Starting phenix.real_space_refine on Fri Aug 22 19:16:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wm5_37641/08_2025/8wm5_37641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wm5_37641/08_2025/8wm5_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wm5_37641/08_2025/8wm5_37641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wm5_37641/08_2025/8wm5_37641.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wm5_37641/08_2025/8wm5_37641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wm5_37641/08_2025/8wm5_37641.map" } 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-2.0-5787/lib/python3.9/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: 2.10, per 1000 atoms: 0.29 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: 0.57 Conformation dependent library (CDL) restraints added in 272.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.20 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: 1.07 Time building geometry restraints manager: 0.73 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: 9743 2.41 - 4.83: 147 4.83 - 7.24: 20 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: 4036 31.96 - 63.92: 241 63.92 - 95.87: 12 95.87 - 127.83: 0 127.83 - 159.79: 2 Dihedral angle restraints: 4291 sinusoidal: 1649 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 4288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 920 0.044 - 0.088: 226 0.088 - 0.132: 42 0.132 - 0.176: 5 0.176 - 0.220: 3 Chirality restraints: 1196 Sorted by residual: 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 -2.57 -2.35 -0.22 2.00e-01 2.50e+01 1.21e+00 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 ... (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: 2.030 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.870 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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= 0.424 Angle : 0.768 12.063 9924 Z= 0.435 Chirality : 0.040 0.220 1196 Planarity : 0.007 0.120 1206 Dihedral : 18.596 159.790 2619 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 aren 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 covalent geometry : bond 0.00687 ( 7316) covalent geometry : angle 0.76805 ( 9924) hydrogen bonds : bond 0.09683 ( 578) hydrogen bonds : angle 4.43576 ( 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 : 0.245 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: 0.0967 time to fit residues: 11.2405 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 : 0.224 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3711 r_free = 0.3711 target = 0.144541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.116638 restraints weight = 7672.153| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.99 r_work: 0.3239 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7316 Z= 0.144 Angle : 0.542 6.468 9924 Z= 0.271 Chirality : 0.038 0.131 1196 Planarity : 0.005 0.060 1206 Dihedral : 13.684 118.807 1207 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.10 % Allowed : 18.87 % 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 aren not related in a simple way. whole: 2.17 (0.27), residues: 946 helix: 2.02 (0.18), residues: 752 sheet: None (None), residues: 0 loop : -0.87 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 207 TYR 0.008 0.001 TYR B 464 PHE 0.013 0.001 PHE B 284 TRP 0.010 0.001 TRP A 265 HIS 0.002 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7316) covalent geometry : angle 0.54171 ( 9924) hydrogen bonds : bond 0.04621 ( 578) hydrogen bonds : angle 3.87778 ( 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 116 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.268 Fit side-chains REVERT: A 366 ARG cc_start: 0.8314 (ttp-110) cc_final: 0.8027 (ttp-110) REVERT: B 366 ARG cc_start: 0.8512 (ttp-110) cc_final: 0.8243 (ttp-110) REVERT: B 463 LEU cc_start: 0.8110 (mm) cc_final: 0.7891 (mm) REVERT: B 480 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6760 (mp) outliers start: 22 outliers final: 5 residues processed: 109 average time/residue: 0.0983 time to fit residues: 14.1285 Evaluate side-chains 92 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 68 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3683 r_free = 0.3683 target = 0.142139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.114426 restraints weight = 7729.728| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.95 r_work: 0.3215 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1269 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= 0.142 Angle : 0.518 6.263 9924 Z= 0.258 Chirality : 0.038 0.125 1196 Planarity : 0.005 0.055 1206 Dihedral : 12.359 78.156 1207 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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 aren not related in a simple way. whole: 2.36 (0.27), residues: 946 helix: 2.14 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -0.83 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 207 TYR 0.008 0.001 TYR A 464 PHE 0.009 0.001 PHE A 298 TRP 0.009 0.001 TRP B 92 HIS 0.003 0.001 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7316) covalent