Starting phenix.real_space_refine on Fri Sep 11 16:23:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6h66_0145/09_2026/6h66_0145.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h66_0145/09_2026/6h66_0145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6h66_0145/09_2026/6h66_0145.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6h66_0145/09_2026/6h66_0145.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6h66_0145/09_2026/6h66_0145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h66_0145/09_2026/6h66_0145.map" model { file = "/net/cci-nas-00/data/ceres_data/6h66_0145/09_2026/6h66_0145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h66_0145/09_2026/6h66_0145.cif" } resolution = 4.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 30 5.49 5 S 33 5.16 5 C 3624 2.51 5 N 1034 2.21 5 O 1175 1.98 5 H 4120 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10017 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 9377 Classifications: {'peptide': 667} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 645} Chain breaks: 7 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'GLU:plan': 13, 'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "X" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 318 Classifications: {'RNAv2': 15} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 8} Link IDs: {'rna3p': 14} Chain: "Y" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 321 Classifications: {'RNAv2': 15} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7936 SG CYS A 907 79.226 42.468 38.240 1.00 94.73 S ATOM 7983 SG CYS A 910 82.212 42.289 38.218 1.00 95.46 S ATOM 8600 SG CYS A 962 80.015 43.857 41.901 1.00 95.10 S ATOM 8615 SG CYS A 964 79.715 45.327 39.850 1.00 99.85 S Time building chain proxies: 1.83, per 1000 atoms: 0.18 Number of scatterers: 10017 At special positions: 0 Unit cell: (99.84, 91.52, 73.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 33 16.00 P 30 15.00 O 1175 8.00 N 1034 7.00 C 3624 6.00 H 4120 1.00 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: 1.17 Conformation dependent library (CDL) restraints added in 236.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 907 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 910 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 962 " Number of angles added : 6 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1276 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 6 sheets defined 55.2% alpha, 6.7% beta 15 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 310 through 318 removed outlier: 3.534A pdb=" N GLU A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 322 Processing helix chain 'A' and resid 335 through 355 removed outlier: 4.022A pdb=" N VAL A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 377 removed outlier: 3.944A pdb=" N ALA A 370 " --> pdb=" O LYS A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 383 removed outlier: 3.927A pdb=" N TYR A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 407 removed outlier: 3.549A pdb=" N VAL A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 428 removed outlier: 3.599A pdb=" N GLU A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 445 through 449 Processing helix chain 'A' and resid 455 through 476 removed outlier: 3.933A pdb=" N MET A 459 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 515 Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.790A pdb=" N LEU A 529 " --> pdb=" O ASN A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 567 removed outlier: 3.825A pdb=" N ILE A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 592 removed outlier: 3.616A pdb=" N GLU A 580 " --> pdb=" O THR A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 616 Processing helix chain 'A' and resid 619 through 643 removed outlier: 3.992A pdb=" N ALA A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 692 removed outlier: 4.291A pdb=" N ASN A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS A 685 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N MET A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 716 removed outlier: 3.845A pdb=" N GLN A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 741 Processing helix chain 'A' and resid 767 through 781 Processing helix chain 'A' and resid 790 through 796 removed outlier: 3.831A pdb=" N GLU A 794 " --> pdb=" O THR A 790 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY A 795 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A 796 " --> pdb=" O ALA A 792 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 790 through 796' Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 840 through 863 removed outlier: 3.863A pdb=" N GLU A 844 " --> pdb=" O VAL A 840 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 855 " --> pdb=" O GLU