 7543 3.29 - 3.83: 12503 3.83 - 4.36: 14418 4.36 - 4.90: 23219 Nonbonded interactions: 58713 Sorted by model distance: nonbonded pdb=" O ARG A 40 " pdb=" NH1 ARG A 40 " model vdw 2.213 3.120 nonbonded pdb=" O PRO A 870 " pdb=" OG1 THR A 880 " model vdw 2.215 3.040 nonbonded pdb=" O ASN A 785 " pdb=" OD1 ASN A 789 " model vdw 2.217 3.040 nonbonded pdb=" N ASP A 341 " pdb=" OG SER A 345 " model vdw 2.223 3.120 nonbonded pdb=" OD1 ASP A 497 " pdb=" N GLY A 498 " model vdw 2.237 3.120 ... (remaining 58708 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.750 Find NCS groups from input model: 0.020 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:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 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 : 0.003 0.046 7434 Z= 0.170 Angle : 0.608 7.021 10191 Z= 0.378 Chirality : 0.037 0.164 1134 Planarity : 0.004 0.050 1181 Dihedral : 19.010 179.362 3110 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.03 % Allowed : 19.41 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.31), residues: 769 helix: 0.63 (0.30), residues: 309 sheet: -0.46 (0.54), residues: 109 loop : -2.03 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 613 TYR 0.013 0.001 TYR A 542 PHE 0.019 0.001 PHE A 771 TRP 0.014 0.001 TRP A 229 HIS 0.010 0.002 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.17 ( 7434) covalent geometry : angle 0.60777 / 0.38 (10191) hydrogen bonds : bond 0.16657 / 10.95 ( 358) hydrogen bonds : angle 6.72235 / 4.85 ( 1008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 185 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ILE cc_start: 0.8688 (mm) cc_final: 0.8441 (mm) REVERT: A 623 TYR cc_start: 0.7488 (m-80) cc_final: 0.7283 (m-80) REVERT: A 793 ARG cc_start: 0.8562 (mtt180) cc_final: 0.8280 (mtt180) outliers start: 7 outliers final: 1 residues processed: 186 average time/residue: 0.0909 time to fit residues: 21.1070 Evaluate side-chains 118 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 530 HIS A 773 GLN A 789 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.085322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.069841 restraints weight = 31536.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.072357 restraints weight = 16447.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.073971 restraints weight = 10303.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.075097 restraints weight = 7320.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.075904 restraints weight = 5628.365| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7434 Z= 0.187 Angle : 0.805 13.058 10191 Z= 0.416 Chirality : 0.045 0.183 1134 Planarity : 0.006 0.048 1181 Dihedral : 17.492 178.857 1501 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.24 % Allowed : 22.21 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.31), residues: 769 helix: 0.61 (0.29), residues: 333 sheet: -0.43 (0.48), residues: 115 loop : -1.83 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 615 TYR 0.042 0.003 TYR A 308 PHE 0.025 0.003 PHE A 604 TRP 0.048 0.003 TRP A 640 HIS 0.010 0.002 HIS A 884 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 ( 7434) covalent geometry : angle 0.80466 / 0.42 (10191) hydrogen bonds : bond 0.05305 / 3.59 ( 358) hydrogen bonds : angle 5.23762 / 3.77 ( 1008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 PHE cc_start: 0.8188 (m-80) cc_final: 0.7587 (m-80) REVERT: A 343 ASP cc_start: 0.8839 (m-30) cc_final: 0.8265 (p0) REVERT: A 391 TRP cc_start: 0.8454 (t-100) cc_final: 0.8194 (t-100) REVERT: A 438 ASP cc_start: 0.8921 (OUTLIER) cc_final: 0.8528 (p0) REVERT: A 532 LEU cc_start: 0.8948 (tp) cc_final: 0.8737 (tp) REVERT: A 607 ARG cc_start: 0.8782 (ptt-90) cc_final: 0.8164 (ptt-90) REVERT: A 608 TYR cc_start: 0.8318 (m-80) cc_final: 0.7703 (m-80) REVERT: A 735 ASN cc_start: 0.8912 (p0) cc_final: 0.8649 (p0) REVERT: A 799 ARG cc_start: 0.8711 (tpt90) cc_final: 0.8502 (mmm160) REVERT: A 872 TYR cc_start: 0.6439 (m-80) cc_final: 0.6114 (m-80) outliers start: 22 outliers final: 10 residues processed: 133 average time/residue: 0.0903 time to fit residues: 15.1512 Evaluate side-chains 118 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 837 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 5 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 0.0970 chunk 28 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 689 HIS A 789 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.085853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.071004 restraints weight = 31607.