Starting phenix.real_space_refine on Fri Sep 11 00:32:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tnx_26022/09_2026/7tnx_26022.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnx_26022/09_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_26022/09_2026/7tnx_26022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnx_26022/09_2026/7tnx_26022.map" model { file = "/net/cci-nas-00/data/ceres_data/7tnx_26022/09_2026/7tnx_26022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnx_26022/09_2026/7tnx_26022.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tnx_26022/09_2026/7tnx_26022.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tnx_26022/09_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-2.2.1-6174/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: {'RNAv2': 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: {'RNAv2': 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: 1.44, per 1000 atoms: 0.25 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: 0.61 Conformation dependent library (CDL) restraints added in 389.5 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: 0.69 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: 1.29 Time building geometry restraints manager: 0.88 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: 6722 1.54 - 3.08: 1294 3.08 - 4.62: 65 4.62 - 6.16: 5 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: 3272 19.34 - 38.68: 231 38.68 - 58.02: 31 58.02 - 77.36: 14 77.36 - 96.70: 10 Dihedral angle restraints: 3558 sinusoidal: 1652 harmonic: 1906 Sorted by residual: dihedral pdb=" C4' C C 13 " pdb=" C3' C C 13 " pdb=" C2' C C 13 " pdb=" C1' C C 13 " ideal model delta sinusoidal sigma weight residual 36.34 -36.90 73.25 1 3.10e+00 1.04e-01 7.11e+02 dihedral pdb=" C4' U B 12 " pdb=" C3' U B 12 " pdb=" C2' U B 12 " pdb=" C1' U B 12 " ideal model delta sinusoidal sigma weight residual 36.34 -35.31 71.65 1 3.10e+00 1.04e-01 6.85e+02 dihedral pdb=" O4' C C 13 " pdb=" C4' C C 13 " pdb=" C3' C C 13 " pdb=" C2' C C 13 " ideal model delta sinusoidal sigma weight residual -35.15 26.46 -61.61 1 4.00e+00 6.25e-02 3.15e+02 ... (remaining 3555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 519 0.056 - 0.112: 290 0.112 - 0.169: 81 0.169 - 0.225: 17 0.225 - 0.281: 12 Chirality restraints: 919 Sorted by residual: chirality pdb=" P G B 2 " pdb=" OP1 G B 2 " pdb=" OP2 G B 2 " pdb=" O5' G B 2 " both_signs ideal model delta sigma weight residual True 2.17 -2.45 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C2' U B 12 " pdb=" C3' U B 12 " pdb=" O2' U B 12 " pdb=" C1' U B 12 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' U B 12 " pdb=" C4' U B 12 " pdb=" O3' U B 12 " pdb=" C2' U B 12 " both_signs ideal model delta sigma weight residual False -2.50 -2.74 0.25 2.00e-01 2.50e+01 1.51e+00 ... (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: 0.490 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.670 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.950 ------------------------------------------------------------------------------- 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= 0.789 Angle : 1.109 7.703 8088 Z= 0.785 Chirality : 0.076 0.281 919 Planarity : 0.004 0.025 943 Dihedral : 14.274 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 0.01052 / 0.78 ( 5915) covalent geometry : angle 1.10943 / 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 : 0.210 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: 0.0949 time to fit residues: 15.5103 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 : 0.206 ------------------------------------------------------------------------------- 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: 4.9990 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: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.138154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.107445 restraints weight = 6847.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.111189 restraints weight = 4307.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.113756 restraints weight = 3196.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.115639 restraints weight = 2614.