geometry : angle 0.51755 ( 9924) hydrogen bonds : bond 0.04471 ( 578) hydrogen bonds : angle 3.82979 ( 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 114 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.248 Fit side-chains REVERT: A 511 THR cc_start: 0.7835 (OUTLIER) cc_final: 0.7634 (p) outliers start: 18 outliers final: 9 residues processed: 112 average time/residue: 0.0867 time to fit residues: 13.0392 Evaluate side-chains 99 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 A residue 511 THR Chi-restraints excluded: chain B residue 192 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 511 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 12 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.144334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116086 restraints weight = 7720.310| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.00 r_work: 0.3206 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7316 Z= 0.146 Angle : 0.526 7.126 9924 Z= 0.260 Chirality : 0.038 0.129 1196 Planarity : 0.005 0.054 1206 Dihedral : 11.908 74.584 1207 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.54 % Allowed : 18.45 % 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 aren not related in a simple way. whole: 2.32 (0.27), residues: 946 helix: 2.09 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -0.74 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 366 TYR 0.007 0.001 TYR A 464 PHE 0.015 0.001 PHE B 284 TRP 0.008 0.001 TRP A 92 HIS 0.002 0.001 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 7316) covalent geometry : angle 0.52576 ( 9924) hydrogen bonds : bond 0.04539 ( 578) hydrogen bonds : angle 3.84733 ( 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 110 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.202 Fit side-chains REVERT: A 67 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.7596 (ttp) REVERT: B 67 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.7622 (ttp) REVERT: B 414 MET cc_start: 0.8846 (ttm) cc_final: 0.8573 (mtp) REVERT: B 463 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7912 (mm) outliers start: 18 outliers final: 9 residues processed: 108 average time/residue: 0.0936 time to fit residues: 13.5482 Evaluate side-chains 94 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 22 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 GLN A 517 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.115412 restraints weight = 7715.986| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.99 r_work: 0.3201 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1627 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 : 0.524 7.423 9924 Z= 0.259 Chirality : 0.039 0.128 1196 Planarity : 0.004 0.053 1206 Dihedral : 11.663 71.655 1207 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.38 % Allowed : 18.45 % 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 aren not related in a simple way. whole: 2.38 (0.27), residues: 946 helix: 2.12 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -0.68 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 366 TYR 0.006 0.001 TYR A 464 PHE 0.010 0.001 PHE B 183 TRP 0.007 0.001 TRP A 92 HIS 0.002 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7316) covalent geometry : angle 0.52360 ( 9924) hydrogen bonds : bond 0.04502 ( 578) hydrogen bonds : angle 3.82916 ( 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 113 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.251 Fit side-chains REVERT: A 67 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7621 (ttp) REVERT: B 67 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7600 (ttp) REVERT: B 186 MET cc_start: 0.7925 (ttm) cc_final: 0.7716 (mtp) REVERT: B 414 MET cc_start: 0.8849 (ttm) cc_final: 0.8562 (mtp) REVERT: B 463 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7927 (mm) outliers start: 24 outliers final: 13 residues processed: 111 average time/residue: 0.0930 time to fit residues: 13.8996 Evaluate side-chains 98 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 511 THR 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 427 VAL 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: 0.7980 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 177 ASN A 431 GLN B 431 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.113436 restraints weight = 7717.446| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.99 r_work: 0.3171 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1816 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 : 0.541 7.691 9924 Z= 0.268 Chirality : 0.039 0.131 1196 Planarity : 0.005 0.054 1206 Dihedral : 11.496 70.563 1207 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.10 % Allowed : 18.87 % 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 aren not related in a simple way. whole: 2.37 (0.27), residues: 946 helix: 2.10 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -0.64 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 366 TYR 0.007 0.001 TYR B 378 PHE 0.010 0.001 PHE A 301 TRP 0.008 0.001 TRP B 92 HIS 0.002 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 