A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 895 removed outlier: 3.985A pdb=" N GLN A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 987 Processing helix chain 'A' and resid 1002 through 1006 removed outlier: 3.562A pdb=" N GLU A1005 " --> pdb=" O LYS A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1019 Processing sheet with id=AA1, first strand: chain 'A' and resid 326 through 327 removed outlier: 6.754A pdb=" N ILE A 326 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE A 441 " --> pdb=" O LEU A 486 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 360 through 364 removed outlier: 6.091A pdb=" N VAL A 360 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N SER A 413 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL A 362 " --> pdb=" O SER A 413 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 722 through 723 Processing sheet with id=AA4, first strand: chain 'A' and resid 913 through 915 removed outlier: 6.549A pdb=" N LEU A 905 " --> pdb=" O VAL A 914 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 921 through 923 Processing sheet with id=AA6, first strand: chain 'A' and resid 940 through 942 removed outlier: 6.350A pdb=" N ILE A 960 " --> pdb=" O TRP A 968 " (cutoff:3.500A) 266 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4109 1.03 - 1.23: 27 1.23 - 1.42: 2506 1.42 - 1.62: 3476 1.62 - 1.81: 52 Bond restraints: 10170 Sorted by residual: bond pdb=" CB MET A 459 " pdb=" CG MET A 459 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.43e+00 bond pdb=" N ASN A 379 " pdb=" CA ASN A 379 " ideal model delta sigma weight residual 1.462 1.448 0.014 7.70e-03 1.69e+04 3.31e+00 bond pdb=" CB VAL A 360 " pdb=" CG1 VAL A 360 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.70e+00 bond pdb=" CG LYS A 466 " pdb=" CD LYS A 466 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.57e+00 bond pdb=" CG LEU A 418 " pdb=" CD1 LEU A 418 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.43e+00 ... (remaining 10165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.63: 17688 10.63 - 21.26: 3 21.26 - 31.88: 0 31.88 - 42.51: 0 42.51 - 53.14: 6 Bond angle restraints: 17697 Sorted by residual: angle pdb=" C LYS A 451 " pdb=" N GLU A 452 " pdb=" H GLU A 452 " ideal model delta sigma weight residual 124.11 70.97 53.14 3.00e+00 1.11e-01 3.14e+02 angle pdb=" C ALA A 497 " pdb=" N LYS A 498 " pdb=" H LYS A 498 " ideal model delta sigma weight residual 124.56 72.49 52.07 3.00e+00 1.11e-01 3.01e+02 angle pdb=" CA GLU A 452 " pdb=" N GLU A 452 " pdb=" H GLU A 452 " ideal model delta sigma weight residual 113.81 62.45 51.36 3.00e+00 1.11e-01 2.93e+02 angle pdb=" C ILE A 399 " pdb=" N SER A 400 " pdb=" H SER A 400 " ideal model delta sigma weight residual 124.49 73.30 51.19 3.00e+00 1.11e-01 2.91e+02 angle pdb=" CA SER A 400 " pdb=" N SER A 400 " pdb=" H SER A 400 " ideal model delta sigma weight residual 114.19 63.54 50.65 3.00e+00 1.11e-01 2.85e+02 ... (remaining 17692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.90: 4451 13.90 - 27.79: 429 27.79 - 41.69: 100 41.69 - 55.58: 45 55.58 - 69.48: 7 Dihedral angle restraints: 5032 sinusoidal: 2827 harmonic: 2205 Sorted by residual: dihedral pdb=" CA LYS A 477 " pdb=" C LYS A 477 " pdb=" N PRO A 478 " pdb=" CA PRO A 478 " ideal model delta harmonic sigma weight residual 180.00 142.23 37.77 0 5.00e+00 4.00e-02 5.71e+01 dihedral pdb=" O5' G X 15 " pdb=" C5' G X 15 " pdb=" C4' G X 15 " pdb=" C3' G X 15 " ideal model delta sinusoidal sigma weight residual 60.00 114.79 -54.79 3 6.40e+00 2.44e-02 5.11e+01 dihedral pdb=" CA GLN A 999 " pdb=" C GLN A 999 " pdb=" N TYR A1000 " pdb=" CA TYR A1000 " ideal model delta harmonic sigma weight residual -180.00 -154.70 -25.30 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 5029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 771 0.058 - 0.116: 152 0.116 - 0.174: 23 0.174 - 0.232: 25 0.232 - 0.290: 4 Chirality restraints: 975 Sorted by residual: chirality pdb=" P C X 3 " pdb=" OP1 C X 3 " pdb=" OP2 C X 3 " pdb=" O5' C X 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.46 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" P G Y 2 " pdb=" OP1 G Y 2 " pdb=" OP2 G Y 2 " pdb=" O5' G Y 2 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" P C Y 8 " pdb=" OP1 C Y 8 " pdb=" OP2 C Y 8 " pdb=" O5' C Y 8 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 972 not shown) Planarity restraints: 1482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 987 " 0.027 2.00e-02 2.50e+03 1.58e-02 7.52e+00 pdb=" CG PHE A 987 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 987 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 987 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 987 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 987 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 987 