Starting phenix.real_space_refine on Thu Jul 2 06:14:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wm5_37641/07_2026/8wm5_37641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wm5_37641/07_2026/8wm5_37641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wm5_37641/07_2026/8wm5_37641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wm5_37641/07_2026/8wm5_37641.map" model { file = "/net/cci-nas-00/data/ceres_data/8wm5_37641/07_2026/8wm5_37641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wm5_37641/07_2026/8wm5_37641.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.106 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 40 5.16 5 C 4724 2.51 5 N 1158 2.21 5 O 1251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7179 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3472 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 19, 'TRANS': 455} Chain: "B" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3472 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 19, 'TRANS': 455} Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "B" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 157 Unusual residues: {'CDL': 1, 'PTY': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 Time building chain proxies: 1.30, per 1000 atoms: 0.18 Number of scatterers: 7179 At special positions: 0 Unit cell: (112.23, 89.61, 71.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 6 15.00 O 1251 8.00 N 1158 7.00 C 4724 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: 0.46 Conformation dependent library (CDL) restraints added in 274.8 milliseconds 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1672 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 84.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 48 through 84 removed outlier: 4.299A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLN A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Proline residue: A 77 - end of helix Processing helix chain 'A' and resid 86 through 104 removed outlier: 4.264A pdb=" N ILE A 94 " --> pdb=" O ARG A 90 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 104 " --> pdb=" O THR A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 115 removed outlier: 4.035A pdb=" N GLY A 109 " --> pdb=" O MET A 105 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 136 Processing helix chain 'A' and resid 140 through 169 Proline residue: A 160 - end of helix removed outlier: 3.842A pdb=" N ALA A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 202 Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.905A pdb=" N PHE A 210 " --> pdb=" O TRP A 206 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 211' Processing helix chain 'A' and resid 212 through 227 removed outlier: 3.955A pdb=" N ILE A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 264 Proline residue: A 261 - end of helix Processing helix chain 'A' and resid 267 through 290 removed outlier: 3.586A pdb=" N ILE A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 302 removed outlier: 3.611A pdb=" N ARG A 302 " --> pdb=" O HIS A 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 299 through 302' Processing helix chain 'A' and resid 303 through 334 Processing helix chain 'A' and resid 338 through 364 Proline residue: A 348 - end of helix Processing helix chain 'A' and resid 368 through 390 Processing helix chain 'A' and resid 401 through 424 removed outlier: 3.906A pdb=" N VAL A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) Proline residue: A 418 - end of helix removed outlier: 3.634A pdb=" N ILE A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 466 removed outlier: 3.930A pdb=" N VAL A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A 447 " --> pdb=" O GLN A 443 " (cutoff:3.500A) Proline residue: A 448 - end of helix removed outlier: 3.648A pdb=" N VAL A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 479 through 506 removed outlier: 3.929A pdb=" N LEU A 483 " --> pdb=" O GLN A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.529A pdb=" N VAL A 515 " --> pdb=" O PRO A 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 84 removed outlier: 4.298A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLN B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Proline residue: B 77 - end of helix Processing helix chain 'B' and resid 86 through 104 removed outlier: 4.264A pdb=" N ILE B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 104 " --> pdb=" O THR B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 115 removed outlier: 4.035A pdb=" N GLY B 109 " --> pdb=" O MET B 105 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 136 Processing helix chain 'B' and resid 140 through 169 Proline residue: B 160 - end of helix removed outlier: 3.842A pdb=" N ALA B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 202 Processing helix chain 'B' and resid 206 through 211 removed outlier: 3.906A pdb=" N PHE B 210 " --> pdb=" O TRP B 206 