Starting phenix.real_space_refine on Thu Jul 2 02:53:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tnx_26022/07_2026/7tnx_26022.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnx_26022/07_2026/7tnx_26022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tnx_26022/07_2026/7tnx_26022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnx_26022/07_2026/7tnx_26022.map" model { file = "/net/cci-nas-00/data/ceres_data/7tnx_26022/07_2026/7tnx_26022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnx_26022/07_2026/7tnx_26022.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tnx_26022/07_2026/7tnx_26022.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tnx_26022/07_2026/7tnx_26022.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 26 5.49 5 S 32 5.16 5 C 3581 2.51 5 N 976 2.21 5 O 1137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5753 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5234 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 619} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 265 Unusual residues: {'GTP': 1} Classifications: {'RNA': 11, 'undetermined': 1} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 10, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain: "C" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 253 Classifications: {'RNA': 12} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 10} 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 4302 SG CYS A 810 24.961 51.835 20.300 1.00 32.46 S ATOM 4741 SG CYS A 864 25.057 50.376 16.542 1.00 45.36 S ATOM 4780 SG CYS A 869 26.399 53.639 17.338 1.00 48.58 S Time building chain proxies: 1.36, per 1000 atoms: 0.24 Number of scatterers: 5753 At special positions: 0 Unit cell: (88.2, 92.4, 82.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 32 16.00 P 26 15.00 O 1137 8.00 N 976 7.00 C 3581 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 281.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1242 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 7 sheets defined 50.9% alpha, 12.2% beta 10 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 244 through 250 removed outlier: 3.840A pdb=" N LEU A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.789A pdb=" N LYS A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 284 Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 333 through 341 Processing helix chain 'A' and resid 347 through 358 removed outlier: 3.625A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.652A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 381 through 396 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 445 through 452 removed outlier: 3.863A pdb=" N LEU A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 487 Processing helix chain 'A' and resid 492 through 496 removed outlier: 3.625A pdb=" N LEU A 496 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 521 Processing helix chain 'A' and resid 529 through 558 Processing helix chain 'A' and resid 559 through 576 removed outlier: 3.845A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 564 " --> pdb=" O MET A 560 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 602 removed outlier: 3.830A pdb=" N GLN A 588 " --> pdb=" O GLN A 584 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.738A pdb=" N GLU A 607 " --> pdb=" O PRO A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 638 through 649 removed outlier: 3.751A pdb=" N LYS A 644 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 771 removed outlier: 3.811A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 794 Processing helix chain 'A' and resid 835 through 840 removed outlier: 3.656A pdb=" N GLU A 840 " --> pdb=" O ALA A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 892 Processing helix chain 'A' and resid 907 through 911 Processing sheet with id=AA1, first strand: chain 'A' and resid 261 through 263 removed outlier: 6.500A pdb=" N ILE A 262 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU A 408 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE A 371 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A 294 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ASP A 372 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N PHE A 296 " --> pdb=" O ASP A 372 