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.073462 restraints weight = 16432.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.075154 restraints weight = 10278.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.076281 restraints weight = 7184.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.076948 restraints weight = 5482.989| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7434 Z= 0.151 Angle : 0.720 8.608 10191 Z= 0.373 Chirality : 0.042 0.188 1134 Planarity : 0.005 0.043 1181 Dihedral : 17.318 177.752 1497 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.41 % Allowed : 20.88 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.31), residues: 769 helix: 0.99 (0.29), residues: 327 sheet: -0.43 (0.46), residues: 118 loop : -1.73 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 326 TYR 0.030 0.002 TYR A 308 PHE 0.023 0.002 PHE A 571 TRP 0.015 0.002 TRP A 640 HIS 0.010 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 7434) covalent geometry : angle 0.71981 / 0.37 (10191) hydrogen bonds : bond 0.04547 / 3.07 ( 358) hydrogen bonds : angle 4.88294 / 3.51 ( 1008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 SER cc_start: 0.8804 (t) cc_final: 0.8461 (m) REVERT: A 64 PHE cc_start: 0.8140 (m-80) cc_final: 0.7561 (m-80) REVERT: A 216 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8392 (ttpt) REVERT: A 242 GLU cc_start: 0.9380 (tm-30) cc_final: 0.9161 (pp20) REVERT: A 328 TRP cc_start: 0.9077 (t60) cc_final: 0.8771 (t60) REVERT: A 343 ASP cc_start: 0.8822 (m-30) cc_final: 0.8290 (p0) REVERT: A 345 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8463 (p) REVERT: A 391 TRP cc_start: 0.8445 (t-100) cc_final: 0.8213 (t-100) REVERT: A 395 VAL cc_start: 0.7511 (m) cc_final: 0.7252 (p) REVERT: A 405 ILE cc_start: 0.9267 (pt) cc_final: 0.9007 (mp) REVERT: A 438 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8520 (p0) REVERT: A 475 MET cc_start: 0.8360 (tmm) cc_final: 0.8147 (tmm) REVERT: A 548 LYS cc_start: 0.8710 (tttt) cc_final: 0.8268 (tttm) REVERT: A 696 MET cc_start: 0.9299 (ptp) cc_final: 0.8610 (pmm) REVERT: A 735 ASN cc_start: 0.8911 (p0) cc_final: 0.8671 (p0) REVERT: A 741 TRP cc_start: 0.6600 (t-100) cc_final: 0.5319 (t-100) REVERT: A 799 ARG cc_start: 0.8737 (tpt90) cc_final: 0.8429 (mmm160) REVERT: A 837 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8842 (t) REVERT: A 869 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8914 (mm-30) REVERT: A 872 TYR cc_start: 0.6666 (m-80) cc_final: 0.6362 (m-80) outliers start: 30 outliers final: 17 residues processed: 134 average time/residue: 0.0871 time to fit residues: 14.8815 Evaluate side-chains 132 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 46 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 69 optimal weight: 0.2980 chunk 54 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 12 optimal weight: 0.1980 chunk 20 optimal weight: 9.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.080587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.065867 restraints weight = 33670.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.068140 restraints weight = 17888.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.069733 restraints weight = 11379.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.070804 restraints weight = 8022.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.071587 restraints weight = 6174.573| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7434 Z= 0.254 Angle : 0.760 9.733 10191 Z= 0.400 Chirality : 0.044 0.213 1134 Planarity : 0.006 0.043 1181 Dihedral : 17.190 176.626 1497 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 6.76 % Allowed : 18.97 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.30), residues: 769 helix: 0.66 (0.28), residues: 336 sheet: -0.46 (0.46), residues: 113 loop : -1.84 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 607 TYR 0.027 0.002 TYR A 308 PHE 0.019 0.003 PHE A 571 TRP 0.015 0.002 TRP A 640 HIS 0.007 0.002 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.25 ( 7434) covalent geometry : angle 0.75968 / 0.40 (10191) hydrogen bonds : bond 0.04933 / 3.30 ( 358) hydrogen bonds : angle 4.81429 / 3.47 ( 1008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 106 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 