Starting phenix.real_space_refine on Tue Mar 3 14:28:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tnx_26022/03_2026/7tnx_26022.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnx_26022/03_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_26022/03_2026/7tnx_26022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnx_26022/03_2026/7tnx_26022.map" model { file = "/net/cci-nas-00/data/ceres_data/7tnx_26022/03_2026/7tnx_26022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnx_26022/03_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-5986/lib/python3.9/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: 1.47, per 1000 atoms: 0.26 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: 0.69 Conformation dependent library (CDL) restraints added in 214.7 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: 0.60 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: 0.89 Time building geometry restraints manager: 0.84 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: 3337 19.34 - 38.68: 225 38.68 - 58.02: 43 58.02 - 77.36: 31 77.36 - 96.70: 10 Dihedral angle restraints: 3646 sinusoidal: 1740 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 3643 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: 0.620 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.140 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 : 15.461 96.698 2404 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 covalent geometry : bond 0.01051 ( 5915) covalent geometry : angle 1.08181 ( 8088) hydrogen bonds : bond 0.08057 ( 272) hydrogen bonds : angle 5.49130 ( 757) metal coordination : bond 0.18254 ( 3) Misc. bond : bond 0.00045 ( 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 : 0.340 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: 0.0879 time to fit residues: 14.3719 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 : 0.172 ------------------------------------------------------------------------------- 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: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.137659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107226 restraints weight = 6842.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.110942 restraints weight = 4310.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.113569 restraints weight = 3192.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.115236 restraints weight = 2601.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.116594 restraints weight = 2268.912| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5919 Z= 0.106 Angle : 0.510 9.191 8088 Z= 0.252 Chirality : 0.038 0.226 919 Planarity : 0.004 0.038 943 Dihedral : 14.253 89.586 1063 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.95 % Favored : 93.90 % Rotamer: Outliers : 1.71 % Allowed : 9.93 % Favored : 88.36 % 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: -1.25 (0.33), residues: 639 helix: 0.98 (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 covalent geometry : bond 0.00236 ( 5915) covalent geometry : angle 0.51008 ( 8088) hydrogen bonds : bond 0.03570 ( 272) hydrogen bonds : angle 3.78350 ( 757) metal coordination : bond 0.00477 ( 3) Misc. bond : bond 0.00042 ( 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 109 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.215 Fit side-chains REVERT: A 255 MET cc_start: 0.8461 (mtt) cc_final: 0.8232 (mtm) REVERT: A 369 MET cc_start: 0.7633 (mtt) cc_final: 0.7395 (mtp) REVERT: A 607 GLU cc_start: 0.8319 (tp30) cc_final: 0.7753 (mt-10) REVERT: A 622 TYR cc_start: 0.8201 (m-80) cc_final: 0.7936 (m-10) REVERT: A 635 LYS cc_start: 0.8273 (ttpt) cc_final: 0.7356 (ttmm) REVERT: A 692 ASN cc_start: 0.8514 (t0) cc_final: 0.8159 (t0) REVERT: A 715 TYR cc_start: 0.8522 (t80) cc_final: 0.8145 (t80) REVERT: A 867 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7530 (mm-40) outliers start: 10 outliers final: 6 residues processed: 102 average time/residue: 0.0753 time to fit residues: 10.2073 Evaluate side-chains 90 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN A 354 ASN A 384 ASN A 517 GLN A 769 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.129659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.099205 restraints weight = 6906.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.102417 restraints weight = 4567.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.104715 restraints weight = 3494.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.105856 restraints weight = 2918.