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 458 removed outlier: 6.859A pdb=" N GLN A 457 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU A 740 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 742 " --> pdb=" O ARG A 461 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 458 removed outlier: 6.859A pdb=" N GLN A 457 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU A 740 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 631 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N TYR A 715 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE A 633 " --> pdb=" O TYR A 715 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR A 630 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ALA A 696 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU A 632 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819 removed outlier: 3.645A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 831 through 833 removed outlier: 4.532A pdb=" N ILE A 916 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 842 through 846 Processing sheet with id=AA7, first strand: chain 'A' and resid 842 through 846 removed outlier: 6.243A pdb=" N LYS A 858 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LYS A 878 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N CYS A 864 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASP A 872 " --> pdb=" O CYS A 864 " (cutoff:3.500A) 251 hydrogen bonds defined for protein. 711 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1673 1.33 - 1.45: 895 1.45 - 1.57: 3253 1.57 - 1.69: 49 1.69 - 1.82: 45 Bond restraints: 5915 Sorted by residual: bond pdb=" N VAL A 414 " pdb=" CA VAL A 414 " ideal model delta sigma weight residual 1.458 1.489 -0.031 9.00e-03 1.23e+04 1.19e+01 bond pdb=" N ILE A 489 " pdb=" CA ILE A 489 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.08e-02 8.57e+03 1.12e+01 bond pdb=" N VAL A 522 " pdb=" CA VAL A 522 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.09e-02 8.42e+03 1.01e+01 bond pdb=" N VAL A 453 " pdb=" CA VAL A 453 " ideal model delta sigma weight residual 1.460 1.485 -0.025 8.60e-03 1.35e+04 8.55e+00 bond pdb=" N VAL A 463 " pdb=" CA VAL A 463 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.11e-02 8.12e+03 8.10e+00 ... (remaining 5910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 6773 1.54 - 3.08: 1258 3.08 - 4.62: 51 4.62 - 6.16: 4 6.16 - 7.70: 2 Bond angle restraints: 8088 Sorted by residual: angle pdb=" N VAL A 453 " pdb=" CA VAL A 453 " pdb=" C VAL A 453 " ideal model delta sigma weight residual 113.71 108.96 4.75 9.50e-01 1.11e+00 2.50e+01 angle pdb=" N THR A 881 " pdb=" CA THR A 881 " pdb=" C THR A 881 " ideal model delta sigma weight residual 114.56 108.88 5.68 1.27e+00 6.20e-01 2.00e+01 angle pdb=" N ARG A 728 " pdb=" CA ARG A 728 " pdb=" C ARG A 728 " ideal model delta sigma weight residual 114.04 108.87 5.17 1.24e+00 6.50e-01 1.74e+01 angle pdb=" N PHE A 789 " pdb=" CA PHE A 789 " pdb=" C PHE A 789 " ideal model delta sigma weight residual 110.97 107.09 3.88 1.09e+00 8.42e-01 1.27e+01 angle pdb=" N ILE A 790 " pdb=" CA ILE A 790 " pdb=" C ILE A 790 " ideal model delta sigma weight residual 110.62 106.64 3.98 1.14e+00 7.69e-01 1.22e+01 ... (remaining 8083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.34: 3306 19.34 - 38.68: 213 38.68 - 58.02: 21 58.02 - 77.36: 8 77.36 - 96.70: 10 Dihedral angle restraints: 3558 sinusoidal: 1652 harmonic: 1906 Sorted by residual: dihedral pdb=" C8 GTP B 1 " pdb=" C1' GTP B 1 " pdb=" N9 GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sinusoidal sigma weight residual 104.59 7.90 96.70 1 2.00e+01 2.50e-03 2.68e+01 dihedral pdb=" CB GLU A 249 " pdb=" CG GLU A 249 " pdb=" CD GLU A 249 " pdb=" OE1 GLU A 249 " ideal model delta sinusoidal sigma weight residual 0.00 88.06 -88.06 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU A 503 " pdb=" CG GLU A 503 " pdb=" CD GLU A 503 " pdb=" OE1 GLU A 503 " ideal model delta sinusoidal sigma weight residual 0.00 -84.83 84.83 1 3.00e+01 1.11e-03 9.71e+00 ... (remaining 3555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 418 0.039 - 0.079: 264 0.079 - 0.118: 180 0.118 - 0.158: 52 0.158 - 0.197: 5 Chirality restraints: 919 Sorted by residual: chirality pdb=" CA ILE A 360 " pdb=" N ILE A 360 " pdb=" C ILE A 360 " pdb=" CB ILE A 360 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" CA ILE A 261 " pdb=" N ILE A 261 " pdb=" C ILE A 261 " pdb=" CB ILE A 261 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA ILE A 790 " pdb=" N ILE A 790 " pdb=" C ILE A 790 " pdb=" CB ILE A 790 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 916 not shown) Planarity restraints: 943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 347 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C THR A 347 " -0.030 2.00e-02 2.50e+03 pdb=" O THR A 347 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO A 348 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 303 " -0.013 2.00e-02 2.50e+03 1.15e-02 2.67e+00 pdb=" CG TYR A 303 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR A 303 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 303 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 303 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 303 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 303 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 303 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 746 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C GLY A 746 " -0.025 2.00e-02 2.50e+03 pdb=" O GLY A 746 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL A 747 " 0.009 2.00e-02 2.50e+03 ... (remaining 940 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 736 2.78 - 3.31: 5868 3.31 - 3.84: 9216 3.84 - 4.37: 11227 4.37 - 4.90: 18370 Nonbonded interactions: 45417 Sorted by model distance: nonbonded pdb=" O2 U B 12 " pdb=" N2 G C 14 " model vdw 2.247 3.120 nonbonded pdb=" O HIS A 557 " pdb=" OH TYR A 715 " model vdw 2.288 3.040 nonbonded pdb=" NH1 ARG A 811 " pdb=" O GLU A 890 " model vdw 2.321 3.120 nonbonded pdb=" OD1 ASN A 259 " pdb=" N VAL A 405 " model vdw 2.322 3.120 nonbonded pdb=" O ILE A 337 " pdb=" ND2 ASN A 341 " model vdw 2.394 3.120 ... (remaining 45412 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.680 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 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 : 0.011 0.200 5919 Z= 0.790 Angle : 1.082 7.703 8088 Z= 0.785 Chirality : 0.065 0.197 919 Planarity : 0.004 0.025 943 Dihedral : 13.307 96.698 2316 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.67 % Favored : 92.18 % Rotamer: Outliers : 0.17 % Allowed : 3.42 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.31), residues: 639 helix: -0.49 (0.29), residues: 294 sheet: -2.90 (0.51), residues: 72 loop : -3.04 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 502 TYR 0.021 0.004 TYR A 303 PHE 0.018 0.003 PHE A 853 TRP 0.010 0.003 TRP A 873 HIS 0.012 0.002 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.01051 / 0.78 ( 5915) covalent geometry : angle 1.08181 / 0.78 ( 8088) hydrogen bonds : bond 0.08057 / 5.25 ( 272) hydrogen bonds : angle 5.49130 / 3.65 ( 757) metal coordination : bond 0.18254 / 9.22 ( 3) Misc. bond : bond 0.00045 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.205 Fit side-chains REVERT: A 340 ASN cc_start: 0.8342 (m-40) cc_final: 0.8062 (m110) REVERT: A 369 MET cc_start: 0.7397 (mtt) cc_final: 0.7022 (mtp) REVERT: A 607 GLU cc_start: 0.8801 (tp30) cc_final: 0.7765 (mt-10) REVERT: A 635 LYS cc_start: 0.8489 (ttpt) cc_final: 0.7716 (ttmm) REVERT: A 715 TYR cc_start: 0.8385 (t80) cc_final: 0.7978 (t80) REVERT: A 716 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7894 (mm-30) REVERT: A 867 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7593 (mm-40) outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 0.0921 time to fit residues: 14.9915 Evaluate side-chains 90 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.137356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.107533 restraints weight = 6850.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.111008 restraints weight = 4432.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.113449 restraints weight = 3342.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.115143 restraints weight = 2755.