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE A 987 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 987 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE A 987 " 0.008 2.00e-02 2.50e+03 pdb=" HE2 PHE A 987 " 0.006 2.00e-02 2.50e+03 pdb=" HZ PHE A 987 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 460 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.88e+00 pdb=" C ARG A 460 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG A 460 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG A 461 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 491 " -0.035 5.00e-02 4.00e+02 5.19e-02 4.30e+00 pdb=" N PRO A 492 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 492 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 492 " -0.029 5.00e-02 4.00e+02 ... (remaining 1479 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 244 2.15 - 2.76: 16443 2.76 - 3.37: 24632 3.37 - 3.99: 32075 3.99 - 4.60: 49773 Nonbonded interactions: 123167 Sorted by model distance: nonbonded pdb=" H LYS A 498 " pdb=" HA LYS A 498 " model vdw 1.532 1.816 nonbonded pdb=" H SER A 400 " pdb=" HA SER A 400 " model vdw 1.576 1.816 nonbonded pdb=" O SER A 357 " pdb=" HG SER A 439 " model vdw 1.657 2.450 nonbonded pdb=" HE2 HIS A 927 " pdb=" O2' U X 5 " model vdw 1.692 2.450 nonbonded pdb=" O ILE A 614 " pdb=" H ILE A 618 " model vdw 1.702 2.450 ... (remaining 123162 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.360 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 : 0.008 0.056 6054 Z= 0.366 Angle : 1.241 45.932 8295 Z= 0.529 Chirality : 0.060 0.290 975 Planarity : 0.006 0.052 939 Dihedral : 10.548 69.479 2381 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.45 % Favored : 89.40 % Rotamer: Outliers : 0.17 % Allowed : 1.05 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.28), residues: 651 helix: -0.66 (0.25), residues: 308 sheet: -3.20 (0.45), residues: 85 loop : -3.36 (0.32), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 599 TYR 0.016 0.003 TYR A 312 PHE 0.046 0.004 PHE A 987 TRP 0.018 0.002 TRP A 582 HIS 0.007 0.002 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00806 / 0.37 ( 6050) covalent geometry : angle 0.91816 / 0.51 ( 8289) hydrogen bonds : bond 0.17167 / 11.03 ( 304) hydrogen bonds : angle 6.56122 / 4.78 ( 826) metal coordination : bond 0.01525 / 0.78 ( 4) metal coordination : angle 31.06001 / 12.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 971 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.282 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 TYR cc_start: 0.7499 (t80) cc_final: 0.7279 (t80) REVERT: A 603 GLU cc_start: 0.7985 (tt0) cc_final: 0.6993 (tm-30) REVERT: A 612 LEU cc_start: 0.9079 (mt) cc_final: 0.8862 (tt) REVERT: A 620 MET cc_start: 0.7779 (ptp) cc_final: 0.7563 (ptp) outliers start: 1 outliers final: 1 residues processed: 174 average time/residue: 0.1960 time to fit residues: 42.4179 Evaluate side-chains 96 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 GLN A 736 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.106802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.089238 restraints weight = 41000.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.093038 restraints weight = 19312.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.095348 restraints weight = 11766.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.096815 restraints weight = 8509.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.097741 restraints weight = 6846.907| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6054 Z= 0.164 Angle : 0.760 23.499 8295 Z= 0.375 Chirality : 0.043 0.159 975 Planarity : 0.005 0.049 939 Dihedral : 9.839 60.280 1060 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.17 % Allowed : 1.05 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.61 (0.31), residues: 651 helix: 0.99 (0.29), residues: 314 sheet: -3.05 (0.50), residues: 76 loop : -3.13 (0.31), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 860 TYR 0.010 0.002 TYR A 939 PHE 0.011 0.001 PHE A 551 TRP 0.008 0.001 TRP A 582 HIS 0.014 0.002 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 ( 6050) covalent geometry : angle 0.72346 / 0.37 ( 8289) hydrogen bonds : bond 0.04032 / 2.63 ( 304) hydrogen bonds : angle 4.82521 / 3.50 ( 826) metal coordination : bond 0.01056 / 0.52 ( 4) metal coordination : angle 8.63535 / 3.