Starting phenix.real_space_refine on Sat May 2 16:08:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lqj_63297/05_2026/9lqj_63297.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lqj_63297/05_2026/9lqj_63297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lqj_63297/05_2026/9lqj_63297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lqj_63297/05_2026/9lqj_63297.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lqj_63297/05_2026/9lqj_63297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lqj_63297/05_2026/9lqj_63297.map" } resolution = 2.68 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 Ca 2 9.91 5 Zn 1 6.06 5 S 15 5.16 5 C 4156 2.51 5 N 1079 2.21 5 O 1722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6975 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 769, 6256 Classifications: {'peptide': 769} Link IDs: {'PTRANS': 27, 'TRANS': 741} Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 95 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 4, 'TRANS': 10} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'HYP:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 95 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 4, 'TRANS': 10} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'HYP:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 95 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 4, 'TRANS': 10} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'HYP:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 404 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3, 'water': 401} Link IDs: {None: 403} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 1.95, per 1000 atoms: 0.28 Number of scatterers: 6975 At special positions: 0 Unit cell: (76.56, 76.56, 99.18, 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 Ca 2 19.99 S 15 16.00 O 1722 8.00 N 1079 7.00 C 4156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 264.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1003 " pdb="ZN ZN A1003 " - pdb=" NE2 HIS A 419 " pdb="ZN ZN A1003 " - pdb=" NE2 HIS A 415 " 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1498 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 4 sheets defined 54.3% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 9 through 16 removed outlier: 3.624A pdb=" N THR A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 26 Processing helix chain 'A' and resid 29 through 33 Processing helix chain 'A' and resid 40 through 48 Processing helix chain 'A' and resid 49 through 64 Processing helix chain 'A' and resid 74 through 92 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 107 through 117 Processing helix chain 'A' and resid 124 through 138 Processing helix chain 'A' and resid 144 through 161 Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 161 through 168 removed outlier: 4.061A pdb=" N LEU A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 194 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 207 through 218 Processing helix chain 'A' and resid 226 through 241 removed outlier: 3.616A pdb=" N ALA A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 265 through 280 removed outlier: 3.658A pdb=" N ASP A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 303 Processing helix chain 'A' and resid 323 through 346 Processing helix chain 'A' and resid 355 through 359 removed outlier: 3.526A pdb=" N ILE A 359 " --> pdb=" O PRO A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.568A pdb=" N LYS A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 408 through 426 Processing helix chain 'A' and resid 434 through 441 removed outlier: 6.196A pdb=" N ASN A 439 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A 440 " --> pdb=" O TYR A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 454 Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 482 through 488 Processing helix chain 'A' and resid 496 through 511 removed outlier: 3.972A pdb=" N TYR A 500 " --> pdb=" O GLU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 removed outlier: 4.046A pdb=" N LEU A 516 " --> pdb=" O ASP A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 541 Processing helix chain 'A' and resid 541 through 558 Processing helix chain 'A' and resid 559 through 562 Processing helix chain 'A' and resid 568 through 573 removed outlier: 3.725A pdb=" N VAL A 573 " --> pdb=" O ASP A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 592 Processing helix chain 'A' and resid 622 through 643 Processing helix chain 'A' and resid 646 through 652 removed outlier: 3.513A pdb=" N TYR A 649 " --> pdb=" O TRP A 646 