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.116406 restraints weight = 2403.375| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5919 Z= 0.112 Angle : 0.513 9.120 8088 Z= 0.254 Chirality : 0.038 0.228 919 Planarity : 0.004 0.038 943 Dihedral : 7.413 89.987 975 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.42 % Favored : 93.43 % Rotamer: Outliers : 1.54 % Allowed : 10.27 % Favored : 88.18 % 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: -1.26 (0.33), residues: 639 helix: 0.97 (0.30), residues: 295 sheet: -2.52 (0.55), residues: 72 loop : -2.46 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 859 TYR 0.007 0.001 TYR A 246 PHE 0.008 0.001 PHE A 460 TRP 0.005 0.001 TRP A 771 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 5915) covalent geometry : angle 0.51335 / 0.25 ( 8088) hydrogen bonds : bond 0.03597 / 2.39 ( 272) hydrogen bonds : angle 3.79601 / 2.58 ( 757) metal coordination : bond 0.00148 / 0.07 ( 3) Misc. bond : bond 0.00042 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.206 Fit side-chains REVERT: A 255 MET cc_start: 0.8461 (mtt) cc_final: 0.8258 (mtm) REVERT: A 369 MET cc_start: 0.7651 (mtt) cc_final: 0.7403 (mtp) REVERT: A 607 GLU cc_start: 0.8278 (tp30) cc_final: 0.7747 (mt-10) REVERT: A 635 LYS cc_start: 0.8302 (ttpt) cc_final: 0.7390 (ttmm) REVERT: A 715 TYR cc_start: 0.8529 (t80) cc_final: 0.8170 (t80) REVERT: A 867 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7520 (mm-40) outliers start: 9 outliers final: 5 residues processed: 100 average time/residue: 0.0697 time to fit residues: 9.3190 Evaluate side-chains 86 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 51 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.135706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.105681 restraints weight = 6843.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.109178 restraints weight = 4458.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.111595 restraints weight = 3376.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.113293 restraints weight = 2785.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.114376 restraints weight = 2436.911| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5919 Z= 0.110 Angle : 0.519 10.049 8088 Z= 0.250 Chirality : 0.038 0.232 919 Planarity : 0.004 0.040 943 Dihedral : 7.284 90.232 974 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.89 % Favored : 92.96 % Rotamer: Outliers : 1.88 % Allowed : 12.33 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.34), residues: 639 helix: 1.62 (0.31), residues: 295 sheet: -2.17 (0.59), residues: 72 loop : -2.22 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 859 TYR 0.011 0.001 TYR A 622 PHE 0.011 0.001 PHE A 459 TRP 0.005 0.001 TRP A 771 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 5915) covalent geometry : angle 0.51932 / 0.25 ( 8088) hydrogen bonds : bond 0.03562 / 2.38 ( 272) hydrogen bonds : angle 3.65488 / 2.49 ( 757) metal coordination : bond 0.00157 / 0.08 ( 3) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.164 Fit side-chains REVERT: A 369 MET cc_start: 0.7694 (mtt) cc_final: 0.7446 (mtp) REVERT: A 607 GLU cc_start: 0.8351 (tp30) cc_final: 0.7853 (mt-10) REVERT: A 635 LYS cc_start: 0.8366 (ttpt) cc_final: 0.7458 (ttmm) REVERT: A 641 ASP cc_start: 0.8115 (t0) cc_final: 0.7876 (t0) REVERT: A 692 ASN cc_start: 0.8618 (t0) cc_final: 0.8343 (t0) REVERT: A 715 TYR cc_start: 0.8656 (t80) cc_final: 0.8337 (t80) REVERT: A 867 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7568 (mm-40) outliers start: 11 outliers final: 8 residues processed: 95 average time/residue: 0.0525 time to fit residues: 6.9699 Evaluate side-chains 90 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 52 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.102482 restraints weight = 6889.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.106064 restraints weight = 4435.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.108429 restraints weight = 3327.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.109785 restraints weight = 2768.