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 971 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.282 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ASP cc_start: 0.7651 (t70) cc_final: 0.7255 (p0) REVERT: A 540 PHE cc_start: 0.6650 (m-10) cc_final: 0.6247 (p90) REVERT: A 585 GLN cc_start: 0.8700 (mp10) cc_final: 0.8318 (tp-100) REVERT: A 603 GLU cc_start: 0.8123 (tt0) cc_final: 0.7216 (tm-30) REVERT: A 864 MET cc_start: 0.7977 (ttt) cc_final: 0.7715 (ttt) REVERT: A 923 ILE cc_start: 0.9262 (pt) cc_final: 0.9011 (pt) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.1272 time to fit residues: 21.9955 Evaluate side-chains 91 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 40 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 42 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 GLN A 993 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.102615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.085270 restraints weight = 41894.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.088734 restraints weight = 19699.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.090915 restraints weight = 12164.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.092296 restraints weight = 8919.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.093123 restraints weight = 7268.266| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6054 Z= 0.259 Angle : 0.836 22.909 8295 Z= 0.412 Chirality : 0.046 0.187 975 Planarity : 0.005 0.040 939 Dihedral : 10.443 67.239 1060 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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: -1.63 (0.31), residues: 651 helix: 1.05 (0.28), residues: 314 sheet: -3.26 (0.48), residues: 77 loop : -3.18 (0.30), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 375 TYR 0.019 0.002 TYR A 579 PHE 0.013 0.002 PHE A 849 TRP 0.007 0.001 TRP A 582 HIS 0.012 0.002 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.26 ( 6050) covalent geometry : angle 0.81003 / 0.41 ( 8289) hydrogen bonds : bond 0.04319 / 2.86 ( 304) hydrogen bonds : angle 4.90585 / 3.57 ( 826) metal coordination : bond 0.01436 / 0.74 ( 4) metal coordination : angle 7.74429 / 3.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 971 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.287 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 TYR cc_start: 0.7673 (t80) cc_final: 0.7345 (t80) REVERT: A 446 CYS cc_start: 0.8366 (m) cc_final: 0.8065 (m) REVERT: A 540 PHE cc_start: 0.6832 (m-10) cc_final: 0.6444 (p90) REVERT: A 603 GLU cc_start: 0.8186 (tt0) cc_final: 0.7149 (tm-30) REVERT: A 723 ILE cc_start: 0.9439 (mt) cc_final: 0.9050 (mm) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1345 time to fit residues: 20.3343 Evaluate side-chains 91 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.104458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.087230 restraints weight = 41569.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.090906 restraints weight = 19237.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.093223 restraints weight = 11662.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.094614 restraints weight = 8430.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.095586 restraints weight = 6816.570| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6054 Z= 0.118 Angle : 0.700 22.959 8295 Z= 0.345 Chirality : 0.042 0.154 975 Planarity : 0.003 0.038 939 Dihedral : 9.404 59.894 1060 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.32), residues: 651 helix: 1.73 (0.28), residues: 316 sheet: -2.90 (0.50), residues: 75 loop : -2.92 (0.33), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 599 TYR 0.013 0.001 TYR A 579 PHE 0.008 0.001 PHE A 849 TRP 0.003 0.001 TRP A 737 HIS 0.006 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 6050) covalent geometry : angle 0.68557 / 0.34 ( 8289) hydrogen bonds : bond 0.03392 / 2.22 ( 304) hydrogen bonds : angle 4.29601 / 3.12 ( 826) metal coordination : bond 0.00424 / 0.21 ( 4) metal coordination : angle 5.21475 / 2.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 971 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.291 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 TYR cc_start: 0.7557 (t80) cc_final: 0.7328 (t80) REVERT: A 540 PHE cc_start: 0.6807 (m-10) cc_final: 0.6417 (p90) REVERT: A 581 GLN cc_start: 0.8595 (tt0) cc_final: 0.8321 (tt0) REVERT: A 585 GLN cc_start: 0.8779 (mp10) cc_final: 0.8412 (tp-100) REVERT: A 603 GLU cc_start: 0.8229 (tt0) cc_final: 0.7166 (tm-30) REVERT: A 723 ILE cc_start: 0.9453 (mt) cc_final: 0.9060 (mm) REVERT: A 864 MET cc_start: 0.7820 (ttt) cc_final: 0.7437 (ttt) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1194 time to fit residues: 17.9281 Evaluate side-chains 87 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 974 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 = 0.3494 r_free = 0.3494 target = 0.100963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.084054 restraints weight = 42138.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.087286 restraints weight = 20754.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.089346 restraints weight = 13314.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.090615 restraints weight = 10021.