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 206 through 211' Processing helix chain 'B' and resid 212 through 227 removed outlier: 3.955A pdb=" N ILE B 216 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 264 Proline residue: B 261 - end of helix Processing helix chain 'B' and resid 267 through 290 removed outlier: 3.586A pdb=" N ILE B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 302 removed outlier: 3.610A pdb=" N ARG B 302 " --> pdb=" O HIS B 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 299 through 302' Processing helix chain 'B' and resid 303 through 334 Processing helix chain 'B' and resid 338 through 364 Proline residue: B 348 - end of helix Processing helix chain 'B' and resid 368 through 390 Processing helix chain 'B' and resid 401 through 424 removed outlier: 3.906A pdb=" N VAL B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) Proline residue: B 418 - end of helix removed outlier: 3.633A pdb=" N ILE B 424 " --> pdb=" O THR B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 466 removed outlier: 3.930A pdb=" N VAL B 435 " --> pdb=" O GLN B 431 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY B 447 " --> pdb=" O GLN B 443 " (cutoff:3.500A) Proline residue: B 448 - end of helix removed outlier: 3.647A pdb=" N VAL B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 479 through 506 removed outlier: 3.929A pdb=" N LEU B 483 " --> pdb=" O GLN B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 515 removed outlier: 3.529A pdb=" N VAL B 515 " --> pdb=" O PRO B 512 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1728 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: 0.94 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1076 1.32 - 1.44: 1865 1.44 - 1.56: 4287 1.56 - 1.69: 14 1.69 - 1.81: 74 Bond restraints: 7316 Sorted by residual: bond pdb=" N PRO B 77 " pdb=" CD PRO B 77 " ideal model delta sigma weight residual 1.473 1.234 0.239 1.40e-02 5.10e+03 2.92e+02 bond pdb=" N PRO A 77 " pdb=" CD PRO A 77 " ideal model delta sigma weight residual 1.473 1.234 0.239 1.40e-02 5.10e+03 2.90e+02 bond pdb=" N PRO B 261 " pdb=" CD PRO B 261 " ideal model delta sigma weight residual 1.473 1.561 -0.088 1.40e-02 5.10e+03 3.98e+01 bond pdb=" N PRO A 261 " pdb=" CD PRO A 261 " ideal model delta sigma weight residual 1.473 1.561 -0.088 1.40e-02 5.10e+03 3.97e+01 bond pdb=" C30 PTY B 602 " pdb=" O4 PTY B 602 " ideal model delta sigma weight residual 1.331 1.453 -0.122 2.00e-02 2.50e+03 3.73e+01 ... (remaining 7311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 9737 2.41 - 4.83: 152 4.83 - 7.24: 21 7.24 - 9.65: 8 9.65 - 12.06: 6 Bond angle restraints: 9924 Sorted by residual: angle pdb=" CA PRO B 261 " pdb=" N PRO B 261 " pdb=" CD PRO B 261 " ideal model delta sigma weight residual 112.00 99.94 12.06 1.40e+00 5.10e-01 7.42e+01 angle pdb=" CA PRO A 261 " pdb=" N PRO A 261 " pdb=" CD PRO A 261 " ideal model delta sigma weight residual 112.00 99.95 12.05 1.40e+00 5.10e-01 7.41e+01 angle pdb=" C ALA A 518 " pdb=" CA ALA A 518 " pdb=" CB ALA A 518 " ideal model delta sigma weight residual 116.54 109.85 6.69 1.15e+00 7.56e-01 3.38e+01 angle pdb=" C ALA B 518 " pdb=" CA ALA B 518 " pdb=" CB ALA B 518 " ideal model delta sigma weight residual 116.54 109.86 6.68 1.15e+00 7.56e-01 3.37e+01 angle pdb=" N PRO B 77 " pdb=" CD PRO B 77 " pdb=" CG PRO B 77 " ideal model delta sigma weight residual 103.20 109.10 -5.90 1.50e+00 4.44e-01 1.55e+01 ... (remaining 9919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.96: 4043 31.96 - 63.92: 250 63.92 - 95.87: 12 95.87 - 127.83: 0 127.83 - 159.79: 2 Dihedral angle restraints: 4307 sinusoidal: 1665 harmonic: 2642 Sorted by residual: dihedral pdb=" N1 PTY B 602 " pdb=" C2 PTY B 602 " pdb=" C3 PTY B 602 " pdb=" O11 PTY B 602 " ideal model delta sinusoidal sigma weight residual 65.33 -94.46 159.79 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" N1 PTY A 602 " pdb=" C2 PTY A 602 " pdb=" C3 PTY A 602 " pdb=" O11 PTY A 602 " ideal model delta sinusoidal sigma weight residual 65.33 -86.45 151.78 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" CA VAL B 74 " pdb=" C VAL B 74 " pdb=" N ALA B 75 " pdb=" CA ALA B 75 " ideal model delta harmonic sigma weight residual -180.00 -163.38 -16.62 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 4304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 857 0.037 - 0.073: 239 0.073 - 0.110: 86 0.110 - 0.146: 9 0.146 - 0.183: 5 Chirality restraints: 1196 Sorted by residual: chirality pdb=" CA VAL B 371 " pdb=" N VAL B 371 " pdb=" C VAL B 371 " pdb=" CB VAL B 371 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CA VAL A 371 " pdb=" N VAL A 371 " pdb=" C VAL A 371 " pdb=" CB VAL A 371 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CA4 CDL B 603 " pdb=" CA3 CDL B 603 " pdb=" CA6 CDL B 603 " pdb=" OA6 CDL B 603 " both_signs ideal model delta sigma weight residual False -2.53 -2.35 -0.18 2.00e-01 2.50e+01 7.99e-01 ... (remaining 1193 