PHE cc_start: 0.8367 (m-80) cc_final: 0.7724 (m-80) REVERT: A 216 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8718 (ttpt) REVERT: A 328 TRP cc_start: 0.9133 (t60) cc_final: 0.8863 (t60) REVERT: A 343 ASP cc_start: 0.8921 (m-30) cc_final: 0.8345 (p0) REVERT: A 345 SER cc_start: 0.8695 (OUTLIER) cc_final: 0.8092 (p) REVERT: A 391 TRP cc_start: 0.8656 (t-100) cc_final: 0.8390 (t-100) REVERT: A 446 VAL cc_start: 0.6063 (OUTLIER) cc_final: 0.5819 (m) REVERT: A 694 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8159 (p) REVERT: A 696 MET cc_start: 0.9362 (ptp) cc_final: 0.8642 (pmm) REVERT: A 735 ASN cc_start: 0.8984 (p0) cc_final: 0.8698 (p0) REVERT: A 741 TRP cc_start: 0.6977 (t-100) cc_final: 0.5572 (t-100) REVERT: A 872 TYR cc_start: 0.7133 (m-80) cc_final: 0.6767 (m-80) outliers start: 46 outliers final: 31 residues processed: 136 average time/residue: 0.0830 time to fit residues: 14.6029 Evaluate side-chains 134 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 829 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 76 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.082895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.067993 restraints weight = 32423.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.070402 restraints weight = 17030.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.071939 restraints weight = 10728.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.073049 restraints weight = 7607.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.073774 restraints weight = 5828.618| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7434 Z= 0.143 Angle : 0.692 10.906 10191 Z= 0.356 Chirality : 0.043 0.298 1134 Planarity : 0.005 0.063 1181 Dihedral : 17.298 178.062 1497 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.85 % Allowed : 21.62 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.31), residues: 769 helix: 1.10 (0.29), residues: 331 sheet: -0.41 (0.45), residues: 125 loop : -1.58 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 793 TYR 0.026 0.002 TYR A 308 PHE 0.019 0.002 PHE A 265 TRP 0.010 0.001 TRP A 720 HIS 0.010 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 7434) covalent geometry : angle 0.69161 / 0.36 (10191) hydrogen bonds : bond 0.04164 / 2.92 ( 358) hydrogen bonds : angle 4.56394 / 3.31 ( 1008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7917 (mmm-85) cc_final: 0.7656 (mmt90) REVERT: A 64 PHE cc_start: 0.8350 (m-80) cc_final: 0.7718 (m-80) REVERT: A 216 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8545 (ttpt) REVERT: A 242 GLU cc_start: 0.9357 (tm-30) cc_final: 0.9140 (pp20) REVERT: A 328 TRP cc_start: 0.9129 (t60) cc_final: 0.8848 (t60) REVERT: A 343 ASP cc_start: 0.8850 (m-30) cc_final: 0.8304 (p0) REVERT: A 391 TRP cc_start: 0.8577 (t-100) cc_final: 0.8327 (t-100) REVERT: A 405 ILE cc_start: 0.9328 (pt) cc_final: 0.9100 (mp) REVERT: A 607 ARG cc_start: 0.8808 (ptt-90) cc_final: 0.8373 (ptt-90) REVERT: A 608 TYR cc_start: 0.8379 (m-80) cc_final: 0.7813 (m-80) REVERT: A 641 ASN cc_start: 0.8638 (t0) cc_final: 0.8399 (t0) REVERT: A 675 LEU cc_start: 0.8675 (tp) cc_final: 0.8431 (tp) REVERT: A 696 MET cc_start: 0.9269 (ptp) cc_final: 0.8760 (pmm) REVERT: A 717 LEU cc_start: 0.9010 (pt) cc_final: 0.8681 (mm) REVERT: A 730 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8555 (pp20) REVERT: A 735 ASN cc_start: 0.8847 (p0) cc_final: 0.8515 (p0) REVERT: A 774 ASP cc_start: 0.9276 (m-30) cc_final: 0.8946 (p0) REVERT: A 851 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8271 (mt) outliers start: 33 outliers final: 18 residues processed: 131 average time/residue: 0.0786 time to fit residues: 13.4264 Evaluate side-chains 122 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.082654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.067785 restraints weight = 32755.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.070165 restraints weight = 17113.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.071763 restraints weight = 10724.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.072896 restraints weight = 7574.