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 305 through 309 removed outlier: 6.666A pdb=" N THR A 361 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N THR A 397 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL A 363 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY A 386 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 593 through 602 removed outlier: 7.622A pdb=" N LEU A 593 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR A 616 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ASP A 595 " --> pdb=" O SER A 614 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N SER A 614 " --> pdb=" O ASP A 595 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL A 667 " --> pdb=" O GLY A 617 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ARG A 666 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL A 661 " --> pdb=" O ARG A 666 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR A 668 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR A 659 " --> pdb=" O THR A 668 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 696 through 699 removed outlier: 6.175A pdb=" N TYR A 696 " --> pdb=" O GLU A 767 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LYS A 769 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY A 698 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN A 729 " --> pdb=" O PHE A 725 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 704 through 705 337 hydrogen bonds defined for protein. 951 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1116 1.31 - 1.43: 1820 1.43 - 1.56: 3735 1.56 - 1.68: 14 1.68 - 1.81: 27 Bond restraints: 6712 Sorted by residual: bond pdb=" C LYS A 597 " pdb=" O LYS A 597 " ideal model delta sigma weight residual 1.235 1.187 0.048 1.30e-02 5.92e+03 1.38e+01 bond pdb=" N LEU A 16 " pdb=" CA LEU A 16 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.25e-02 6.40e+03 9.03e+00 bond pdb=" N LEU A 593 " pdb=" CA LEU A 593 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.21e-02 6.83e+03 9.02e+00 bond pdb=" N VAL A 469 " pdb=" CA VAL A 469 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.30e-02 5.92e+03 7.59e+00 bond pdb=" N ASP A 381 " pdb=" CA ASP A 381 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.23e-02 6.61e+03 7.47e+00 ... (remaining 6707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 8843 1.67 - 3.34: 182 3.34 - 5.02: 32 5.02 - 6.69: 26 6.69 - 8.36: 3 Bond angle restraints: 9086 Sorted by residual: angle pdb=" N HYP B 17 " pdb=" CA HYP B 17 " pdb=" CB HYP B 17 " ideal model delta sigma weight residual 103.00 108.46 -5.46 1.10e+00 8.26e-01 2.46e+01 angle pdb=" N HYP B 23 " pdb=" CA HYP B 23 " pdb=" CB HYP B 23 " ideal model delta sigma weight residual 103.00 108.39 -5.39 1.10e+00 8.26e-01 2.40e+01 angle pdb=" N HYP C 20 " pdb=" CA HYP C 20 " pdb=" CB HYP C 20 " ideal model delta sigma weight residual 103.00 108.22 -5.22 1.10e+00 8.26e-01 2.25e+01 angle pdb=" N HYP C 26 " pdb=" CA HYP C 26 " pdb=" CB HYP C 26 " ideal model delta sigma weight residual 103.00 108.12 -5.12 1.10e+00 8.26e-01 2.16e+01 angle pdb=" N HYP C 17 " pdb=" CA HYP C 17 " pdb=" CB HYP C 17 " ideal model delta sigma weight residual 103.00 108.07 -5.07 1.10e+00 8.26e-01 2.12e+01 ... (remaining 9081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.17: 3688 14.17 - 28.35: 218 28.35 - 42.52: 62 42.52 - 56.70: 27 56.70 - 70.87: 5 Dihedral angle restraints: 4000 sinusoidal: 1632 harmonic: 2368 Sorted by residual: dihedral pdb=" CA LYS A 597 " pdb=" CB LYS A 597 " pdb=" CG LYS A 597 " pdb=" CD LYS A 597 " ideal model delta sinusoidal sigma weight residual 60.00 118.84 -58.84 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA GLN A 270 " pdb=" CB GLN A 270 " pdb=" CG GLN A 270 " pdb=" CD GLN A 270 " ideal model delta sinusoidal sigma weight residual -60.00 -116.87 56.87 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA ARG A 433 " pdb=" CB ARG A 433 " pdb=" CG ARG A 433 " pdb=" CD ARG A 433 " ideal model delta sinusoidal sigma weight residual 180.00 124.17 55.83 3 1.50e+01 4.44e-03 9.37e+00 ... (remaining 3997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 778 0.053 - 0.107: 138 0.107 - 0.160: 33 0.160 - 0.214: 4 0.214 - 0.267: 1 Chirality restraints: 954 Sorted by residual: chirality pdb=" CA HYP D 17 " pdb=" N HYP D 17 " pdb=" C HYP D 17 " pdb=" CB HYP D 17 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA LEU A 33 " pdb=" N LEU A 33 " pdb=" C LEU A 33 " pdb=" CB LEU A 33 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.40e-01 chirality pdb=" CG LEU A 16 " pdb=" CB LEU A 16 " pdb=" CD1 