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 260 " 0.086 5.00e-02 4.00e+02 1.20e-01 2.31e+01 pdb=" N PRO B 261 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 260 " -0.086 5.00e-02 4.00e+02 1.20e-01 2.30e+01 pdb=" N PRO A 261 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO A 261 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 261 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 433 " 0.037 5.00e-02 4.00e+02 5.68e-02 5.15e+00 pdb=" N PRO A 434 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 434 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 434 " 0.032 5.00e-02 4.00e+02 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.01: 3 2.01 - 2.73: 372 2.73 - 3.45: 11235 3.45 - 4.18: 17012 4.18 - 4.90: 32209 Nonbonded interactions: 60831 Sorted by model distance: nonbonded pdb=" O10 PTY A 602 " pdb=" O14 PTY A 602 " model vdw 1.284 3.040 nonbonded pdb=" O10 PTY B 602 " pdb=" O14 PTY B 602 " model vdw 1.469 3.040 nonbonded pdb=" OA4 CDL B 603 " pdb=" OA8 CDL B 603 " model vdw 1.613 3.040 nonbonded pdb=" OA4 CDL B 603 " pdb=" OA6 CDL B 603 " model vdw 2.083 3.040 nonbonded pdb=" C8 PTY A 602 " pdb=" O14 PTY A 602 " model vdw 2.161 3.270 ... (remaining 60826 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 'A' selection = (chain 'B' and resid 45 through 602) } 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: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.260 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 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 : 0.007 0.239 7316 Z= 0.430 Angle : 0.778 12.063 9924 Z= 0.431 Chirality : 0.040 0.183 1196 Planarity : 0.007 0.120 1206 Dihedral : 18.633 159.790 2635 Min Nonbonded Distance : 1.284 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.33 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 25.77 % Favored : 74.23 % 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: 1.57 (0.27), residues: 946 helix: 1.66 (0.18), residues: 736 sheet: None (None), residues: 0 loop : -1.15 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 207 TYR 0.005 0.001 TYR A 378 PHE 0.009 0.001 PHE A 398 TRP 0.010 0.001 TRP A 265 HIS 0.002 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.43 ( 7316) covalent geometry : angle 0.77796 / 0.43 ( 9924) hydrogen bonds : bond 0.09683 / 6.47 ( 578) hydrogen bonds : angle 4.43576 / 3.11 ( 1728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.154 Fit side-chains REVERT: B 73 ILE cc_start: 0.8652 (mm) cc_final: 0.8450 (mm) REVERT: B 304 ARG cc_start: 0.7543 (ttt180) cc_final: 0.6621 (ttp80) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.0838 time to fit residues: 9.7159 Evaluate side-chains 84 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN B 151 GLN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.144857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.116931 restraints weight = 7665.805| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.00 r_work: 0.3243 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7316 Z= 0.143 Angle : 0.542 6.502 9924 Z= 0.270 Chirality : 0.038 0.116 1196 Planarity : 0.005 0.060 1206 Dihedral : 13.715 123.379 1223 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.68 % Allowed : 19.72 % Favored : 77.61 % 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: 2.18 (0.27), residues: 946 helix: 2.03 (0.18), residues: 752 sheet: None (None), residues: 0 loop : -0.89 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 207 TYR 0.008 0.001 TYR B 464 PHE 0.013 0.001 PHE B 284 TRP 0.009 0.001 TRP A 265 HIS 0.002 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 7316) covalent geometry : angle 0.54159 / 0.27 ( 9924) hydrogen bonds : bond 0.04642 / 3.17 ( 578) hydrogen bonds : angle 3.87727 / 2.74 ( 1728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.164 Fit side-chains REVERT: A 353 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7925 (ttt) REVERT: A 366 ARG cc_start: 0.8304 (ttp-110) cc_final: 0.8007 (ttp-110) REVERT: B 463 LEU cc_start: 0.8122 (mm) cc_final: 0.7898 (mm) REVERT: B 480 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6773 (mp) outliers start: 19 outliers final: 5 residues processed: 105 average time/residue: 0.0711 time to fit residues: 10.0998 Evaluate side-chains 92 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 480 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 48 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.140190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.112577 restraints weight = 7761.389| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.93 r_work: 0.3196 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7316 Z= 0.164 Angle : 0.538 6.435 9924 Z= 0.268 Chirality : 0.039 0.143 1196 Planarity : 0.005 0.055 1206 Dihedral : 12.463 85.405 1223 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.54 % Allowed : 19.86 % Favored : 77.61 % 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 (0.27), residues: 946 helix: 2.11 (0.18), residues: 754 sheet: None (None), residues: 0 loop : -0.77 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 207 TYR 0.007 0.001 TYR A 378 PHE 0.010 0.001 PHE A 301 TRP 0.008 0.001 TRP A 265 HIS 0.002 0.001 HIS B 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 ( 7316) covalent geometry : angle 0.53772 / 0.27 ( 9924) hydrogen bonds : bond 0.04724 / 3.25 ( 578) hydrogen bonds : angle 3.89473 / 2.77 ( 1728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.156 Fit side-chains REVERT: A 186 MET cc_start: 0.8133 (ttp) cc_final: 0.7919 (ttp) REVERT: B 480 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6868 (mp) outliers start: 18 outliers final: 8 residues processed: 115 average time/residue: 0.0694 time to fit residues: 10.6807 Evaluate side-chains 102 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 511 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 12 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 52 optimal weight: 0.4980 chunk 22 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 GLN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 GLN B 514 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.145080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117104 restraints weight = 7694.905| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.96 r_work: 0.3222 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7316 Z= 0.126 Angle : 0.510 7.161 9924 Z= 0.252 Chirality : 0.038 0.125 1196 Planarity : 0.004 0.053 1206 Dihedral : 11.700 74.936 1223 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.68 % Allowed : 18.31 % Favored : 79.01 % 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: 2.40 (0.27), residues: 946 helix: 2.16 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -0.76 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 366 TYR 0.007 0.001 TYR B 464 PHE 0.011 0.001 PHE B 183 TRP 0.008 0.001 TRP A 92 HIS 0.002 0.001 HIS B 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 7316) covalent geometry : angle 0.50952 / 0.25 ( 9924) hydrogen bonds : bond 0.04306 / 2.97 ( 578) hydrogen bonds : angle 3.79626 / 2.70 ( 1728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.232 Fit side-chains REVERT: A 67 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.7610 (ttp) REVERT: A 463 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7940 (mm) REVERT: B 67 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7593 (ttp) REVERT: B 414 MET cc_start: 0.8820 (ttm) cc_final: 0.8550 (mtp) REVERT: B 463 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7910 (mm) outliers start: 19 outliers final: 8 residues processed: 108 average time/residue: 0.0941 time to fit residues: 13.5665 Evaluate side-chains 96 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 463 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 517 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.113080 restraints weight = 7712.309| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.96 r_work: 0.3202 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7316 Z= 0.143 Angle : 0.528 7.111 9924 Z= 0.259 Chirality : 0.039 0.128 1196 Planarity : 0.004 0.053 1206 Dihedral : 11.508 71.944 1223 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.24 % Allowed : 18.31 % Favored : 78.45 % 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: 2.45 (0.27), residues: 946 helix: 2.20 (0.18), residues: 752 sheet: None (None), residues: 0 loop : -0.69 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 207 TYR 0.007 0.001 TYR B 464 PHE 0.010 0.001 PHE A 183 TRP 0.008 0.001 TRP B 92 HIS 0.002 0.001 HIS B 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 7316) covalent geometry : angle 0.52791 / 0.26 ( 9924) hydrogen bonds : bond 0.04514 / 3.12 ( 578) hydrogen bonds : angle 3.81941 / 2.71 ( 1728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.215 Fit side-chains REVERT: A 67 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.7664 (ttp) REVERT: A 463 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7962 (mm) REVERT: B 67 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7599 (ttp) REVERT: B 186 MET cc_start: 0.7898 (ttm) cc_final: 0.7671 (ttp) REVERT: B 304 ARG cc_start: 0.7487 (ttt180) cc_final: 0.5914 (ttp80) REVERT: B 463 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7945 (mm) outliers start: 23 outliers final: 10 residues processed: 111 average time/residue: 0.0898 time to fit residues: 13.3653 Evaluate side-chains 97 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 511 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 431 GLN B 431 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.139221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.111513 restraints weight = 7705.718| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.95 r_work: 0.3178 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7316 Z= 0.156 Angle : 0.538 7.751 9924 Z= 0.266 Chirality : 0.039 0.131 1196 Planarity : 0.005 0.053 1206 Dihedral : 11.277 70.606 1223 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.38 % Allowed : 18.59 % Favored : 78.03 % 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: 2.43 (0.27), residues: 946 helix: 2.17 (0.18), residues: 752 sheet: None (None), residues: 0 loop : -0.66 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 366 TYR 0.006 0.001 TYR A 378 PHE 0.010 0.001 PHE A 301 TRP 0.007 0.001 TRP B 92 HIS 0.002 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 7316) covalent geometry : angle 0.53775 / 0.27 ( 9924) hydrogen bonds : bond 0.04692 / 3.24 ( 578) hydrogen bonds : angle 3.84592 / 2.74 ( 1728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.257 Fit side-chains REVERT: A 67 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.7639 (ttp) REVERT: A 186 MET cc_start: 0.7940 (ttm) cc_final: 0.7732 (ttp) REVERT: A 463 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7955 (mm) REVERT: B 67 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.7592 (ttp) REVERT: B 106 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8947 (mp) REVERT: B 186 MET cc_start: 0.8101 (ttm) cc_final: 0.7893 (mtp) REVERT: B 304 ARG cc_start: 0.7417 (ttt180) cc_final: 0.5822 (ttp80) REVERT: B 463 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7938 (mm) outliers start: 24 outliers final: 13 residues processed: 106 average time/residue: 0.0819 time to fit residues: 11.4778 Evaluate side-chains 98 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 511 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.138389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.110801 restraints weight = 7683.092| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.94 r_work: 0.3172 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7316 Z= 0.161 Angle : 0.543 8.101 9924 Z= 0.268 Chirality : 0.040 0.152 1196 Planarity : 0.004 0.053 1206 Dihedral : 11.108 70.162 1223 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.10 % Allowed : 18.59 % Favored : 78.31 % 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: 2.41 (0.27), residues: 946 helix: 2.13 (0.18), residues: 754 sheet: None (None), residues: 0 loop : -0.56 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 366 TYR 0.006 0.001 TYR A 378 PHE 0.010 0.001 PHE A 301 TRP 0.007 0.001 TRP B 265 HIS 0.002 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 7316) covalent geometry : angle 0.54307 / 0.27 ( 9924) hydrogen bonds : bond 0.04764 / 3.28 ( 578) hydrogen bonds : angle 3.85429 / 2.75 ( 1728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.211 Fit side-chains REVERT: A 67 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.7671 (ttp) REVERT: A 463 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7975 (mm) REVERT: B 67 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7620 (ttp) REVERT: B 106 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8946 (mp) REVERT: B 304 ARG cc_start: 0.7365 (ttt180) cc_final: 0.5840 (ttp80) REVERT: B 463 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7932 (mm) REVERT: B 511 THR cc_start: 0.7764 (OUTLIER) cc_final: 0.7554 (p) outliers start: 22 outliers final: 12 residues processed: 98 average time/residue: 0.0825 time to fit residues: 10.6285 Evaluate side-chains 94 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 511 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 92 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.112659 restraints weight = 7715.803| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.96 r_work: 0.3193 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7316 Z= 0.140 Angle : 0.531 8.731 9924 Z= 0.260 Chirality : 0.039 0.160 1196 Planarity : 0.004 0.052 1206 Dihedral : 10.976 70.224 1223 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.54 % Allowed : 19.01 % Favored : 78.45 % 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: 2.42 (0.27), residues: 946 helix: 2.15 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.70 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 366 TYR 0.005 0.001 TYR B 464 PHE 0.010 0.001 PHE B 183 TRP 0.007 0.001 TRP B 265 HIS 0.002 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 7316) covalent geometry : angle 0.53130 / 0.26 ( 9924) hydrogen bonds : bond 0.04517 / 3.12 ( 578) hydrogen bonds : angle 3.81337 / 2.72 ( 1728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.219 Fit side-chains REVERT: A 67 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7649 (ttp) REVERT: A 304 ARG cc_start: 0.7398 (ttt180) cc_final: 0.5863 (ttp80) REVERT: A 463 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7981 (mm) REVERT: B 67 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7576 (ttp) REVERT: B 304 ARG cc_start: 0.7446 (ttt180) cc_final: 0.5890 (ttp80) REVERT: B 414 MET cc_start: 0.8848 (ttm) cc_final: 0.8553 (mtp) REVERT: B 463 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7940 (mm) REVERT: B 511 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7574 (p) outliers start: 