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.116782 restraints weight = 2267.163| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1453 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 : 0.596 9.573 8088 Z= 0.273 Chirality : 0.045 0.318 919 Planarity : 0.004 0.040 943 Dihedral : 9.884 135.644 975 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.95 % Favored : 93.90 % Rotamer: Outliers : 1.88 % Allowed : 9.93 % 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: -1.33 (0.33), residues: 639 helix: 0.93 (0.30), residues: 296 sheet: -2.74 (0.51), residues: 78 loop : -2.44 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 859 TYR 0.008 0.001 TYR A 246 PHE 0.009 0.001 PHE A 460 TRP 0.004 0.001 TRP A 771 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 5915) covalent geometry : angle 0.59650 / 0.27 ( 8088) hydrogen bonds : bond 0.03710 / 2.55 ( 272) hydrogen bonds : angle 3.81224 / 2.59 ( 757) metal coordination : bond 0.00155 / 0.07 ( 3) Misc. bond : bond 0.00040 / 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 110 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.209 Fit side-chains REVERT: A 255 MET cc_start: 0.8460 (mtt) cc_final: 0.8220 (mtm) REVERT: A 369 MET cc_start: 0.7616 (mtt) cc_final: 0.7369 (mtp) REVERT: A 607 GLU cc_start: 0.8339 (tp30) cc_final: 0.7755 (mt-10) REVERT: A 635 LYS cc_start: 0.8269 (ttpt) cc_final: 0.7352 (ttmm) REVERT: A 692 ASN cc_start: 0.8491 (t0) cc_final: 0.8172 (t0) REVERT: A 715 TYR cc_start: 0.8558 (t80) cc_final: 0.8185 (t80) REVERT: A 867 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7531 (mm-40) outliers start: 11 outliers final: 8 residues processed: 102 average time/residue: 0.0744 time to fit residues: 10.2345 Evaluate side-chains 93 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 790 ILE 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: 2.9990 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 ASN A 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.131419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.100748 restraints weight = 6891.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.104255 restraints weight = 4420.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.106660 restraints weight = 3314.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.108189 restraints weight = 2748.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.109364 restraints weight = 2419.350| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5919 Z= 0.161 Angle : 0.626 10.048 8088 Z= 0.287 Chirality : 0.045 0.273 919 Planarity : 0.004 0.042 943 Dihedral : 10.258 152.717 974 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.36 % Favored : 92.49 % Rotamer: Outliers : 2.40 % Allowed : 12.84 % Favored : 84.76 % 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 (0.34), residues: 639 helix: 1.51 (0.31), residues: 291 sheet: -2.23 (0.59), residues: 72 loop : -2.22 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 859 TYR 0.013 0.001 TYR A 622 PHE 0.011 0.001 PHE A 459 TRP 0.004 0.001 TRP A 873 HIS 0.004 0.001 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 5915) covalent geometry : angle 0.62643 / 0.29 ( 8088) hydrogen bonds : bond 0.04187 / 2.85 ( 272) hydrogen bonds : angle 3.79119 / 2.59 ( 757) metal coordination : bond 0.00254 / 0.13 ( 3) Misc. bond : bond 0.00039 / 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 105 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.214 Fit side-chains REVERT: A 346 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8349 (pp) REVERT: A 369 MET cc_start: 0.7772 (mtt) cc_final: 0.7523 (mtp) REVERT: A 422 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7144 (mt-10) REVERT: A 434 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8036 (tp) REVERT: A 591 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8406 (mm-30) REVERT: A 607 GLU cc_start: 0.8413 (tp30) cc_final: 0.7849 (mt-10) REVERT: A 635 LYS cc_start: 0.8456 (ttpt) cc_final: 0.7585 (ttmm) REVERT: A 715 TYR cc_start: 0.8741 (t80) cc_final: 0.8447 (t80) REVERT: A 717 TYR cc_start: 0.8162 (t80) cc_final: 0.7782 (t80) REVERT: A 867 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7595 (mm-40) outliers start: 14 outliers final: 11 residues processed: 98 average time/residue: 0.0650 time to fit residues: 8.8688 Evaluate side-chains 91 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 481 ASP 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 653 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 790 ILE 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: 2.9990 chunk 43 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 17 optimal weight: 0.0980 chunk 52 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 444 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.135944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105248 restraints weight = 6857.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.108994 restraints weight = 4347.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.111623 restraints weight = 3237.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.113225 restraints weight = 2638.