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.073522 restraints weight = 5815.483| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7434 Z= 0.143 Angle : 0.686 10.316 10191 Z= 0.356 Chirality : 0.043 0.300 1134 Planarity : 0.004 0.050 1181 Dihedral : 17.232 177.794 1497 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.12 % Allowed : 21.18 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.31), residues: 769 helix: 1.05 (0.29), residues: 329 sheet: -0.40 (0.45), residues: 127 loop : -1.58 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 TYR 0.041 0.002 TYR A 760 PHE 0.039 0.002 PHE A 202 TRP 0.013 0.001 TRP A 229 HIS 0.009 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 7434) covalent geometry : angle 0.68647 / 0.36 (10191) hydrogen bonds : bond 0.03984 / 2.78 ( 358) hydrogen bonds : angle 4.58592 / 3.33 ( 1008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7912 (mmm-85) cc_final: 0.7639 (mmt90) REVERT: A 64 PHE cc_start: 0.8397 (m-80) cc_final: 0.7740 (m-80) REVERT: A 216 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8605 (ttpt) REVERT: A 242 GLU cc_start: 0.9350 (tm-30) cc_final: 0.9144 (pp20) REVERT: A 328 TRP cc_start: 0.9159 (t60) cc_final: 0.8886 (t60) REVERT: A 343 ASP cc_start: 0.8792 (m-30) cc_final: 0.8229 (p0) REVERT: A 391 TRP cc_start: 0.8608 (t-100) cc_final: 0.8370 (t-100) REVERT: A 641 ASN cc_start: 0.8713 (t0) cc_final: 0.8433 (t0) REVERT: A 696 MET cc_start: 0.9243 (ptp) cc_final: 0.8727 (pmm) REVERT: A 730 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8537 (pp20) REVERT: A 735 ASN cc_start: 0.8789 (p0) cc_final: 0.8473 (p0) REVERT: A 774 ASP cc_start: 0.9265 (m-30) cc_final: 0.8925 (p0) REVERT: A 851 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8262 (mt) outliers start: 28 outliers final: 19 residues processed: 118 average time/residue: 0.0871 time to fit residues: 13.2800 Evaluate side-chains 119 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 63 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.081787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.066623 restraints weight = 33176.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.068981 restraints weight = 17610.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.070605 restraints weight = 11118.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.071676 restraints weight = 7913.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.072517 restraints weight = 6113.142| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7434 Z= 0.166 Angle : 0.683 9.640 10191 Z= 0.353 Chirality : 0.043 0.268 1134 Planarity : 0.004 0.043 1181 Dihedral : 17.199 177.743 1497 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 5.15 % Allowed : 20.44 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.31), residues: 769 helix: 1.09 (0.29), residues: 331 sheet: -0.50 (0.45), residues: 127 loop : -1.63 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 326 TYR 0.027 0.002 TYR A 760 PHE 0.020 0.002 PHE A 202 TRP 0.013 0.001 TRP A 229 HIS 0.011 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 ( 7434) covalent geometry : angle 0.68251 / 0.35 (10191) hydrogen bonds : bond 0.04030 / 2.79 ( 358) hydrogen bonds : angle 4.53764 / 3.30 ( 1008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7905 (mmm-85) cc_final: 0.7452 (mmt90) REVERT: A 64 PHE cc_start: 0.8490 (m-80) cc_final: 0.7615 (m-10) REVERT: A 216 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8600 (ttpt) REVERT: A 328 TRP cc_start: 0.9181 (t60) cc_final: 0.8912 (t60) REVERT: A 343 ASP cc_start: 0.8842 (m-30) cc_final: 0.8300 (p0) REVERT: A 391 TRP cc_start: 0.8664 (t-100) cc_final: 0.8440 (t-100) REVERT: A 506 MET cc_start: 0.9045 (mmt) cc_final: 0.8700 (mmt) REVERT: A 641 ASN cc_start: 0.8794 (t0) cc_final: 0.8477 (t0) REVERT: A 694 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8390 (p) REVERT: A 696 MET cc_start: 0.9285 (ptp) cc_final: 0.8779 (pmm) REVERT: A 730 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8539 (pp20) REVERT: A 735 ASN cc_start: 0.8763 (p0) cc_final: 0.8472 (p0) REVERT: A 774 ASP cc_start: 0.9273 (m-30) cc_final: 0.8938 (p0) REVERT: A 793 ARG cc_start: 0.9137 (mtt180) cc_final: 0.8848 (mtp180) REVERT: A 851 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8256 (mt) outliers start: 35 outliers final: 24 residues processed: 121 average time/residue: 0.0820 time to fit residues: 12.8684 Evaluate side-chains 124 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 8.9990 chunk 42 optimal weight: 0.0070 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 overall best weight: 0.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.083150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.067962 restraints weight = 32773.