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.107243 restraints weight = 2617.959| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5919 Z= 0.181 Angle : 0.588 9.753 8088 Z= 0.284 Chirality : 0.041 0.239 919 Planarity : 0.004 0.043 943 Dihedral : 14.168 93.284 1062 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.20 % Favored : 92.64 % Rotamer: Outliers : 2.57 % Allowed : 12.84 % Favored : 84.59 % 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 (0.35), residues: 639 helix: 1.54 (0.31), residues: 288 sheet: -2.52 (0.56), residues: 78 loop : -2.11 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 859 TYR 0.008 0.001 TYR A 879 PHE 0.012 0.002 PHE A 459 TRP 0.005 0.001 TRP A 873 HIS 0.005 0.001 HIS A 871 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 5915) covalent geometry : angle 0.58806 ( 8088) hydrogen bonds : bond 0.04189 ( 272) hydrogen bonds : angle 3.86370 ( 757) metal coordination : bond 0.00320 ( 3) Misc. bond : bond 0.00028 ( 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 97 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.247 Fit side-chains REVERT: A 346 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8351 (pp) REVERT: A 369 MET cc_start: 0.7764 (mtt) cc_final: 0.7503 (mtp) REVERT: A 422 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7172 (mt-10) REVERT: A 434 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8037 (tp) REVERT: A 607 GLU cc_start: 0.8397 (tp30) cc_final: 0.7859 (mt-10) REVERT: A 635 LYS cc_start: 0.8516 (ttpt) cc_final: 0.7535 (ttmm) REVERT: A 715 TYR cc_start: 0.8786 (t80) cc_final: 0.8568 (t80) REVERT: A 717 TYR cc_start: 0.8194 (t80) cc_final: 0.7645 (t80) REVERT: A 867 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7636 (mm-40) outliers start: 15 outliers final: 12 residues processed: 89 average time/residue: 0.0634 time to fit residues: 7.8451 Evaluate side-chains 87 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 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 718 VAL Chi-restraints excluded: chain A residue 766 LEU 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: 4.9990 chunk 41 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.131468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.100311 restraints weight = 6892.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.103956 restraints weight = 4410.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.106373 restraints weight = 3293.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.108018 restraints weight = 2726.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.108790 restraints weight = 2407.683| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 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 0.034 5919 Z= 0.141 Angle : 0.547 10.935 8088 Z= 0.265 Chirality : 0.040 0.197 919 Planarity : 0.004 0.042 943 Dihedral : 14.112 91.512 1062 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.73 % Favored : 93.11 % Rotamer: Outliers : 2.91 % Allowed : 15.24 % 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: -0.48 (0.35), residues: 639 helix: 1.67 (0.31), residues: 288 sheet: -2.11 (0.60), residues: 74 loop : -2.04 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 859 TYR 0.006 0.001 TYR A 313 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 covalent geometry : bond 0.00330 ( 5915) covalent geometry : angle 0.54657 ( 8088) hydrogen bonds : bond 0.03926 ( 272) hydrogen bonds : angle 3.78451 ( 757) metal coordination : bond 0.00214 ( 3) Misc. bond : bond 0.00029 ( 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: 17 poor density : 87 time to evaluate : 0.204 Fit side-chains REVERT: A 346 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8421 (pp) REVERT: A 369 MET cc_start: 0.7754 (mtt) cc_final: 0.7499 (mtp) REVERT: A 562 ASP cc_start: 0.8175 (t0) cc_final: 0.7932 (t0) REVERT: A 607 GLU cc_start: 0.8403 (tp30) cc_final: 0.7865 (mt-10) REVERT: A 635 LYS cc_start: 0.8505 (ttpt) cc_final: 0.7547 (ttmm) REVERT: A 655 PHE cc_start: 0.8943 (p90) cc_final: 0.8533 (p90) REVERT: A 715 TYR cc_start: 0.8784 (t80) cc_final: 0.8563 (t80) REVERT: A 717 TYR cc_start: 0.8302 (t80) cc_final: 0.7680 (t80) outliers start: 17 outliers final: 12 residues processed: 94 average time/residue: 0.0608 time to fit residues: 7.9838 Evaluate side-chains 89 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 18 optimal weight: 0.0970 chunk 37 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.133790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.103140 restraints weight = 6999.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.106639 restraints weight = 4541.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.109008 restraints weight = 3440.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.110772 restraints weight = 2848.