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.111261 restraints weight = 2454.474| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5919 Z= 0.140 Angle : 0.551 11.546 8088 Z= 0.266 Chirality : 0.039 0.200 919 Planarity : 0.004 0.041 943 Dihedral : 7.319 91.279 974 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.89 % Favored : 92.96 % Rotamer: Outliers : 3.08 % Allowed : 13.70 % Favored : 83.22 % 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: -0.41 (0.35), residues: 639 helix: 1.73 (0.31), residues: 293 sheet: -2.00 (0.61), residues: 74 loop : -2.10 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 859 TYR 0.013 0.001 TYR A 622 PHE 0.010 0.001 PHE A 459 TRP 0.004 0.001 TRP A 771 HIS 0.004 0.001 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 5915) covalent geometry : angle 0.55100 / 0.27 ( 8088) hydrogen bonds : bond 0.03817 / 2.50 ( 272) hydrogen bonds : angle 3.74322 / 2.53 ( 757) metal coordination : bond 0.00191 / 0.10 ( 3) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.205 Fit side-chains REVERT: A 255 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8407 (mpp) REVERT: A 369 MET cc_start: 0.7752 (mtt) cc_final: 0.7507 (mtp) REVERT: A 434 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8023 (tp) REVERT: A 607 GLU cc_start: 0.8350 (tp30) cc_final: 0.7840 (mt-10) REVERT: A 622 TYR cc_start: 0.8315 (m-10) cc_final: 0.7886 (m-80) REVERT: A 635 LYS cc_start: 0.8487 (ttpt) cc_final: 0.7627 (ttmm) REVERT: A 641 ASP cc_start: 0.8077 (t0) cc_final: 0.7799 (t0) REVERT: A 655 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8222 (p90) REVERT: A 715 TYR cc_start: 0.8714 (t80) cc_final: 0.8468 (t80) REVERT: A 867 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7620 (mm-40) outliers start: 18 outliers final: 13 residues processed: 94 average time/residue: 0.0610 time to fit residues: 8.0655 Evaluate side-chains 94 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 18 optimal weight: 0.2980 chunk 37 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.136271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.105953 restraints weight = 6976.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.109649 restraints weight = 4493.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.112172 restraints weight = 3366.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.113854 restraints weight = 2770.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.114823 restraints weight = 2423.195| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5919 Z= 0.095 Angle : 0.501 10.305 8088 Z= 0.243 Chirality : 0.038 0.164 919 Planarity : 0.003 0.040 943 Dihedral : 7.078 88.687 974 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.26 % Favored : 93.58 % Rotamer: Outliers : 3.25 % Allowed : 14.90 % Favored : 81.85 % 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: -0.19 (0.35), residues: 639 helix: 1.92 (0.31), residues: 293 sheet: -1.88 (0.61), residues: 74 loop : -1.99 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 859 TYR 0.014 0.001 TYR A 622 PHE 0.008 0.001 PHE A 459 TRP 0.006 0.001 TRP A 771 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 ( 5915) covalent geometry : angle 0.50094 / 0.24 ( 8088) hydrogen bonds : bond 0.03310 / 2.18 ( 272) hydrogen bonds : angle 3.54094 / 2.39 ( 757) metal coordination : bond 0.00098 / 0.05 ( 3) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.167 Fit side-chains REVERT: A 393 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7918 (tm-30) REVERT: A 434 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7852 (tt) REVERT: A 435 ASP cc_start: 0.8189 (t0) cc_final: 0.7893 (t0) REVERT: A 591 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8376 (mm-30) REVERT: A 607 GLU cc_start: 0.8304 (tp30) cc_final: 0.7853 (mt-10) REVERT: A 635 LYS cc_start: 0.8434 (ttpt) cc_final: 0.7574 (ttmm) REVERT: A 641 ASP cc_start: 0.8024 (t0) cc_final: 0.7771 (t0) REVERT: A 655 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.7899 (p90) REVERT: A 715 TYR cc_start: 0.8648 (t80) cc_final: 0.8390 (t80) REVERT: A 867 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7552 (mm-40) outliers start: 19 outliers final: 14 residues processed: 102 average time/residue: 0.0667 time to fit residues: 9.3662 Evaluate side-chains 99 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 41 optimal weight: 0.0970 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.138167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.107037 restraints weight = 6864.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.110835 restraints weight = 4373.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.113314 restraints weight = 3264.