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.070404 restraints weight = 17297.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.072030 restraints weight = 10759.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.073173 restraints weight = 7584.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.073952 restraints weight = 5815.746| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7434 Z= 0.132 Angle : 0.676 9.516 10191 Z= 0.346 Chirality : 0.042 0.193 1134 Planarity : 0.004 0.042 1181 Dihedral : 17.183 177.813 1497 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.82 % Allowed : 22.35 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.31), residues: 769 helix: 1.18 (0.29), residues: 330 sheet: -0.35 (0.47), residues: 120 loop : -1.48 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 49 TYR 0.025 0.001 TYR A 760 PHE 0.020 0.002 PHE A 571 TRP 0.018 0.001 TRP A 741 HIS 0.012 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 7434) covalent geometry : angle 0.67626 / 0.35 (10191) hydrogen bonds : bond 0.03753 / 2.63 ( 358) hydrogen bonds : angle 4.47670 / 3.27 ( 1008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7856 (mmm-85) cc_final: 0.7531 (mmt90) REVERT: A 216 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8525 (ttpt) REVERT: A 328 TRP cc_start: 0.9187 (t60) cc_final: 0.8924 (t60) REVERT: A 391 TRP cc_start: 0.8611 (t-100) cc_final: 0.8397 (t-100) REVERT: A 506 MET cc_start: 0.9011 (mmt) cc_final: 0.8654 (mmt) REVERT: A 623 TYR cc_start: 0.8882 (m-10) cc_final: 0.8678 (m-10) REVERT: A 641 ASN cc_start: 0.8766 (t0) cc_final: 0.8400 (t0) REVERT: A 672 MET cc_start: 0.7503 (tpp) cc_final: 0.7242 (tpp) REVERT: A 696 MET cc_start: 0.9276 (ptp) cc_final: 0.8735 (pmm) REVERT: A 717 LEU cc_start: 0.9002 (pt) cc_final: 0.8738 (mm) REVERT: A 730 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8482 (pp20) REVERT: A 735 ASN cc_start: 0.8682 (p0) cc_final: 0.8432 (p0) REVERT: A 774 ASP cc_start: 0.9269 (m-30) cc_final: 0.8920 (p0) REVERT: A 851 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8221 (mt) outliers start: 26 outliers final: 21 residues processed: 119 average time/residue: 0.1084 time to fit residues: 16.4541 Evaluate side-chains 123 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 56 optimal weight: 0.0770 chunk 36 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.081919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066859 restraints weight = 32713.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.069183 restraints weight = 17319.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.070773 restraints weight = 10988.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.071928 restraints weight = 7787.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.072622 restraints weight = 6003.284| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7434 Z= 0.154 Angle : 0.706 11.191 10191 Z= 0.360 Chirality : 0.041 0.178 1134 Planarity : 0.004 0.049 1181 Dihedral : 17.156 177.646 1497 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.82 % Allowed : 22.50 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.31), residues: 769 helix: 1.17 (0.29), residues: 331 sheet: -0.30 (0.50), residues: 110 loop : -1.52 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 326 TYR 0.022 0.002 TYR A 760 PHE 0.020 0.002 PHE A 604 TRP 0.015 0.001 TRP A 229 HIS 0.010 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 7434) covalent geometry : angle 0.70558 / 0.36 (10191) hydrogen bonds : bond 0.03814 / 2.65 ( 358) hydrogen bonds : angle 4.49551 / 3.29 ( 1008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 SER cc_start: 0.8471 (t) cc_final: 0.8079 (p) REVERT: A 34 ARG cc_start: 0.7851 (mmm-85) cc_final: 0.7509 (mmt90) REVERT: A 64 PHE cc_start: 0.8646 (m-80) cc_final: 0.8413 (m-80) REVERT: A 216 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8504 (ttpt) REVERT: A 328 TRP cc_start: 0.9205 (t60) cc_final: 0.8939 (t60) REVERT: A 391 TRP cc_start: 0.8676 (t-100) cc_final: 0.8455 (t-100) REVERT: A 506 MET cc_start: 0.9013 (mmt) cc_final: 0.8654 (mmt) REVERT: A 641 ASN cc_start: 0.8844 (t0) cc_final: 0.8472 (t0) REVERT: A 696 MET cc_start: 0.9287 (ptp) cc_final: 0.8755 (pmm) REVERT: A 717 LEU cc_start: 0.8995 (pt) cc_final: 0.8738 (mm) REVERT: A 730 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8473 (pp20) REVERT: A 735 ASN cc_start: 0.8691 (p0) cc_final: 0.8448 (p0) REVERT: A 774 ASP cc_start: 0.9284 (m-30) cc_final: 0.8933 (p0) REVERT: A 793 ARG cc_start: 0.9185 (mtt180) cc_final: 0.8925 (mtp180) REVERT: A 851 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8171 (mt) outliers start: 26 outliers final: 20 residues processed: 117 average time/residue: 0.1008 time to fit residues: 15.1990 Evaluate side-chains 122 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 GLN A 530 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.081598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.066440 restraints weight = 33302.