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.111868 restraints weight = 2497.097| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2562 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= 0.109 Angle : 0.521 10.596 8088 Z= 0.252 Chirality : 0.039 0.185 919 Planarity : 0.004 0.041 943 Dihedral : 14.048 90.006 1062 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.89 % Favored : 92.96 % Rotamer: Outliers : 2.91 % Allowed : 16.61 % 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: -0.34 (0.35), residues: 639 helix: 1.76 (0.31), residues: 294 sheet: -1.91 (0.62), residues: 74 loop : -2.06 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 859 TYR 0.009 0.001 TYR A 313 PHE 0.009 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 covalent geometry : bond 0.00249 ( 5915) covalent geometry : angle 0.52121 ( 8088) hydrogen bonds : bond 0.03547 ( 272) hydrogen bonds : angle 3.58657 ( 757) metal coordination : bond 0.00150 ( 3) Misc. bond : bond 0.00030 ( 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 104 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.215 Fit side-chains REVERT: A 369 MET cc_start: 0.7702 (mtt) cc_final: 0.7449 (mtp) REVERT: A 435 ASP cc_start: 0.8184 (t0) cc_final: 0.7862 (t0) REVERT: A 562 ASP cc_start: 0.8158 (t70) cc_final: 0.7887 (t0) REVERT: A 591 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8373 (mm-30) REVERT: A 607 GLU cc_start: 0.8335 (tp30) cc_final: 0.7878 (mt-10) REVERT: A 715 TYR cc_start: 0.8761 (t80) cc_final: 0.8546 (t80) outliers start: 17 outliers final: 14 residues processed: 94 average time/residue: 0.0665 time to fit residues: 8.7140 Evaluate side-chains 94 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.131975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.100332 restraints weight = 6914.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.104150 restraints weight = 4310.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.106787 restraints weight = 3179.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.108442 restraints weight = 2597.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.109749 restraints weight = 2267.354| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2742 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= 0.133 Angle : 0.554 10.356 8088 Z= 0.266 Chirality : 0.040 0.220 919 Planarity : 0.004 0.042 943 Dihedral : 13.981 91.018 1062 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.20 % Favored : 92.64 % Rotamer: Outliers : 3.60 % Allowed : 15.92 % 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: -0.24 (0.35), residues: 639 helix: 1.79 (0.31), residues: 295 sheet: -1.85 (0.63), residues: 74 loop : -1.96 (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 622 PHE 0.019 0.001 PHE A 853 TRP 0.004 0.001 TRP A 771 HIS 0.003 0.001 HIS A 871 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 5915) covalent geometry : angle 0.55433 ( 8088) hydrogen bonds : bond 0.03709 ( 272) hydrogen bonds : angle 3.62868 ( 757) metal coordination : bond 0.00209 ( 3) Misc. bond : bond 0.00027 ( 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 102 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.172 Fit side-chains REVERT: A 346 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8416 (pp) REVERT: A 369 MET cc_start: 0.7736 (mtt) cc_final: 0.7488 (mtp) REVERT: A 562 ASP cc_start: 0.8222 (t70) cc_final: 0.7884 (t0) REVERT: A 591 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8354 (mm-30) REVERT: A 607 GLU cc_start: 0.8392 (tp30) cc_final: 0.7878 (mt-10) REVERT: A 635 LYS cc_start: 0.8478 (ttpt) cc_final: 0.7561 (ttmm) outliers start: 21 outliers final: 17 residues processed: 92 average time/residue: 0.0680 time to fit residues: 8.5911 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 : 0.142 ------------------------------------------------------------------------------- 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 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 766 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 60 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 HIS A 608 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.133251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.102512 restraints weight = 6910.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.105942 restraints weight = 4528.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.108437 restraints weight = 3433.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.110129 restraints weight = 2836.