7316) covalent geometry : angle 0.54141 ( 9924) hydrogen bonds : bond 0.04761 ( 578) hydrogen bonds : angle 3.87378 ( 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 108 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.282 Fit side-chains REVERT: A 67 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.7692 (ttp) REVERT: A 511 THR cc_start: 0.7797 (OUTLIER) cc_final: 0.7584 (p) REVERT: B 67 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7605 (ttp) REVERT: B 463 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7946 (mm) outliers start: 22 outliers final: 13 residues processed: 104 average time/residue: 0.0823 time to fit residues: 11.2249 Evaluate side-chains 98 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 511 THR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 100 THR 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 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: 1.9990 chunk 31 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.111854 restraints weight = 7643.932| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.95 r_work: 0.3181 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1916 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 : 0.548 8.138 9924 Z= 0.269 Chirality : 0.039 0.135 1196 Planarity : 0.005 0.053 1206 Dihedral : 11.304 70.188 1207 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.10 % Allowed : 19.01 % Favored : 77.89 % 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 aren 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 0.008 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 92 HIS 0.002 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 7316) covalent geometry : angle 0.54760 ( 9924) hydrogen bonds : bond 0.04721 ( 578) hydrogen bonds : angle 3.87578 ( 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 104 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.154 Fit side-chains REVERT: A 67 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.7639 (ttp) REVERT: A 511 THR cc_start: 0.7761 (OUTLIER) cc_final: 0.7551 (p) REVERT: B 67 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7575 (ttp) REVERT: B 463 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7936 (mm) REVERT: B 511 THR cc_start: 0.7764 (OUTLIER) cc_final: 0.7551 (p) outliers start: 22 outliers final: 12 residues processed: 102 average time/residue: 0.0817 time to fit residues: 10.9124 Evaluate side-chains 96 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 511 THR 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 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: 0.5980 chunk 62 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 85 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 84 optimal weight: 0.0980 chunk 12 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.141720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114101 restraints weight = 7683.701| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.96 r_work: 0.3217 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7316 Z= 0.128 Angle : 0.523 8.661 9924 Z= 0.256 Chirality : 0.038 0.157 1196 Planarity : 0.004 0.053 1206 Dihedral : 11.039 70.539 1207 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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 aren not related in a simple way. whole: 2.55 (0.27), residues: 946 helix: 2.23 (0.18), residues: 754 sheet: None (None), residues: 0 loop : -0.54 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 366 TYR 0.006 0.001 TYR A 464 PHE 0.011 0.001 PHE A 183 TRP 0.009 0.001 TRP A 92 HIS 0.002 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7316) covalent geometry : angle 0.52312 ( 9924) hydrogen bonds : bond 0.04335 ( 578) hydrogen bonds : angle 3.76938 ( 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 97 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.265 Fit side-chains REVERT: A 67 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7609 (ttp) REVERT: A 304 ARG cc_start: 0.7427 (ttt180) cc_final: 0.5914 (ttp80) REVERT: A 414 MET cc_start: 0.8818 (ttm) cc_final: 0.8518 (mtp) REVERT: A 511 THR cc_start: 0.7750 (OUTLIER) cc_final: 0.7532 (p) REVERT: B 67 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.7596 (ttp) REVERT: B 304 ARG cc_start: 0.7468 (ttt180) cc_final: 0.5919 (ttp80) REVERT: B 414 MET cc_start: 0.8820 (ttm) cc_final: 0.8537 (mtp) REVERT: B 463 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7867 (mm) REVERT: B 511 THR cc_start: 0.7778 (OUTLIER) cc_final: 0.7559 (p) outliers start: 18 outliers final: 10 residues processed: 95 average time/residue: 0.0752 time to fit residues: 9.4820 Evaluate side-chains 88 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.139 ------------------------------------------------------------------------------- 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 511 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 0.0970 chunk 66 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.141105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.113573 restraints weight = 7621.515| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.94 