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.091453 restraints weight = 8310.845| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.6014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6054 Z= 0.247 Angle : 0.807 23.023 8295 Z= 0.399 Chirality : 0.046 0.204 975 Planarity : 0.004 0.038 939 Dihedral : 9.948 61.766 1060 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 23.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % 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: -1.22 (0.32), residues: 651 helix: 1.42 (0.28), residues: 315 sheet: -3.07 (0.47), residues: 87 loop : -2.99 (0.33), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 461 TYR 0.010 0.002 TYR A1018 PHE 0.012 0.002 PHE A 849 TRP 0.005 0.001 TRP A 582 HIS 0.009 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.25 ( 6050) covalent geometry : angle 0.79384 / 0.40 ( 8289) hydrogen bonds : bond 0.04134 / 2.76 ( 304) hydrogen bonds : angle 4.71089 / 3.41 ( 826) metal coordination : bond 0.00892 / 0.45 ( 4) metal coordination : angle 5.37719 / 2.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 971 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.294 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: 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 342 TYR cc_start: 0.7498 (t80) cc_final: 0.7266 (t80) REVERT: A 488 LEU cc_start: 0.8903 (mt) cc_final: 0.8178 (mt) REVERT: A 540 PHE cc_start: 0.6846 (m-10) cc_final: 0.6417 (p90) REVERT: A 603 GLU cc_start: 0.8106 (tt0) cc_final: 0.7019 (tm-30) REVERT: A 723 ILE cc_start: 0.9518 (mt) cc_final: 0.9167 (mm) REVERT: A 864 MET cc_start: 0.7825 (ttt) cc_final: 0.7439 (ttt) REVERT: A 1009 ARG cc_start: 0.7756 (mmp80) cc_final: 0.7500 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1386 time to fit residues: 19.7545 Evaluate side-chains 82 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 581 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.102448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.084980 restraints weight = 41320.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.088526 restraints weight = 18940.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.090743 restraints weight = 11589.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.092128 restraints weight = 8464.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.092954 restraints weight = 6892.956| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6054 Z= 0.168 Angle : 0.702 22.779 8295 Z= 0.353 Chirality : 0.042 0.143 975 Planarity : 0.003 0.036 939 Dihedral : 9.443 58.543 1060 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.33), residues: 651 helix: 1.77 (0.28), residues: 318 sheet: -2.70 (0.55), residues: 75 loop : -3.00 (0.32), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 461 TYR 0.014 0.002 TYR A 579 PHE 0.009 0.001 PHE A 551 TRP 0.004 0.001 TRP A 968 HIS 0.005 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 ( 6050) covalent geometry : angle 0.69564 / 0.35 ( 8289) hydrogen bonds : bond 0.03500 / 2.31 ( 304) hydrogen bonds : angle 4.41068 / 3.19 ( 826) metal coordination : bond 0.00458 / 0.23 ( 4) metal coordination : angle 3.66252 / 1.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 971 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.308 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: 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: symmetry clash REVERT: A 446 CYS cc_start: 0.7999 (m) cc_final: 0.7751 (m) REVERT: A 488 LEU cc_start: 0.8841 (mt) cc_final: 0.8197 (mt) REVERT: A 540 PHE cc_start: 0.7005 (m-10) cc_final: 0.6393 (p90) REVERT: A 559 MET cc_start: 0.7530 (ttt) cc_final: 0.7023 (ttp) REVERT: A 603 GLU cc_start: 0.8290 (tt0) cc_final: 0.7123 (tm-30) REVERT: A 723 ILE cc_start: 0.9512 (mt) cc_final: 0.9161 (mm) REVERT: A 1009 ARG cc_start: 0.7703 (mmp80) cc_final: 0.7412 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1181 time to fit residues: 17.4699 Evaluate side-chains 87 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 683 ASN ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.100572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.082903 restraints weight = 41429.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.086369 restraints weight = 19165.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.088553 restraints weight = 11862.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.089987 restraints weight = 8766.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.090813 restraints weight = 7166.083| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.6817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6054 Z= 0.276 Angle : 0.826 23.141 8295 Z= 0.409 Chirality : 0.046 0.194 975 Planarity : 0.004 0.037 939 Dihedral : 10.067 57.879 1060 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 24.