LEU A 16 " pdb=" CD2 LEU A 16 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 951 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 395 " -0.017 2.00e-02 2.50e+03 1.31e-02 3.00e+00 pdb=" CG PHE A 395 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 395 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 395 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 395 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 395 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 395 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 197 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C PRO A 197 " 0.023 2.00e-02 2.50e+03 pdb=" O PRO A 197 " -0.009 2.00e-02 2.50e+03 pdb=" N GLU A 198 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 75 " 0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO A 76 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " 0.018 5.00e-02 4.00e+02 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 147 2.46 - 3.07: 4740 3.07 - 3.68: 11515 3.68 - 4.29: 18761 4.29 - 4.90: 30245 Nonbonded interactions: 65408 Sorted by model distance: nonbonded pdb=" OD1 ASN A 685 " pdb="CA CA A1002 " model vdw 1.847 2.510 nonbonded pdb=" O HYP D 26 " pdb="ZN ZN A1003 " model vdw 1.887 2.230 nonbonded pdb=" OE1 GLU A 447 " pdb="ZN ZN A1003 " model vdw 1.887 2.230 nonbonded pdb=" O PRO A 565 " pdb=" O HOH A1101 " model vdw 2.208 3.040 nonbonded pdb=" OE2 GLU A 198 " pdb=" O HOH A1102 " model vdw 2.209 3.040 ... (remaining 65403 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } 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 individual isotropic 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: 0.880 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.130 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 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 : 0.005 0.057 6714 Z= 0.270 Angle : 0.649 8.360 9086 Z= 0.399 Chirality : 0.045 0.267 954 Planarity : 0.003 0.032 1175 Dihedral : 11.126 70.869 2502 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.00 % Allowed : 3.58 % Favored : 94.42 % 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: 1.76 (0.31), residues: 767 helix: 1.88 (0.27), residues: 387 sheet: 0.79 (0.47), residues: 112 loop : 0.40 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 83 TYR 0.011 0.001 TYR A 498 PHE 0.029 0.001 PHE A 395 TRP 0.004 0.001 TRP A 444 HIS 0.003 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 6712) covalent geometry : angle 0.64926 ( 9086) hydrogen bonds : bond 0.14550 ( 337) hydrogen bonds : angle 5.86132 ( 951) metal coordination : bond 0.00476 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 9 THR cc_start: 0.9216 (p) cc_final: 0.9015 (t) REVERT: A 35 ASP cc_start: 0.7763 (t0) cc_final: 0.7152 (t0) REVERT: A 93 LYS cc_start: 0.8716 (mptt) cc_final: 0.8449 (tptp) REVERT: A 105 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8284 (mm-30) REVERT: A 106 ARG cc_start: 0.8753 (ptp-110) cc_final: 0.7979 (ptm-80) REVERT: A 116 LYS cc_start: 0.9639 (ttpt) cc_final: 0.9387 (ptmm) REVERT: A 169 ASP cc_start: 0.8298 (t0) cc_final: 0.7932 (t0) REVERT: A 392 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8129 (mt-10) REVERT: A 490 LYS cc_start: 0.8514 (mttt) cc_final: 0.8274 (mttp) REVERT: A 496 GLU cc_start: 0.8509 (tt0) cc_final: 0.8027 (tp30) REVERT: A 542 TYR cc_start: 0.8251 (t80) cc_final: 0.8022 (t80) REVERT: A 594 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8272 (mmmm) REVERT: A 599 GLU cc_start: 0.7778 (tt0) cc_final: 0.7510 (tt0) REVERT: A 658 ASN cc_start: 0.8623 (m-40) cc_final: 0.8323 (t0) REVERT: A 749 LYS cc_start: 0.9413 (mtpt) cc_final: 0.9173 (mtpm) outliers start: 14 outliers final: 1 residues processed: 115 average time/residue: 0.7267 time to fit residues: 86.9811 Evaluate side-chains 75 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 594 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 74 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 49 ASN A 127 GLN A 149 ASN A 156 GLN A 374 ASN A 558 ASN A 732 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.107025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.081114 restraints weight = 11637.801| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.82 r_work: 0.3078 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6714 Z= 0.130 Angle : 0.517 5.071 9086 Z= 0.270 Chirality : 0.044 0.205 954 Planarity : 0.004 0.047 1175 Dihedral : 4.532 60.748 917 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.86 % Allowed : 9.16 % Favored : 88.98 % 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: 