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.110797 restraints weight = 2493.228| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2813 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= 0.112 Angle : 0.531 9.128 8088 Z= 0.258 Chirality : 0.039 0.212 919 Planarity : 0.004 0.041 943 Dihedral : 13.952 89.653 1062 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.20 % Favored : 92.64 % Rotamer: Outliers : 3.94 % Allowed : 15.58 % 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: -0.08 (0.36), residues: 639 helix: 1.91 (0.31), residues: 295 sheet: -1.66 (0.64), residues: 74 loop : -1.89 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 859 TYR 0.009 0.001 TYR A 622 PHE 0.016 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 covalent geometry : bond 0.00257 ( 5915) covalent geometry : angle 0.53144 ( 8088) hydrogen bonds : bond 0.03514 ( 272) hydrogen bonds : angle 3.54314 ( 757) metal coordination : bond 0.00148 ( 3) Misc. bond : bond 0.00038 ( 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 105 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.207 Fit side-chains REVERT: A 249 GLU cc_start: 0.7954 (tt0) cc_final: 0.7589 (tt0) REVERT: A 346 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8413 (pp) REVERT: A 369 MET cc_start: 0.7636 (mtt) cc_final: 0.7370 (mtp) REVERT: A 393 GLN cc_start: 0.8306 (tm-30) cc_final: 0.8080 (tm-30) REVERT: A 445 ASN cc_start: 0.8532 (m110) cc_final: 0.8096 (m110) REVERT: A 562 ASP cc_start: 0.8168 (t70) cc_final: 0.7805 (t0) REVERT: A 579 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6288 (t80) REVERT: A 591 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8367 (mm-30) REVERT: A 607 GLU cc_start: 0.8365 (tp30) cc_final: 0.7904 (mt-10) REVERT: A 635 LYS cc_start: 0.8477 (ttpt) cc_final: 0.7562 (ttmm) REVERT: A 789 PHE cc_start: 0.7976 (t80) cc_final: 0.7575 (t80) outliers start: 23 outliers final: 18 residues processed: 94 average time/residue: 0.0662 time to fit residues: 8.6123 Evaluate side-chains 99 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 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 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 766 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.133052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.101533 restraints weight = 6850.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105303 restraints weight = 4274.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.108023 restraints weight = 3155.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.109686 restraints weight = 2572.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.110953 restraints weight = 2244.295| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2876 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= 0.119 Angle : 0.538 8.086 8088 Z= 0.262 Chirality : 0.039 0.213 919 Planarity : 0.004 0.042 943 Dihedral : 13.910 89.738 1062 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.77 % Allowed : 15.58 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.36), residues: 639 helix: 1.95 (0.31), residues: 296 sheet: -1.63 (0.63), residues: 74 loop : -1.84 (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 0.002 0.000 HIS A 871 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5915) covalent geometry : angle 0.53808 ( 8088) hydrogen bonds : bond 0.03520 ( 272) hydrogen bonds : angle 3.54027 ( 757) metal coordination : bond 0.00157 ( 3) Misc. bond : bond 0.00030 ( 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 103 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.206 Fit side-chains REVERT: A 346 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8407 (pp) REVERT: A 369 MET cc_start: 0.7646 (mtt) cc_final: 0.7368 (mtp) REVERT: A 460 PHE cc_start: 0.8468 (m-80) cc_final: 0.8266 (m-80) REVERT: A 562 ASP cc_start: 0.8242 (t70) cc_final: 0.7830 (t0) REVERT: A 591 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8395 (mm-30) REVERT: A 607 GLU cc_start: 0.8410 (tp30) cc_final: 0.7896 (mt-10) REVERT: A 635 LYS cc_start: 0.8410 (ttpt) cc_final: 0.7499 (ttmm) REVERT: A 789 PHE cc_start: 0.7997 (t80) cc_final: 0.7583 (t80) outliers start: 22 outliers final: 17 residues processed: 92 average time/residue: 0.0578 time to fit residues: 7.6024 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 : 0.202 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 57 optimal weight: 0.0170 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.133586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.101838 restraints weight = 6908.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.105628 restraints weight = 4299.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.108253 restraints weight = 3179.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110056 restraints weight = 2590.