18 outliers final: 11 residues processed: 93 average time/residue: 0.0860 time to fit residues: 10.5829 Evaluate side-chains 89 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 511 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.141398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.113540 restraints weight = 7661.969| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.96 r_work: 0.3175 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7316 Z= 0.158 Angle : 0.549 8.783 9924 Z= 0.269 Chirality : 0.039 0.164 1196 Planarity : 0.004 0.051 1206 Dihedral : 10.891 71.269 1223 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.82 % Allowed : 19.15 % Favored : 78.03 % 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: 2.41 (0.27), residues: 946 helix: 2.13 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.62 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 366 TYR 0.007 0.001 TYR B 378 PHE 0.010 0.001 PHE A 301 TRP 0.008 0.001 TRP B 265 HIS 0.002 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 7316) covalent geometry : angle 0.54905 / 0.27 ( 9924) hydrogen bonds : bond 0.04731 / 3.26 ( 578) hydrogen bonds : angle 3.84927 / 2.74 ( 1728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.159 Fit side-chains REVERT: A 67 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.7664 (ttp) REVERT: A 304 ARG cc_start: 0.7409 (ttt180) cc_final: 0.5908 (ttp80) REVERT: A 463 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7965 (mm) REVERT: B 67 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7616 (ttp) REVERT: B 304 ARG cc_start: 0.7413 (ttt180) cc_final: 0.5890 (ttp80) REVERT: B 463 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7939 (mm) REVERT: B 511 THR cc_start: 0.7783 (OUTLIER) cc_final: 0.7564 (p) outliers start: 20 outliers final: 11 residues processed: 96 average time/residue: 0.0799 time to fit residues: 10.0885 Evaluate side-chains 94 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 511 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.112293 restraints weight = 7642.495| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.93 r_work: 0.3187 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7316 Z= 0.144 Angle : 0.538 8.952 9924 Z= 0.263 Chirality : 0.039 0.172 1196 Planarity : 0.004 0.052 1206 Dihedral : 10.680 72.770 1223 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.25 % Allowed : 19.58 % Favored : 78.17 % 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: 2.46 (0.27), residues: 946 helix: 2.17 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.64 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 366 TYR 0.006 0.001 TYR A 464 PHE 0.010 0.001 PHE A 183 TRP 0.007 0.001 TRP B 265 HIS 0.003 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 7316) covalent geometry : angle 0.53816 / 0.26 ( 9924) hydrogen bonds : bond 0.04572 / 3.15 ( 578) hydrogen bonds : angle 3.81453 / 2.71 ( 1728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.169 Fit side-chains REVERT: A 67 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7642 (ttp) REVERT: A 304 ARG cc_start: 0.7386 (ttt180) cc_final: 0.5845 (ttp80) REVERT: A 463 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7965 (mm) REVERT: B 67 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7565 (ttp) REVERT: B 304 ARG cc_start: 0.7395 (ttt180) cc_final: 0.5893 (ttp80) REVERT: B 414 MET cc_start: 0.8851 (ttm) cc_final: 0.8555 (mtp) REVERT: B 463 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7915 (mm) REVERT: B 511 THR cc_start: 0.7763 (OUTLIER) cc_final: 0.7542 (p) outliers start: 16 outliers final: 11 residues processed: 92 average time/residue: 0.1112 time to fit residues: 13.4805 Evaluate side-chains 89 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 511 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 12 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.140916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.113395 restraints weight = 7666.909| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.94 r_work: 0.3206 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7316 Z= 0.134 Angle : 0.534 9.228 9924 Z= 0.261 Chirality : 0.038 0.174 1196 Planarity : 0.004 0.052 1206 Dihedral : 10.504 73.974 1223 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.54 % Allowed : 19.30 % Favored : 78.17 % 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: 2.53 (0.27), residues: 946 helix: 2.21 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.58 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 366 TYR 0.006 0.001 TYR A 464 PHE 0.010 0.001 PHE A 183 TRP 0.007 0.001 TRP B 265 HIS 0.002 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 7316) covalent geometry : angle 0.53442 / 0.26 ( 9924) hydrogen bonds : bond 0.04453 / 3.06 ( 578) hydrogen bonds : angle 3.78647 / 2.69 ( 1728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1595.40 seconds wall clock time: 28 minutes 5.59 seconds (1685.59 seconds total)