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.114640 restraints weight = 2304.854| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5919 Z= 0.106 Angle : 0.571 11.070 8088 Z= 0.264 Chirality : 0.044 0.245 919 Planarity : 0.003 0.041 943 Dihedral : 10.362 162.555 974 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.10 % Favored : 93.74 % Rotamer: Outliers : 2.40 % Allowed : 15.24 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.35), residues: 639 helix: 1.79 (0.31), residues: 294 sheet: -2.27 (0.56), residues: 80 loop : -2.03 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 859 TYR 0.009 0.001 TYR A 313 PHE 0.009 0.001 PHE A 459 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 0.00234 / 0.11 ( 5915) covalent geometry : angle 0.57131 / 0.26 ( 8088) hydrogen bonds : bond 0.03727 / 2.50 ( 272) hydrogen bonds : angle 3.64480 / 2.47 ( 757) metal coordination : bond 0.00123 / 0.06 ( 3) Misc. bond : bond 0.00022 / 0.01 ( 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 102 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.259 Fit side-chains REVERT: A 369 MET cc_start: 0.7702 (mtt) cc_final: 0.7460 (mtp) REVERT: A 591 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8338 (mm-30) REVERT: A 635 LYS cc_start: 0.8458 (ttpt) cc_final: 0.7555 (ttmm) REVERT: A 715 TYR cc_start: 0.8702 (t80) cc_final: 0.8401 (t80) REVERT: A 717 TYR cc_start: 0.8188 (t80) cc_final: 0.7696 (t80) REVERT: A 867 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7601 (mm-40) outliers start: 14 outliers final: 12 residues processed: 94 average time/residue: 0.0706 time to fit residues: 9.1165 Evaluate side-chains 92 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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 457 GLN Chi-restraints excluded: chain A residue 491 LYS 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 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: 0.7980 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.0040 chunk 13 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.134567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.104094 restraints weight = 6991.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107566 restraints weight = 4524.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.110119 restraints weight = 3415.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.111765 restraints weight = 2823.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.112914 restraints weight = 2473.116| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2496 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= 0.116 Angle : 0.585 11.038 8088 Z= 0.268 Chirality : 0.044 0.250 919 Planarity : 0.004 0.042 943 Dihedral : 10.369 167.230 974 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.73 % Favored : 93.11 % Rotamer: Outliers : 3.25 % Allowed : 15.07 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.35), residues: 639 helix: 1.76 (0.31), residues: 295 sheet: -1.88 (0.62), residues: 74 loop : -2.11 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 859 TYR 0.007 0.001 TYR A 313 PHE 0.009 0.001 PHE A 856 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 0.00267 / 0.12 ( 5915) covalent geometry : angle 0.58463 / 0.27 ( 8088) hydrogen bonds : bond 0.03739 / 2.50 ( 272) hydrogen bonds : angle 3.57135 / 2.43 ( 757) metal coordination : bond 0.00138 / 0.07 ( 3) Misc. bond : bond 0.00030 / 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 108 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.188 Fit side-chains REVERT: A 346 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8399 (pp) REVERT: A 369 MET cc_start: 0.7717 (mtt) cc_final: 0.7482 (mtp) REVERT: A 422 GLU cc_start: 0.7305 (mt-10) cc_final: 0.7084 (mt-10) REVERT: A 591 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8369 (mm-30) REVERT: A 607 GLU cc_start: 0.8428 (tp30) cc_final: 0.7825 (mt-10) REVERT: A 635 LYS cc_start: 0.8492 (ttpt) cc_final: 0.7582 (ttmm) REVERT: A 715 TYR cc_start: 0.8700 (t80) cc_final: 0.8394 (t80) REVERT: A 717 TYR cc_start: 0.8246 (t80) cc_final: 0.7602 (t80) REVERT: A 867 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7657 (mm-40) outliers start: 19 outliers final: 13 residues processed: 99 average time/residue: 0.0639 time to fit residues: 8.7449 Evaluate side-chains 97 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 346 LEU 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 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 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: 1.9990 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 769 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.132509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.101825 restraints weight = 6927.