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.32), residues: 651 helix: 1.22 (0.28), residues: 325 sheet: -3.08 (0.50), residues: 87 loop : -3.03 (0.33), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 461 TYR 0.011 0.002 TYR A1018 PHE 0.022 0.002 PHE A 551 TRP 0.005 0.001 TRP A 737 HIS 0.006 0.002 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.28 ( 6050) covalent geometry : angle 0.81723 / 0.41 ( 8289) hydrogen bonds : bond 0.04286 / 2.87 ( 304) hydrogen bonds : angle 4.85009 / 3.53 ( 826) metal coordination : bond 0.00893 / 0.45 ( 4) metal coordination : angle 4.44718 / 2.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 971 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.295 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: 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: symmetry clash REVERT: A 446 CYS cc_start: 0.8104 (m) cc_final: 0.7893 (m) REVERT: A 488 LEU cc_start: 0.8920 (mt) cc_final: 0.8320 (mt) REVERT: A 540 PHE cc_start: 0.6927 (m-10) cc_final: 0.6374 (p90) REVERT: A 603 GLU cc_start: 0.8343 (tt0) cc_final: 0.7219 (tm-30) REVERT: A 613 GLN cc_start: 0.8489 (pm20) cc_final: 0.8150 (pm20) REVERT: A 723 ILE cc_start: 0.9519 (mt) cc_final: 0.9180 (mm) REVERT: A 864 MET cc_start: 0.7894 (ttt) cc_final: 0.7461 (ttt) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1204 time to fit residues: 16.1247 Evaluate side-chains 82 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 61 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 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 = 0.3511 r_free = 0.3511 target = 0.102683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.085028 restraints weight = 40822.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.088620 restraints weight = 18254.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.090867 restraints weight = 11079.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.092219 restraints weight = 8086.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.093143 restraints weight = 6644.065| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.6917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6054 Z= 0.178 Angle : 0.725 22.827 8295 Z= 0.363 Chirality : 0.043 0.148 975 Planarity : 0.003 0.032 939 Dihedral : 9.643 58.875 1060 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.33), residues: 651 helix: 1.61 (0.28), residues: 319 sheet: -2.73 (0.58), residues: 75 loop : -3.06 (0.31), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 599 TYR 0.014 0.001 TYR A 579 PHE 0.009 0.001 PHE A 849 TRP 0.005 0.001 TRP A1003 HIS 0.015 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 ( 6050) covalent geometry : angle 0.71951 / 0.36 ( 8289) hydrogen bonds : bond 0.03691 / 2.48 ( 304) hydrogen bonds : angle 4.55527 / 3.33 ( 826) metal coordination : bond 0.00629 / 0.32 ( 4) metal coordination : angle 3.45321 / 1.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 971 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.292 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: 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 342 TYR cc_start: 0.7748 (t80) cc_final: 0.7281 (t80) REVERT: A 446 CYS cc_start: 0.8102 (m) cc_final: 0.7818 (m) REVERT: A 488 LEU cc_start: 0.8812 (mt) cc_final: 0.8168 (mt) REVERT: A 540 PHE cc_start: 0.6903 (m-10) cc_final: 0.6335 (p90) REVERT: A 864 MET cc_start: 0.7751 (ttt) cc_final: 0.7336 (ttt) REVERT: A 877 GLN cc_start: 0.8268 (mt0) cc_final: 0.7778 (mm-40) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1056 time to fit residues: 15.2726 Evaluate side-chains 84 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 63 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 615 ASN ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.105128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.087676 restraints weight = 40366.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.091283 restraints weight = 18060.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.093560 restraints weight = 10988.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.094980 restraints weight = 8009.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.095923 restraints weight = 6505.358| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6054 Z= 0.098 Angle : 0.659 22.912 8295 Z= 0.330 Chirality : 0.041 0.149 975 Planarity : 0.003 0.028 939 Dihedral : 9.010 58.319 1060 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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 (0.33), residues: 651 helix: 2.25 (0.28), residues: 319 sheet: -2.58 (0.58), residues: 75 loop : -2.84 (0.32), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 599 TYR 0.017 0.001 TYR A 579 PHE 0.006 0.001 PHE A 675 TRP 0.006 0.001 TRP A 737 HIS 0.009 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 ( 6050) covalent geometry : angle 0.65446 / 0.33 ( 8289) hydrogen bonds : bond 0.03147 / 2.11 ( 304) hydrogen bonds : angle 4.07718 / 2.98 ( 826) metal coordination : bond 0.00163 / 0.08 ( 4) metal coordination : angle 2.95374 / 1.