r_work: 0.3207 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2023 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= 0.139 Angle : 0.536 8.910 9924 Z= 0.262 Chirality : 0.039 0.161 1196 Planarity : 0.004 0.053 1206 Dihedral : 10.906 72.008 1207 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.13 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 aren not related in a simple way. whole: 2.55 (0.27), residues: 946 helix: 2.22 (0.18), residues: 754 sheet: None (None), residues: 0 loop : -0.49 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 366 TYR 0.006 0.001 TYR B 378 PHE 0.009 0.001 PHE B 183 TRP 0.008 0.001 TRP B 92 HIS 0.002 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7316) covalent geometry : angle 0.53628 ( 9924) hydrogen bonds : bond 0.04489 ( 578) hydrogen bonds : angle 3.79217 ( 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 92 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.257 Fit side-chains REVERT: A 67 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.7606 (ttp) REVERT: A 304 ARG cc_start: 0.7385 (ttt180) cc_final: 0.5857 (ttp80) REVERT: A 511 THR cc_start: 0.7709 (OUTLIER) cc_final: 0.7489 (p) REVERT: B 67 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7639 (ttp) REVERT: B 304 ARG cc_start: 0.7451 (ttt180) cc_final: 0.5906 (ttp80) REVERT: B 463 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7865 (mm) REVERT: B 511 THR cc_start: 0.7728 (OUTLIER) cc_final: 0.7517 (p) outliers start: 16 outliers final: 11 residues processed: 90 average time/residue: 0.0857 time to fit residues: 10.1004 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 : 0.153 ------------------------------------------------------------------------------- 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 511 THR 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: 0.0570 chunk 23 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.140108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.112531 restraints weight = 7608.603| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.94 r_work: 0.3195 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7316 Z= 0.149 Angle : 0.549 8.959 9924 Z= 0.267 Chirality : 0.039 0.175 1196 Planarity : 0.005 0.052 1206 Dihedral : 10.804 73.479 1207 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.68 % Allowed : 19.30 % 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 aren not related in a simple way. whole: 2.53 (0.27), residues: 946 helix: 2.20 (0.18), residues: 754 sheet: None (None), residues: 0 loop : -0.46 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 366 TYR 0.006 0.001 TYR A 378 PHE 0.009 0.001 PHE A 301 TRP 0.007 0.001 TRP B 265 HIS 0.002 0.001 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 7316) covalent geometry : angle 0.54914 ( 9924) hydrogen bonds : bond 0.04640 ( 578) hydrogen bonds : angle 3.81903 ( 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 95 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.253 Fit side-chains REVERT: A 67 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7645 (ttp) REVERT: A 186 MET cc_start: 0.8080 (ttm) cc_final: 0.7861 (mtp) REVERT: A 304 ARG cc_start: 0.7348 (ttt180) cc_final: 0.5829 (ttp80) REVERT: B 67 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.7651 (ttp) REVERT: B 304 ARG cc_start: 0.7387 (ttt180) cc_final: 0.5882 (ttp80) REVERT: B 463 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7863 (mm) REVERT: B 511 THR cc_start: 0.7779 (OUTLIER) cc_final: 0.7563 (p) outliers start: 19 outliers final: 13 residues processed: 93 average time/residue: 0.0926 time to fit residues: 11.1974 Evaluate side-chains 91 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 201 LEU 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 511 THR 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: 0.9980 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 63 optimal weight: 0.0470 chunk 85 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.141297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.113766 restraints weight = 7670.398| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.95 r_work: 0.3211 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2127 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= 0.138 Angle : 0.548 9.235 9924 Z= 0.265 Chirality : 0.039 0.240 1196 Planarity : 0.004 0.053 1206 Dihedral : 10.681 74.694 1207 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.81 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 aren not related in a simple way. whole: 2.54 (0.27), residues: 946 helix: 2.20 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.51 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 366 TYR 0.005 0.001 TYR A 378 PHE 0.010 0.001 PHE B 183 TRP 0.008 0.001 TRP B 92 HIS 0.002 0.001 HIS B 517 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7316) covalent geometry : angle 0.54830 ( 9924) hydrogen bonds : bond 0.04498 ( 578) hydrogen bonds : angle 3.78200 ( 1728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1618.83 seconds wall clock time: 28 minutes 25.95 seconds (1705.95 seconds total)