2.14 (0.31), residues: 767 helix: 2.16 (0.27), residues: 384 sheet: 0.89 (0.48), residues: 114 loop : 0.70 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 7 TYR 0.023 0.001 TYR A 87 PHE 0.026 0.001 PHE A 395 TRP 0.005 0.001 TRP A 444 HIS 0.002 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6712) covalent geometry : angle 0.51658 ( 9086) hydrogen bonds : bond 0.03714 ( 337) hydrogen bonds : angle 4.66880 ( 951) metal coordination : bond 0.00626 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8659 (mp0) cc_final: 0.8404 (pm20) REVERT: A 42 ASP cc_start: 0.8728 (p0) cc_final: 0.8381 (p0) REVERT: A 94 GLU cc_start: 0.8497 (mp0) cc_final: 0.8264 (mp0) REVERT: A 105 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8265 (mm-30) REVERT: A 106 ARG cc_start: 0.8938 (ptp-110) cc_final: 0.8367 (ptm-80) REVERT: A 256 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8394 (mm-30) REVERT: A 369 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8054 (pm20) REVERT: A 440 ASP cc_start: 0.9015 (m-30) cc_final: 0.8748 (m-30) REVERT: A 496 GLU cc_start: 0.8506 (tt0) cc_final: 0.8041 (tp30) REVERT: A 599 GLU cc_start: 0.8353 (tt0) cc_final: 0.8071 (tt0) REVERT: A 658 ASN cc_start: 0.8689 (m-40) cc_final: 0.8313 (t0) REVERT: A 679 ASN cc_start: 0.8612 (m-40) cc_final: 0.8311 (m-40) REVERT: A 749 LYS cc_start: 0.9442 (mtpt) cc_final: 0.9218 (mtpm) outliers start: 13 outliers final: 6 residues processed: 91 average time/residue: 0.6517 time to fit residues: 62.2263 Evaluate side-chains 75 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 621 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 0.0470 chunk 15 optimal weight: 0.5980 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.105782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.080213 restraints weight = 11550.854| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.82 r_work: 0.3082 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6714 Z= 0.111 Angle : 0.483 4.988 9086 Z= 0.253 Chirality : 0.043 0.208 954 Planarity : 0.003 0.040 1175 Dihedral : 4.108 52.381 913 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.15 % Allowed : 10.44 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.31), residues: 767 helix: 2.31 (0.27), residues: 383 sheet: 0.90 (0.47), residues: 114 loop : 0.75 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 7 TYR 0.023 0.001 TYR A 87 PHE 0.024 0.001 PHE A 395 TRP 0.004 0.001 TRP A 444 HIS 0.003 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6712) covalent geometry : angle 0.48302 ( 9086) hydrogen bonds : bond 0.03312 ( 337) hydrogen bonds : angle 4.45722 ( 951) metal coordination : bond 0.00500 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.9235 (m-30) cc_final: 0.8505 (p0) REVERT: A 31 GLU cc_start: 0.8641 (mp0) cc_final: 0.8400 (pm20) REVERT: A 42 ASP cc_start: 0.8764 (p0) cc_final: 0.8369 (p0) REVERT: A 94 GLU cc_start: 0.8640 (mp0) cc_final: 0.8157 (mp0) REVERT: A 105 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8304 (mm-30) REVERT: A 106 ARG cc_start: 0.9019 (ptp-110) cc_final: 0.8421 (ptm-80) REVERT: A 164 ARG cc_start: 0.9245 (ttm-80) cc_final: 0.8721 (mtm110) REVERT: A 191 ARG cc_start: 0.8718 (ttp80) cc_final: 0.8505 (ttp80) REVERT: A 256 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8449 (mm-30) REVERT: A 369 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8095 (pm20) REVERT: A 401 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7820 (mt-10) REVERT: A 440 ASP cc_start: 0.8965 (m-30) cc_final: 0.8693 (m-30) REVERT: A 496 GLU cc_start: 0.8477 (tt0) cc_final: 0.8006 (tp30) REVERT: A 599 GLU cc_start: 0.8398 (tt0) cc_final: 0.8178 (tt0) REVERT: A 658 ASN cc_start: 0.8765 (m-40) cc_final: 0.8282 (t0) REVERT: A 679 ASN cc_start: 0.8653 (m-40) cc_final: 0.8378 (m-40) REVERT: A 749 LYS cc_start: 0.9437 (mtpt) cc_final: 0.9156 (mtpm) outliers start: 15 outliers final: 5 residues processed: 84 average time/residue: 0.7303 time to fit residues: 64.0287 Evaluate side-chains 76 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 621 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 31 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.104988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.079348 restraints weight = 11655.737| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.83 r_work: 0.3122 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6714 Z= 0.119 Angle : 0.475 4.985 9086 Z= 0.249 Chirality : 0.043 0.206 954 Planarity : 0.003 0.030 1175 Dihedral : 4.001 49.723 913 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.86 % Allowed : 10.44 % Favored : 87.70 % 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: 2.34 (0.31), residues: 767 helix: 2.39 (0.27), residues: 384 sheet: 1.17 (0.47), residues: 110 loop : 0.60 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 7 TYR 0.025 0.001 TYR A 87 PHE 0.023 0.001 PHE A 395 TRP 0.004 0.001 TRP A 444 HIS 0.003 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 6712) covalent geometry : angle 0.47550 ( 9086) hydrogen bonds : bond 0.03241 ( 337) hydrogen bonds : angle 4.37609 ( 951) metal coordination : bond 0.00605 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.9210 (m-30) cc_final: 0.8480 (p0) REVERT: A 31 GLU cc_start: 0.8709 (mp0) cc_final: 0.8372 (pm20) REVERT: A 42 ASP cc_start: 0.8835 (p0) cc_final: 0.8438 (p0) REVERT: A 45 GLU cc_start: 0.8833 (tp30) cc_final: 0.8546 (tp30) REVERT: A 93 LYS cc_start: 0.8444 (tppp) cc_final: 0.8211 (tptp) REVERT: A 94 GLU cc_start: 0.8579 (mp0) cc_final: 0.8343 (mp0) REVERT: A 105 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8330 (mm-30) REVERT: A 106 ARG cc_start: 0.9071 (ptp-110) cc_final: 0.8445 (ptm-80) REVERT: A 164 ARG cc_start: 0.9231 (ttm-80) cc_final: 0.8743 (mtm110) REVERT: A 191 ARG cc_start: 0.8695 (ttp80) cc_final: 0.8454 (ttp80) REVERT: A 256 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8463 (mm-30) REVERT: A 369 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8120 (pm20) REVERT: A 401 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: A 440 ASP cc_start: 0.8994 (m-30) cc_final: 0.8729 (m-30) REVERT: A 496 GLU cc_start: 0.8468 (tt0) cc_final: 0.7989 (tp30) REVERT: A 658 ASN cc_start: 0.8851 (m-40) cc_final: 0.8322 (t0) REVERT: A 679 ASN cc_start: 0.8699 (m-40) cc_final: 0.8428 (m-40) REVERT: A 749 LYS cc_start: 0.9450 (mtpt) cc_final: 0.9156 (mtpm) outliers start: 13 outliers final: 5 residues processed: 83 average time/residue: 0.7157 time to fit residues: 62.2222 Evaluate side-chains 78 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 513 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 63 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.104626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.079244 restraints weight = 11783.979| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.78 r_work: 0.3018 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6714 Z= 0.145 Angle : 0.492 4.985 9086 Z= 0.257 Chirality : 0.044 0.209 954 Planarity : 0.003 0.029 1175 Dihedral : 3.913 49.777 912 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.29 % Allowed : 12.30 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.30), residues: 767 helix: 2.38 (0.27), residues: 384 sheet: 1.11 (0.47), residues: 110 loop : 0.55 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 7 TYR 0.025 0.001 TYR A 87 PHE 0.025 0.001 PHE A 395 TRP 0.004 0.001 TRP A 444 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 6712) covalent geometry : angle 0.49155 ( 9086) hydrogen bonds : bond 0.03347 ( 337) hydrogen bonds : angle 4.41237 ( 951) metal coordination : bond 0.00785 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8544 (tppp) cc_final: 0.8228 (tppt) REVERT: A 20 ASP cc_start: 0.9248 (m-30) cc_final: 0.8532 (p0) REVERT: A 31 GLU cc_start: 0.8679 (mp0) cc_final: 0.8380 (pm20) REVERT: A 45 GLU cc_start: 0.8849 (tp30) cc_final: 0.8559 (tp30) REVERT: A 93 LYS cc_start: 0.8512 (tppp) cc_final: 0.8259 (tptp) REVERT: A 94 GLU cc_start: 0.8609 (mp0) cc_final: 0.8351 (mp0) REVERT: A 105 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8354 (mm-30) REVERT: A 106 ARG cc_start: 0.9095 (ptp-110) cc_final: 0.8454 (ptm-80) REVERT: A 164 ARG cc_start: 0.9245 (ttm-80) cc_final: 0.8759 (mtm110) REVERT: A 191 ARG cc_start: 0.8693 (ttp80) cc_final: 0.8445 (ttp80) REVERT: A 256 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8512 (mm-30) REVERT: A 369 GLU cc_start: 0.8360 (mp0) cc_final: 0.8066 (pm20) REVERT: A 401 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: A 440 ASP cc_start: 0.8995 (m-30) cc_final: 0.8736 (m-30) REVERT: A 496 GLU cc_start: 0.8476 (tt0) cc_final: 0.8077 (tp30) REVERT: A 658 ASN cc_start: 0.8912 (m-40) cc_final: 0.8321 (t0) REVERT: A 679 ASN cc_start: 0.8704 (m-40) cc_final: 0.8448 (m-40) REVERT: A 749 LYS cc_start: 0.9445 (mtpt) cc_final: 0.9146 (mtpm) outliers start: 9 outliers final: 4 residues processed: 77 average time/residue: 0.7311 time to fit residues: 58.8214 Evaluate side-chains 74 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 567 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 69 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 