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.105297 restraints weight = 4544.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.107567 restraints weight = 3459.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.109349 restraints weight = 2878.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110313 restraints weight = 2530.971| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5919 Z= 0.141 Angle : 0.602 9.970 8088 Z= 0.279 Chirality : 0.045 0.256 919 Planarity : 0.004 0.043 943 Dihedral : 10.432 170.070 974 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.04 % Favored : 92.80 % Rotamer: Outliers : 3.25 % Allowed : 16.44 % Favored : 80.31 % 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: -0.23 (0.35), residues: 639 helix: 1.80 (0.31), residues: 296 sheet: -1.79 (0.63), residues: 74 loop : -1.98 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 859 TYR 0.006 0.001 TYR A 426 PHE 0.020 0.001 PHE A 655 TRP 0.004 0.001 TRP A 771 HIS 0.003 0.001 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 5915) covalent geometry : angle 0.60175 / 0.28 ( 8088) hydrogen bonds : bond 0.03954 / 2.64 ( 272) hydrogen bonds : angle 3.61460 / 2.47 ( 757) metal coordination : bond 0.00234 / 0.12 ( 3) Misc. bond : bond 0.00027 / 0.01 ( 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 100 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.141 Fit side-chains REVERT: A 346 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8416 (pp) REVERT: A 369 MET cc_start: 0.7737 (mtt) cc_final: 0.7491 (mtp) REVERT: A 422 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7161 (mt-10) REVERT: A 591 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8360 (mm-30) REVERT: A 607 GLU cc_start: 0.8423 (tp30) cc_final: 0.7797 (mt-10) REVERT: A 635 LYS cc_start: 0.8503 (ttpt) cc_final: 0.7597 (ttmm) REVERT: A 715 TYR cc_start: 0.8749 (t80) cc_final: 0.8512 (t80) REVERT: A 867 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7642 (mm-40) outliers start: 19 outliers final: 16 residues processed: 90 average time/residue: 0.0653 time to fit residues: 8.1730 Evaluate side-chains 97 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 346 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 491 LYS 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 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=2.50 ------------------------------------------------------------------------------- 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: 3.9990 chunk 49 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.131273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.100096 restraints weight = 6996.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.103630 restraints weight = 4458.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.106245 restraints weight = 3351.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107698 restraints weight = 2758.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.109070 restraints weight = 2437.810| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5919 Z= 0.150 Angle : 0.614 9.943 8088 Z= 0.286 Chirality : 0.045 0.263 919 Planarity : 0.004 0.042 943 Dihedral : 10.480 171.573 974 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.51 % Favored : 92.33 % Rotamer: Outliers : 3.77 % Allowed : 15.75 % Favored : 80.48 % 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: -0.13 (0.36), residues: 639 helix: 1.86 (0.31), residues: 290 sheet: -1.72 (0.63), residues: 74 loop : -1.84 (0.39), residues: 275 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 0.014 0.001 PHE A 655 TRP 0.004 0.001 TRP A 771 HIS 0.003 0.001 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 5915) covalent geometry : angle 0.61446 / 0.29 ( 8088) hydrogen bonds : bond 0.04046 / 2.68 ( 272) hydrogen bonds : angle 3.76314 / 2.54 ( 757) metal coordination : bond 0.00223 / 0.11 ( 3) Misc. bond : bond 0.00014 / 0.01 ( 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 104 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.211 Fit side-chains REVERT: A 249 GLU cc_start: 0.7916 (tt0) cc_final: 0.7694 (tt0) REVERT: A 346 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8461 (pp) REVERT: A 369 MET cc_start: 0.7696 (mtt) cc_final: 0.7420 (mtp) REVERT: A 591 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8373 (mm-30) REVERT: A 607 GLU cc_start: 0.8445 (tp30) cc_final: 0.7812 (mt-10) REVERT: A 635 LYS cc_start: 0.8530 (ttpt) cc_final: 0.7621 (ttmm) REVERT: A 802 ASP cc_start: 0.7897 (t0) cc_final: 0.7635 (t0) outliers start: 22 outliers final: 17 residues processed: 94 average time/residue: 0.0636 time to fit residues: 8.4573 Evaluate side-chains 94 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 346 LEU Chi-restraints excluded: chain A residue 442 VAL 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 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 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: 5.9990 chunk 32 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.130414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.099838 restraints weight = 6936.