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.115281 restraints weight = 2682.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.116416 restraints weight = 2336.772| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5919 Z= 0.097 Angle : 0.523 9.740 8088 Z= 0.252 Chirality : 0.038 0.218 919 Planarity : 0.004 0.040 943 Dihedral : 6.979 88.068 974 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.73 % Favored : 93.11 % Rotamer: Outliers : 3.08 % Allowed : 15.07 % Favored : 81.85 % 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: -0.11 (0.36), residues: 639 helix: 1.87 (0.31), residues: 300 sheet: -1.72 (0.63), residues: 74 loop : -1.95 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 859 TYR 0.014 0.001 TYR A 622 PHE 0.016 0.001 PHE A 853 TRP 0.006 0.001 TRP A 771 HIS 0.003 0.000 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 ( 5915) covalent geometry : angle 0.52332 / 0.25 ( 8088) hydrogen bonds : bond 0.03300 / 2.15 ( 272) hydrogen bonds : angle 3.48150 / 2.36 ( 757) metal coordination : bond 0.00092 / 0.05 ( 3) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.209 Fit side-chains REVERT: A 249 GLU cc_start: 0.7941 (tt0) cc_final: 0.7684 (tt0) REVERT: A 393 GLN cc_start: 0.8247 (tm-30) cc_final: 0.8016 (tm-30) REVERT: A 434 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7399 (tt) REVERT: A 591 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8380 (mm-30) REVERT: A 607 GLU cc_start: 0.8399 (tp30) cc_final: 0.7863 (mt-10) REVERT: A 622 TYR cc_start: 0.8208 (m-10) cc_final: 0.7954 (m-80) REVERT: A 635 LYS cc_start: 0.8379 (ttpt) cc_final: 0.7510 (ttmm) REVERT: A 655 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8108 (p90) REVERT: A 715 TYR cc_start: 0.8591 (t80) cc_final: 0.8244 (t80) REVERT: A 789 PHE cc_start: 0.7923 (t80) cc_final: 0.7611 (t80) REVERT: A 867 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7704 (mm-40) outliers start: 18 outliers final: 16 residues processed: 100 average time/residue: 0.0622 time to fit residues: 8.6839 Evaluate side-chains 102 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 51 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 608 ASN A 769 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.133961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.101966 restraints weight = 6920.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.105833 restraints weight = 4306.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.108503 restraints weight = 3181.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.110376 restraints weight = 2589.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.111171 restraints weight = 2248.794| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5919 Z= 0.122 Angle : 0.542 8.851 8088 Z= 0.262 Chirality : 0.039 0.215 919 Planarity : 0.004 0.042 943 Dihedral : 7.016 89.406 974 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.20 % Favored : 92.64 % Rotamer: Outliers : 3.25 % Allowed : 15.92 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.36), residues: 639 helix: 1.90 (0.31), residues: 296 sheet: -1.60 (0.64), residues: 74 loop : -1.90 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 859 TYR 0.013 0.001 TYR A 622 PHE 0.015 0.001 PHE A 853 TRP 0.005 0.001 TRP A 771 HIS 0.003 0.001 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 5915) covalent geometry : angle 0.54170 / 0.26 ( 8088) hydrogen bonds : bond 0.03528 / 2.31 ( 272) hydrogen bonds : angle 3.53123 / 2.39 ( 757) metal coordination : bond 0.00177 / 0.09 ( 3) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.224 Fit side-chains REVERT: A 591 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8402 (mm-30) REVERT: A 607 GLU cc_start: 0.8358 (tp30) cc_final: 0.7883 (mt-10) REVERT: A 635 LYS cc_start: 0.8472 (ttpt) cc_final: 0.7629 (ttmm) REVERT: A 715 TYR cc_start: 0.8658 (t80) cc_final: 0.8385 (t80) REVERT: A 867 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7671 (mm-40) outliers start: 19 outliers final: 16 residues processed: 92 average time/residue: 0.0645 time to fit residues: 8.3012 Evaluate side-chains 94 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.0870 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.134356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.103254 restraints weight = 6864.