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.068774 restraints weight = 17641.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.070339 restraints weight = 11220.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.071484 restraints weight = 7997.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.072326 restraints weight = 6181.468| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7434 Z= 0.166 Angle : 0.720 12.296 10191 Z= 0.368 Chirality : 0.041 0.178 1134 Planarity : 0.004 0.057 1181 Dihedral : 17.158 177.712 1497 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.68 % Allowed : 23.09 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.31), residues: 769 helix: 1.11 (0.29), residues: 331 sheet: -0.47 (0.48), residues: 117 loop : -1.61 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 356 TYR 0.023 0.002 TYR A 760 PHE 0.017 0.002 PHE A 604 TRP 0.014 0.001 TRP A 229 HIS 0.010 0.002 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 7434) covalent geometry : angle 0.71976 / 0.37 (10191) hydrogen bonds : bond 0.03841 / 2.68 ( 358) hydrogen bonds : angle 4.54416 / 3.32 ( 1008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 SER cc_start: 0.8480 (t) cc_final: 0.8083 (p) REVERT: A 34 ARG cc_start: 0.7864 (mmm-85) cc_final: 0.7540 (mmt90) REVERT: A 64 PHE cc_start: 0.8693 (m-80) cc_final: 0.8341 (m-80) REVERT: A 328 TRP cc_start: 0.9215 (t60) cc_final: 0.8947 (t60) REVERT: A 391 TRP cc_start: 0.8682 (t-100) cc_final: 0.8470 (t-100) REVERT: A 506 MET cc_start: 0.9021 (mmt) cc_final: 0.8680 (mmt) REVERT: A 641 ASN cc_start: 0.8860 (t0) cc_final: 0.8477 (t0) REVERT: A 694 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8448 (p) REVERT: A 696 MET cc_start: 0.9284 (ptp) cc_final: 0.8792 (pmm) REVERT: A 730 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8472 (pp20) REVERT: A 735 ASN cc_start: 0.8662 (p0) cc_final: 0.8423 (p0) REVERT: A 774 ASP cc_start: 0.9293 (m-30) cc_final: 0.8935 (p0) REVERT: A 793 ARG cc_start: 0.9167 (mtt180) cc_final: 0.8943 (mtp180) REVERT: A 851 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8164 (mt) outliers start: 25 outliers final: 19 residues processed: 114 average time/residue: 0.0987 time to fit residues: 14.5224 Evaluate side-chains 121 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 76 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 47 optimal weight: 0.0020 chunk 68 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.082085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.066811 restraints weight = 33319.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.069215 restraints weight = 17605.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.070787 restraints weight = 11135.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.071881 restraints weight = 7958.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.072648 restraints weight = 6177.764| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.5360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7434 Z= 0.149 Angle : 0.704 11.979 10191 Z= 0.362 Chirality : 0.041 0.176 1134 Planarity : 0.004 0.057 1181 Dihedral : 17.144 177.950 1497 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.53 % Allowed : 23.68 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.31), residues: 769 helix: 1.19 (0.29), residues: 330 sheet: -0.39 (0.47), residues: 120 loop : -1.60 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 356 TYR 0.023 0.002 TYR A 760 PHE 0.018 0.002 PHE A 369 TRP 0.014 0.001 TRP A 229 HIS 0.010 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 7434) covalent geometry : angle 0.70383 / 0.36 (10191) hydrogen bonds : bond 0.03777 / 2.64 ( 358) hydrogen bonds : angle 4.50713 / 3.29 ( 1008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1267.82 seconds wall clock time: 22 minutes 34.06 seconds (1354.06 seconds total)