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 971 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.297 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: 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 342 TYR cc_start: 0.7632 (t80) cc_final: 0.7169 (t80) REVERT: A 446 CYS cc_start: 0.7960 (m) cc_final: 0.7666 (m) REVERT: A 488 LEU cc_start: 0.8749 (mt) cc_final: 0.8198 (mt) REVERT: A 613 GLN cc_start: 0.8156 (pm20) cc_final: 0.7883 (pm20) REVERT: A 864 MET cc_start: 0.7981 (ttt) cc_final: 0.7572 (ttt) REVERT: A 926 MET cc_start: 0.9062 (mtp) cc_final: 0.8750 (mtp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1272 time to fit residues: 17.7717 Evaluate side-chains 85 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 30.0000 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 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 = 0.3524 r_free = 0.3524 target = 0.103300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.085602 restraints weight = 41116.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.089210 restraints weight = 18618.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.091431 restraints weight = 11378.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.092847 restraints weight = 8321.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.093654 restraints weight = 6783.456| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.7102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6054 Z= 0.159 Angle : 0.697 23.048 8295 Z= 0.348 Chirality : 0.042 0.163 975 Planarity : 0.003 0.031 939 Dihedral : 9.314 58.514 1060 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.36 (0.33), residues: 651 helix: 2.24 (0.28), residues: 320 sheet: -2.57 (0.60), residues: 73 loop : -2.91 (0.32), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 599 TYR 0.014 0.001 TYR A 579 PHE 0.009 0.001 PHE A 675 TRP 0.004 0.001 TRP A 737 HIS 0.010 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 ( 6050) covalent geometry : angle 0.69235 / 0.35 ( 8289) hydrogen bonds : bond 0.03396 / 2.30 ( 304) hydrogen bonds : angle 4.22073 / 3.09 ( 826) metal coordination : bond 0.00316 / 0.16 ( 4) metal coordination : angle 3.19479 / 1.35 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 971 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.302 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: 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 339 VAL cc_start: 0.9254 (m) cc_final: 0.9044 (p) REVERT: A 342 TYR cc_start: 0.7728 (t80) cc_final: 0.7274 (t80) REVERT: A 446 CYS cc_start: 0.7971 (m) cc_final: 0.7757 (m) REVERT: A 488 LEU cc_start: 0.8783 (mt) cc_final: 0.8272 (mt) REVERT: A 613 GLN cc_start: 0.8264 (pm20) cc_final: 0.7902 (pm20) REVERT: A 864 MET cc_start: 0.7992 (ttt) cc_final: 0.7536 (ttt) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1023 time to fit residues: 14.4136 Evaluate side-chains 82 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 16 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 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 = 0.3491 r_free = 0.3491 target = 0.100924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.083844 restraints weight = 41509.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.087178 restraints weight = 19263.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.089274 restraints weight = 12010.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.090581 restraints weight = 8917.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.091288 restraints weight = 7350.525| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.7366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6054 Z= 0.225 Angle : 0.775 23.102 8295 Z= 0.384 Chirality : 0.045 0.171 975 Planarity : 0.003 0.033 939 Dihedral : 9.813 59.585 1060 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -0.70 (0.33), residues: 651 helix: 1.84 (0.29), residues: 324 sheet: -2.71 (0.59), residues: 75 loop : -2.99 (0.31), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 461 TYR 0.011 0.002 TYR A 579 PHE 0.012 0.001 PHE A 675 TRP 0.005 0.001 TRP A1003 HIS 0.012 0.002 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.23 ( 6050) covalent geometry : angle 0.76912 / 0.38 ( 8289) hydrogen bonds : bond 0.03904 / 2.63 ( 304) hydrogen bonds : angle 4.51545 / 3.29 ( 826) metal coordination : bond 0.00742 / 0.37 ( 4) metal coordination : angle 3.75493 / 1.74 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1810.95 seconds wall clock time: 31 minutes 49.65 seconds (1909.65 seconds total)