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.106884 restraints weight = 4402.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.109392 restraints weight = 3293.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.111211 restraints weight = 2715.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.112355 restraints weight = 2372.353| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5919 Z= 0.117 Angle : 0.536 8.011 8088 Z= 0.261 Chirality : 0.039 0.210 919 Planarity : 0.004 0.040 943 Dihedral : 6.983 89.025 974 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 3.42 % Allowed : 15.07 % Favored : 81.51 % 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: -0.02 (0.36), residues: 639 helix: 1.93 (0.31), residues: 295 sheet: -1.56 (0.64), residues: 74 loop : -1.85 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 859 TYR 0.007 0.001 TYR A 622 PHE 0.013 0.001 PHE A 853 TRP 0.005 0.001 TRP A 771 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 5915) covalent geometry : angle 0.53640 / 0.26 ( 8088) hydrogen bonds : bond 0.03541 / 2.29 ( 272) hydrogen bonds : angle 3.56438 / 2.41 ( 757) metal coordination : bond 0.00144 / 0.07 ( 3) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.212 Fit side-chains REVERT: A 393 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7928 (tm-30) REVERT: A 435 ASP cc_start: 0.8289 (t70) cc_final: 0.8053 (t70) REVERT: A 445 ASN cc_start: 0.8515 (m110) cc_final: 0.8091 (m110) REVERT: A 591 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8404 (mm-30) REVERT: A 635 LYS cc_start: 0.8489 (ttpt) cc_final: 0.7653 (ttmm) REVERT: A 715 TYR cc_start: 0.8706 (t80) cc_final: 0.8493 (t80) REVERT: A 867 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7697 (mm-40) outliers start: 20 outliers final: 19 residues processed: 98 average time/residue: 0.0581 time to fit residues: 8.0491 Evaluate side-chains 100 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 0.0050 chunk 4 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 58 optimal weight: 0.2980 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.136737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.105630 restraints weight = 6943.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.109433 restraints weight = 4402.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.112160 restraints weight = 3257.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.113993 restraints weight = 2652.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.115189 restraints weight = 2310.554| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5919 Z= 0.105 Angle : 0.532 7.805 8088 Z= 0.261 Chirality : 0.039 0.215 919 Planarity : 0.004 0.040 943 Dihedral : 6.896 88.161 974 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.77 % Allowed : 15.07 % Favored : 81.16 % 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: 0.09 (0.36), residues: 639 helix: 2.02 (0.31), residues: 295 sheet: -1.48 (0.64), residues: 74 loop : -1.80 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 859 TYR 0.011 0.001 TYR A 622 PHE 0.012 0.001 PHE A 853 TRP 0.006 0.001 TRP A 771 HIS 0.003 0.000 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 5915) covalent geometry : angle 0.53176 / 0.26 ( 8088) hydrogen bonds : bond 0.03366 / 2.18 ( 272) hydrogen bonds : angle 3.50763 / 2.37 ( 757) metal coordination : bond 0.00104 / 0.05 ( 3) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.159 Fit side-chains REVERT: A 393 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7891 (tm-30) REVERT: A 435 ASP cc_start: 0.8308 (t70) cc_final: 0.8097 (t70) REVERT: A 445 ASN cc_start: 0.8520 (m110) cc_final: 0.8266 (m110) REVERT: A 460 PHE cc_start: 0.8474 (m-80) cc_final: 0.8272 (m-80) REVERT: A 591 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8330 (mm-30) REVERT: A 607 GLU cc_start: 0.8483 (tp30) cc_final: 0.7941 (mt-10) REVERT: A 622 TYR cc_start: 0.8237 (m-10) cc_final: 0.7843 (m-10) REVERT: A 635 LYS cc_start: 0.8452 (ttpt) cc_final: 0.7591 (ttmm) REVERT: A 655 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8225 (p90) REVERT: A 715 TYR cc_start: 0.8673 (t80) cc_final: 0.8411 (t80) outliers start: 22 outliers final: 18 residues processed: 99 average time/residue: 0.0561 time to fit residues: 7.7395 Evaluate side-chains 102 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 5 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 0.0370 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.136572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.106105 restraints weight = 6926.