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.103234 restraints weight = 4571.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.105446 restraints weight = 3487.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.107186 restraints weight = 2909.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.108127 restraints weight = 2567.015| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5919 Z= 0.156 Angle : 0.625 9.023 8088 Z= 0.293 Chirality : 0.045 0.269 919 Planarity : 0.004 0.043 943 Dihedral : 10.542 173.103 974 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.60 % Allowed : 15.24 % 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: -0.15 (0.36), residues: 639 helix: 1.79 (0.31), residues: 296 sheet: -1.70 (0.64), residues: 74 loop : -1.87 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 859 TYR 0.016 0.001 TYR A 622 PHE 0.013 0.001 PHE A 655 TRP 0.003 0.001 TRP A 771 HIS 0.003 0.001 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 5915) covalent geometry : angle 0.62533 / 0.29 ( 8088) hydrogen bonds : bond 0.04100 / 2.71 ( 272) hydrogen bonds : angle 3.74325 / 2.53 ( 757) metal coordination : bond 0.00242 / 0.12 ( 3) Misc. bond : bond 0.00013 / 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 99 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.173 Fit side-chains REVERT: A 346 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8465 (pp) REVERT: A 369 MET cc_start: 0.7631 (mtt) cc_final: 0.7378 (mtp) REVERT: A 435 ASP cc_start: 0.8262 (t70) cc_final: 0.8008 (t70) REVERT: A 497 SER cc_start: 0.7836 (t) cc_final: 0.7618 (t) REVERT: A 591 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8387 (mm-30) REVERT: A 607 GLU cc_start: 0.8444 (tp30) cc_final: 0.7833 (mt-10) REVERT: A 802 ASP cc_start: 0.7986 (t0) cc_final: 0.7715 (t0) outliers start: 21 outliers final: 17 residues processed: 89 average time/residue: 0.0605 time to fit residues: 7.6918 Evaluate side-chains 95 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 346 LEU Chi-restraints excluded: chain A residue 442 VAL 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 579 PHE 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 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: 0.5980 chunk 16 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.133210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.101248 restraints weight = 6971.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.105115 restraints weight = 4354.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.107714 restraints weight = 3217.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.109545 restraints weight = 2626.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.110926 restraints weight = 2281.157| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2975 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= 0.121 Angle : 0.594 8.100 8088 Z= 0.278 Chirality : 0.044 0.279 919 Planarity : 0.004 0.042 943 Dihedral : 10.528 174.639 974 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.25 % Allowed : 15.75 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.36), residues: 639 helix: 1.89 (0.31), residues: 296 sheet: -1.65 (0.64), residues: 74 loop : -1.84 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 859 TYR 0.008 0.001 TYR A 622 PHE 0.009 0.001 PHE A 856 TRP 0.005 0.001 TRP A 771 HIS 0.003 0.000 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 5915) covalent geometry : angle 0.59396 / 0.28 ( 8088) hydrogen bonds : bond 0.03808 / 2.50 ( 272) hydrogen bonds : angle 3.64488 / 2.47 ( 757) metal coordination : bond 0.00178 / 0.09 ( 3) Misc. bond : bond 0.00018 / 0.01 ( 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 105 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.208 Fit side-chains REVERT: A 346 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8411 (pp) REVERT: A 369 MET cc_start: 0.7622 (mtt) cc_final: 0.7326 (mtp) REVERT: A 393 GLN cc_start: 0.8258 (tm-30) cc_final: 0.8000 (tm-30) REVERT: A 435 ASP cc_start: 0.8234 (t70) cc_final: 0.7980 (t70) REVERT: A 445 ASN cc_start: 0.8574 (m110) cc_final: 0.8205 (m110) REVERT: A 591 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8414 (mm-30) REVERT: A 607 GLU cc_start: 0.8484 (tp30) cc_final: 0.7832 (mt-10) REVERT: A 802 ASP cc_start: 0.7999 (t0) cc_final: 0.7731 (t0) outliers start: 19 outliers final: 17 residues processed: 97 average time/residue: 0.0600 time to fit residues: 8.4298 Evaluate side-chains 98 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 346 LEU Chi-restraints excluded: chain A residue 442 VAL 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 579 PHE 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 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: 1.9990 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.128250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.097834 restraints weight = 7054.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.101064 restraints weight = 4621.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.103420 restraints weight = 3519.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.104873 restraints weight = 2937.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.106057 restraints weight = 2599.145| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5919 Z= 0.201 Angle : 0.682 9.599 8088 Z= 0.321 Chirality : 0.047 0.275 919 Planarity : 0.004 0.043 943 Dihedral : 10.601 174.967 974 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 3.25 % Allowed : 15.75 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.35), residues: 639 helix: 1.75 (0.31), residues: 296 sheet: -1.76 (0.63), residues: 74 loop : -1.86 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 811 TYR 0.012 0.001 TYR A 715 PHE 0.020 0.002 PHE A 853 TRP 0.006 0.001 TRP A 873 HIS 0.004 0.001 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 ( 5915) covalent geometry : angle 0.68211 / 0.32 ( 8088) hydrogen bonds : bond 0.04289 / 2.82 ( 272) hydrogen bonds : angle 3.81006 / 2.58 ( 757) metal coordination : bond 0.00336 / 0.17 ( 3) Misc. bond : bond 0.00019 / 0.01 ( 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 97 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.196 Fit side-chains REVERT: A 346 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8505 (pp) REVERT: A 369 MET cc_start: 0.7712 (mtt) cc_final: 0.7417 (mtp) REVERT: A 393 GLN cc_start: 0.8381 (tm-30) cc_final: 0.8101 (tm-30) REVERT: A 445 ASN cc_start: 0.8565 (m110) cc_final: 0.8202 (m110) REVERT: A 591 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8373 (mm-30) REVERT: A 607 GLU cc_start: 0.8366 (tp30) cc_final: 0.7850 (mt-10) REVERT: A 802 ASP cc_start: 0.7982 (t0) cc_final: 0.7764 (t0) outliers start: 19 outliers final: 17 residues processed: 88 average time/residue: 0.0595 time to fit residues: 7.5139 Evaluate side-chains 93 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 346 LEU Chi-restraints excluded: chain A residue 442 VAL 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 579 PHE 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 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: 3.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.0870 chunk 4 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.132261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.101880 restraints weight = 6880.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.105102 restraints weight = 4526.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.107652 restraints weight = 3463.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.109439 restraints weight = 2854.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.110198 restraints weight = 2497.717| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5919 Z= 0.131 Angle : 0.629 9.030 8088 Z= 0.297 Chirality : 0.045 0.283 919 Planarity : 0.004 0.042 943 Dihedral : 10.594 175.952 974 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 3.25 % Allowed : 15.41 % 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: -0.08 (0.36), residues: 639 helix: 1.88 (0.31), residues: 296 sheet: -1.72 (0.62), residues: 74 loop : -1.84 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 859 TYR 0.014 0.001 TYR A 715 PHE 0.029 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 0.00303 / 0.13 ( 5915) covalent geometry : angle 0.62922 / 0.30 ( 8088) hydrogen bonds : bond 0.03884 / 2.53 ( 272) hydrogen bonds : angle 3.69435 / 2.50 ( 757) metal coordination : bond 0.00170 / 0.09 ( 3) Misc. bond : bond 0.00015 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1082.08 seconds wall clock time: 19 minutes 24.80 seconds (1164.80 seconds total)