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.111166 restraints weight = 2257.318| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5919 Z= 0.114 Angle : 0.539 7.849 8088 Z= 0.261 Chirality : 0.039 0.213 919 Planarity : 0.004 0.041 943 Dihedral : 13.893 89.304 1062 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % 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: 0.04 (0.36), residues: 639 helix: 1.98 (0.31), residues: 296 sheet: -1.59 (0.63), residues: 74 loop : -1.82 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 859 TYR 0.009 0.001 TYR A 622 PHE 0.014 0.001 PHE A 853 TRP 0.005 0.001 TRP A 771 HIS 0.002 0.000 HIS A 871 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 5915) covalent geometry : angle 0.53857 ( 8088) hydrogen bonds : bond 0.03437 ( 272) hydrogen bonds : angle 3.50477 ( 757) metal coordination : bond 0.00146 ( 3) Misc. bond : bond 0.00028 ( 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 100 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.215 Fit side-chains REVERT: A 346 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8412 (pp) REVERT: A 369 MET cc_start: 0.7629 (mtt) cc_final: 0.7338 (mtp) REVERT: A 393 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7930 (tm-30) REVERT: A 435 ASP cc_start: 0.8271 (t70) cc_final: 0.8001 (t70) REVERT: A 445 ASN cc_start: 0.8554 (m110) cc_final: 0.8309 (m110) REVERT: A 562 ASP cc_start: 0.8211 (t70) cc_final: 0.7797 (t0) REVERT: A 591 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8321 (mm-30) outliers start: 19 outliers final: 16 residues processed: 92 average time/residue: 0.0534 time to fit residues: 7.0534 Evaluate side-chains 95 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.132048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.100193 restraints weight = 6929.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.104036 restraints weight = 4301.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.106615 restraints weight = 3159.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.108473 restraints weight = 2574.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.109653 restraints weight = 2235.080| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5919 Z= 0.135 Angle : 0.560 7.901 8088 Z= 0.273 Chirality : 0.040 0.215 919 Planarity : 0.004 0.042 943 Dihedral : 13.876 89.960 1062 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.91 % Allowed : 16.78 % 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: 0.02 (0.36), residues: 639 helix: 1.95 (0.31), residues: 296 sheet: -1.61 (0.63), residues: 74 loop : -1.79 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 859 TYR 0.008 0.001 TYR A 622 PHE 0.029 0.001 PHE A 460 TRP 0.004 0.001 TRP A 771 HIS 0.002 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 5915) covalent geometry : angle 0.56003 ( 8088) hydrogen bonds : bond 0.03578 ( 272) hydrogen bonds : angle 3.55660 ( 757) metal coordination : bond 0.00195 ( 3) Misc. bond : bond 0.00027 ( 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: 17 poor density : 80 time to evaluate : 0.260 Fit side-chains REVERT: A 346 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8444 (pp) REVERT: A 369 MET cc_start: 0.7669 (mtt) cc_final: 0.7379 (mtp) REVERT: A 435 ASP cc_start: 0.8250 (t70) cc_final: 0.7977 (t70) REVERT: A 445 ASN cc_start: 0.8545 (m110) cc_final: 0.8151 (m110) REVERT: A 562 ASP cc_start: 0.8262 (t70) cc_final: 0.8001 (m-30) REVERT: A 591 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8325 (mm-30) outliers start: 17 outliers final: 16 residues processed: 89 average time/residue: 0.0597 time to fit residues: 7.6989 Evaluate side-chains 94 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.132863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.102480 restraints weight = 6803.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.105985 restraints weight = 4432.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.108387 restraints weight = 3332.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110164 restraints weight = 2757.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.111024 restraints weight = 2404.126| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3022 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= 0.123 Angle : 0.558 8.228 8088 Z= 0.272 Chirality : 0.040 0.211 919 Planarity : 0.004 0.041 943 Dihedral : 13.874 89.393 1062 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % 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: 0.05 (0.36), residues: 639 helix: 1.94 (0.31), residues: 297 sheet: -1.62 (0.62), residues: 74 loop : -1.74 (0.40), residues: 268 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 0.017 0.001 PHE A 655 TRP 0.005 0.001 TRP A 771 HIS 0.002 0.000 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 5915) covalent geometry : angle 0.55791 ( 8088) hydrogen bonds : bond 0.03529 ( 272) hydrogen bonds : angle 3.55196 ( 757) metal coordination : bond 0.00152 ( 3) Misc. bond : bond 0.00030 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 999.07 seconds wall clock time: 17 minutes 56.72 seconds (1076.72 seconds total)