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.109620 restraints weight = 4485.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.112248 restraints weight = 3380.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.113881 restraints weight = 2785.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.115118 restraints weight = 2438.154| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5919 Z= 0.105 Angle : 0.540 8.268 8088 Z= 0.265 Chirality : 0.039 0.238 919 Planarity : 0.004 0.040 943 Dihedral : 6.828 87.768 974 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.08 % Allowed : 14.90 % Favored : 82.02 % 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: 0.09 (0.36), residues: 639 helix: 2.02 (0.31), residues: 294 sheet: -1.49 (0.63), residues: 74 loop : -1.77 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 859 TYR 0.010 0.001 TYR A 622 PHE 0.012 0.001 PHE A 853 TRP 0.009 0.001 TRP A 646 HIS 0.003 0.000 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 ( 5915) covalent geometry : angle 0.53956 / 0.26 ( 8088) hydrogen bonds : bond 0.03344 / 2.17 ( 272) hydrogen bonds : angle 3.50581 / 2.38 ( 757) metal coordination : bond 0.00097 / 0.05 ( 3) Misc. bond : bond 0.00031 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.157 Fit side-chains REVERT: A 283 LYS cc_start: 0.8905 (ttpp) cc_final: 0.8669 (ttpp) REVERT: A 373 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7828 (tp30) REVERT: A 393 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7883 (tm-30) REVERT: A 435 ASP cc_start: 0.8313 (t70) cc_final: 0.8100 (t70) REVERT: A 445 ASN cc_start: 0.8469 (m110) cc_final: 0.8060 (m110) REVERT: A 460 PHE cc_start: 0.8504 (m-80) cc_final: 0.8277 (m-80) REVERT: A 497 SER cc_start: 0.7471 (t) cc_final: 0.7244 (t) REVERT: A 591 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8348 (mm-30) REVERT: A 607 GLU cc_start: 0.8475 (tp30) cc_final: 0.7936 (mt-10) REVERT: A 622 TYR cc_start: 0.8199 (m-10) cc_final: 0.7837 (m-10) REVERT: A 635 LYS cc_start: 0.8458 (ttpt) cc_final: 0.7614 (ttmm) REVERT: A 655 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8218 (p90) REVERT: A 715 TYR cc_start: 0.8628 (t80) cc_final: 0.8347 (t80) REVERT: A 867 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7681 (mm-40) outliers start: 18 outliers final: 17 residues processed: 98 average time/residue: 0.0587 time to fit residues: 8.1607 Evaluate side-chains 103 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.0670 chunk 3 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.137675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.106560 restraints weight = 6819.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.110256 restraints weight = 4318.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.112979 restraints weight = 3216.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.114393 restraints weight = 2633.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.115861 restraints weight = 2321.773| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5919 Z= 0.106 Angle : 0.547 11.434 8088 Z= 0.265 Chirality : 0.039 0.225 919 Planarity : 0.004 0.040 943 Dihedral : 6.771 87.648 974 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.08 % Allowed : 15.58 % Favored : 81.34 % 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: 0.10 (0.36), residues: 639 helix: 1.96 (0.31), residues: 296 sheet: -1.45 (0.63), residues: 74 loop : -1.72 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 859 TYR 0.010 0.001 TYR A 622 PHE 0.012 0.001 PHE A 853 TRP 0.007 0.001 TRP A 646 HIS 0.003 0.000 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 5915) covalent geometry : angle 0.54680 / 0.26 ( 8088) hydrogen bonds : bond 0.03356 / 2.17 ( 272) hydrogen bonds : angle 3.50780 / 2.38 ( 757) metal coordination : bond 0.00103 / 0.05 ( 3) Misc. bond : bond 0.00029 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1039.16 seconds wall clock time: 18 minutes 40.95 seconds (1120.95 seconds total)