35 optimal weight: 0.2980 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 91 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.110195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.085200 restraints weight = 12053.348| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.58 r_work: 0.2974 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6714 Z= 0.188 Angle : 0.518 5.035 9086 Z= 0.269 Chirality : 0.045 0.214 954 Planarity : 0.003 0.033 1175 Dihedral : 4.002 49.869 912 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.29 % Allowed : 12.73 % Favored : 85.98 % 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: 2.20 (0.30), residues: 767 helix: 2.31 (0.27), residues: 384 sheet: 1.03 (0.47), residues: 110 loop : 0.51 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 7 TYR 0.028 0.001 TYR A 87 PHE 0.027 0.001 PHE A 395 TRP 0.004 0.001 TRP A 444 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 6712) covalent geometry : angle 0.51798 ( 9086) hydrogen bonds : bond 0.03584 ( 337) hydrogen bonds : angle 4.49098 ( 951) metal coordination : bond 0.01009 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.9200 (m-30) cc_final: 0.8542 (p0) REVERT: A 31 GLU cc_start: 0.8709 (mp0) cc_final: 0.8426 (pm20) REVERT: A 42 ASP cc_start: 0.8821 (p0) cc_final: 0.8467 (p0) REVERT: A 45 GLU cc_start: 0.8902 (tp30) cc_final: 0.8659 (tp30) REVERT: A 93 LYS cc_start: 0.8588 (tppp) cc_final: 0.7995 (tptp) REVERT: A 105 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8478 (mm-30) REVERT: A 106 ARG cc_start: 0.9095 (ptp-110) cc_final: 0.8491 (ptm-80) REVERT: A 164 ARG cc_start: 0.9140 (ttm-80) cc_final: 0.8770 (mtm110) REVERT: A 191 ARG cc_start: 0.8973 (ttp80) cc_final: 0.8742 (ttp80) REVERT: A 256 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8638 (mm-30) REVERT: A 369 GLU cc_start: 0.8431 (mp0) cc_final: 0.8215 (pm20) REVERT: A 496 GLU cc_start: 0.8610 (tt0) cc_final: 0.8345 (tp30) REVERT: A 658 ASN cc_start: 0.9002 (m-40) cc_final: 0.8570 (t0) REVERT: A 679 ASN cc_start: 0.8856 (m-40) cc_final: 0.8585 (m-40) REVERT: A 692 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.7186 (pp) REVERT: A 749 LYS cc_start: 0.9548 (mtpt) cc_final: 0.9289 (mtpm) REVERT: A 752 VAL cc_start: 0.8787 (OUTLIER) cc_final: 0.8532 (m) outliers start: 9 outliers final: 5 residues processed: 73 average time/residue: 0.6855 time to fit residues: 52.4664 Evaluate side-chains 72 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 752 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 55 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.098307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.072386 restraints weight = 11871.935| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.68 r_work: 0.2880 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6714 Z= 0.147 Angle : 0.499 5.835 9086 Z= 0.260 Chirality : 0.044 0.206 954 Planarity : 0.003 0.029 1175 Dihedral : 3.954 49.753 912 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.57 % Allowed : 13.16 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.30), residues: 767 helix: 2.35 (0.27), residues: 384 sheet: 0.99 (0.47), residues: 110 loop : 0.50 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 7 TYR 0.025 0.001 TYR A 87 PHE 0.026 0.001 PHE A 395 TRP 0.004 0.001 TRP A 444 HIS 0.003 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6712) covalent geometry : angle 0.49928 ( 9086) hydrogen bonds : bond 0.03383 ( 337) hydrogen bonds : angle 4.42898 ( 951) metal coordination : bond 0.00726 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8605 (tppp) cc_final: 0.8302 (tppt) REVERT: A 20 ASP cc_start: 0.9233 (m-30) cc_final: 0.8567 (p0) REVERT: A 31 GLU cc_start: 0.8726 (mp0) cc_final: 0.8407 (pm20) REVERT: A 42 ASP cc_start: 0.8912 (p0) cc_final: 0.8529 (p0) REVERT: A 45 GLU cc_start: 0.8912 (tp30) cc_final: 0.8667 (tp30) REVERT: A 93 LYS cc_start: 0.8538 (tppp) cc_final: 0.7929 (tptp) REVERT: A 105 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8432 (mm-30) REVERT: A 106 ARG cc_start: 0.9128 (ptp-110) cc_final: 0.8482 (ptm-80) REVERT: A 164 ARG cc_start: 0.9205 (ttm-80) cc_final: 0.8791 (mtm110) REVERT: A 191 ARG cc_start: 0.8909 (ttp80) cc_final: 0.8659 (ttp80) REVERT: A 256 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8585 (mm-30) REVERT: A 369 GLU cc_start: 0.8464 (mp0) cc_final: 0.8188 (pm20) REVERT: A 496 GLU cc_start: 0.8585 (tt0) cc_final: 0.8289 (tp30) REVERT: A 658 ASN cc_start: 0.8973 (m-40) cc_final: 0.8475 (t0) REVERT: A 679 ASN cc_start: 0.8831 (m-40) cc_final: 0.8605 (m-40) REVERT: A 692 ILE cc_start: 0.7276 (OUTLIER) cc_final: 0.7066 (pp) REVERT: A 749 LYS cc_start: 0.9527 (mtpt) cc_final: 0.9249 (mtpm) REVERT: A 752 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8399 (m) outliers start: 11 outliers final: 7 residues processed: 75 average time/residue: 0.7130 time to fit residues: 56.0181 Evaluate side-chains 77 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 752 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.098499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.072709 restraints weight = 11874.892| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.70 r_work: 0.2883 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6714 Z= 0.134 Angle : 0.502 6.079 9086 Z= 0.262 Chirality : 0.044 0.204 954 Planarity : 0.003 0.029 1175 Dihedral : 3.920 49.456 912 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.43 % Allowed : 13.88 % Favored : 84.69 % 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: 2.25 (0.30), residues: 767 helix: 2.37 (0.27), residues: 384 sheet: 0.99 (0.47), residues: 110 loop : 0.53 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 7 TYR 0.026 0.001 TYR A 87 PHE 0.025 0.001 PHE A 395 TRP 0.004 0.001 TRP A 444 HIS 0.003 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6712) covalent geometry : angle 0.50246 ( 9086) hydrogen bonds : bond 0.03275 ( 337) hydrogen bonds : angle 4.37654 ( 951) metal coordination : bond 0.00678 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8601 (tppp) cc_final: 0.8302 (tppt) REVERT: A 20 ASP cc_start: 0.9249 (m-30) cc_final: 0.8559 (p0) REVERT: A 42 ASP cc_start: 0.8912 (p0) cc_final: 0.8546 (p0) REVERT: A 45 GLU cc_start: 0.8927 (tp30) cc_final: 0.8687 (tp30) REVERT: A 93 LYS cc_start: 0.8531 (tppp) cc_final: 0.8125 (tptp) REVERT: A 94 GLU cc_start: 0.8707 (mp0) cc_final: 0.8448 (mp0) REVERT: A 105 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8412 (mm-30) REVERT: A 106 ARG cc_start: 0.9139 (ptp-110) cc_final: 0.8454 (ptm-80) REVERT: A 164 ARG cc_start: 0.9164 (ttm-80) cc_final: 0.8780 (mtm110) REVERT: A 191 ARG cc_start: 0.8920 (ttp80) cc_final: 0.8683 (ttp80) REVERT: A 256 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8578 (mm-30) REVERT: A 369 GLU cc_start: 0.8473 (mp0) cc_final: 0.8215 (pm20) REVERT: A 496 GLU cc_start: 0.8582 (tt0) cc_final: 0.8289 (tp30) REVERT: A 658 ASN cc_start: 0.8985 (m-40) cc_final: 0.8481 (t0) REVERT: A 679 ASN cc_start: 0.8826 (m-40) cc_final: 0.8484 (m-40) REVERT: A 749 LYS cc_start: 0.9525 (mtpt) cc_final: 0.9239 (mtpm) REVERT: A 752 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8411 (m) outliers start: 10 outliers final: 7 residues processed: 81 average time/residue: 0.6802 time to fit residues: 57.7791 Evaluate side-chains 77 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 752 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 69 optimal weight: 7.9990 chunk 40 optimal weight: 0.0020 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.098700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.072953 restraints weight = 11824.256| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.71 r_work: 0.2907 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6714 Z= 0.114 Angle : 0.514 7.020 9086 Z= 0.267 Chirality : 0.043 0.198 954 Planarity : 0.003 0.029 1175 Dihedral : 3.905 49.892 912 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.43 % Allowed : 14.31 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.31), residues: 767 helix: 2.39 (0.27), residues: 384 sheet: 1.00 (0.47), residues: 110 loop : 0.54 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 7 TYR 0.025 0.001 TYR A 87 PHE 0.024 0.001 PHE A 395 TRP 0.012 0.001 TRP A 723 HIS 0.003 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6712) covalent geometry : angle 0.51393 ( 9086) hydrogen bonds : bond 0.03165 ( 337) hydrogen bonds : angle 4.32274 ( 951) metal coordination : bond 0.00518 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.258 Fit side-chains REVERT: A 6 LYS cc_start: 0.8617 (tppp) cc_final: 0.8386 (tppt) REVERT: A 20 ASP cc_start: 0.9236 (m-30) cc_final: 0.8550 (p0) REVERT: A 42 ASP cc_start: 0.8920 (p0) cc_final: 0.8527 (p0) REVERT: A 45 GLU cc_start: 0.8922 (tp30) cc_final: 0.8679 (tp30) REVERT: A 93 LYS cc_start: 0.8540 (tppp) cc_final: 0.8128 (tptp) REVERT: A 94 GLU cc_start: 0.8712 (mp0) cc_final: 0.8498 (mp0) REVERT: A 105 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8411 (mm-30) REVERT: A 106 ARG cc_start: 0.9137 (ptp-110) cc_final: 0.8501 (ptm-80) REVERT: A 164 ARG cc_start: 0.9154 (ttm-80) cc_final: 0.8799 (mtm110) REVERT: A 191 ARG cc_start: 0.8937 (ttp80) cc_final: 0.8703 (ttp80) REVERT: A 256 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8546 (mm-30) REVERT: A 369 GLU cc_start: 0.8488 (mp0) cc_final: 0.8278 (pm20) REVERT: A 496 GLU cc_start: 0.8572 (tt0) cc_final: 0.8287 (tp30) REVERT: A 658 ASN cc_start: 0.8978 (m-40) cc_final: 0.8474 (t0) REVERT: A 679 ASN cc_start: 0.8845 (m-40) cc_final: 0.8461 (m-40) REVERT: A 749 LYS cc_start: 0.9507 (mtpt) cc_final: 0.9216 (mtpm) REVERT: A 752 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8393 (m) outliers start: 10 outliers final: 5 residues processed: 80 average time/residue: 0.6785 time to fit residues: 56.8452 Evaluate side-chains 74 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 752 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 68 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 71 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.100223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.074782 restraints weight = 11919.516| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.69 r_work: 0.2936 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6714 Z= 0.108 Angle : 0.525 7.936 9086 Z= 0.269 Chirality : 0.043 0.199 954 Planarity : 0.003 0.029 1175 Dihedral : 3.881 49.799 912 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.00 % Allowed : 15.16 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.31), residues: 767 helix: 2.42 (0.27), residues: 384 sheet: 1.07 (0.48), residues: 110 loop : 0.57 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 7 TYR 0.025 0.001 TYR A 87 PHE 0.024 0.001 PHE A 395 TRP 0.012 0.001 TRP A 723 HIS 0.003 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6712) covalent geometry : angle 0.52531 ( 9086) hydrogen bonds : bond 0.03052 ( 337) hydrogen bonds : angle 4.27125 ( 951) metal coordination : bond 0.00461 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1534 Ramachandran restraints generated. 767 Oldfield, 0 Emsley, 767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.283 Fit side-chains REVERT: A 6 LYS cc_start: 0.8626 (tppp) cc_final: 0.8405 (tppt) REVERT: A 20 ASP cc_start: 0.9248 (m-30) cc_final: 0.8535 (p0) REVERT: A 42 ASP cc_start: 0.8943 (p0) cc_final: 0.8552 (p0) REVERT: A 45 GLU cc_start: 0.8925 (tp30) cc_final: 0.8694 (tp30) REVERT: A 93 LYS cc_start: 0.8527 (tppp) cc_final: 0.8115 (tptp) REVERT: A 94 GLU cc_start: 0.8746 (mp0) cc_final: 0.8530 (mp0) REVERT: A 105 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8439 (mm-30) REVERT: A 106 ARG cc_start: 0.9208 (ptp-110) cc_final: 0.8507 (ptm-80) REVERT: A 164 ARG cc_start: 0.9138 (ttm-80) cc_final: 0.8796 (mtm110) REVERT: A 191 ARG cc_start: 0.8940 (ttp80) cc_final: 0.8709 (ttp80) REVERT: A 256 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8566 (mm-30) REVERT: A 369 GLU cc_start: 0.8483 (mp0) cc_final: 0.8266 (pm20) REVERT: A 387 MET cc_start: 0.9006 (tpp) cc_final: 0.8498 (tpp) REVERT: A 496 GLU cc_start: 0.8539 (tt0) cc_final: 0.8283 (tp30) REVERT: A 658 ASN cc_start: 0.8954 (m-40) cc_final: 0.8455 (t0) REVERT: A 679 ASN cc_start: 0.8859 (m-40) cc_final: 0.8479 (m-40) REVERT: A 749 LYS cc_start: 0.9512 (mtpt) cc_final: 0.9230 (mtpm) REVERT: A 752 VAL cc_start: 0.8677 (OUTLIER) cc_final: 0.8412 (m) outliers start: 7 outliers final: 6 residues processed: 71 average time/residue: 0.6954 time to fit residues: 51.7407 Evaluate side-chains 74 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 752 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.098565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.072874 restraints weight = 11815.088| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.70 r_work: 0.2891 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6714 Z= 0.164 Angle : 0.542 7.129 9086 Z= 0.279 Chirality : 0.045 0.210 954 Planarity : 0.003 0.029 1175 Dihedral : 3.898 48.241 912 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.00 % Allowed : 14.74 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.31), residues: 767 helix: 2.39 (0.27), residues: 384 sheet: 1.04 (0.48), residues: 110 loop : 0.56 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 7 TYR 0.027 0.001 TYR A 87 PHE 0.026 0.001 PHE A 395 TRP 0.004 0.001 TRP A 228 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6712) covalent geometry : angle 0.54232 ( 9086) hydrogen bonds : bond 0.03293 ( 337) hydrogen bonds : angle 4.34183 ( 951) metal coordination : bond 0.00843 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2116.58 seconds wall clock time: 37 minutes 5.29 seconds (2225.29 seconds total)