Starting phenix.real_space_refine on Sun May 11 00:47:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wm5_37641/05_2025/8wm5_37641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wm5_37641/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wm5_37641/05_2025/8wm5_37641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wm5_37641/05_2025/8wm5_37641.map" model { file = "/net/cci-nas-00/data/ceres_data/8wm5_37641/05_2025/8wm5_37641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wm5_37641/05_2025/8wm5_37641.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.46, per 1000 atoms: 0.76 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: 2.34 Conformation dependent library (CDL) restraints added in 896.9 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: 0.64 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: 2.09 Time building geometry restraints manager: 2.52 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 519 or resid 601 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: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.950 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.150 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP A 265 HIS 0.002 0.001 HIS A 392 PHE 0.009 0.001 PHE A 398 TYR 0.005 0.001 TYR A 378 ARG 0.006 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.09683 ( 578) hydrogen bonds : angle 4.43576 ( 1728) covalent geometry : bond 0.00687 ( 7316) covalent geometry : angle 0.76805 ( 9924) *********************** 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 : 0.723 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: 0.2229 time to fit residues: 25.6534 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 : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 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 = 44)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116661 restraints weight = 7641.464| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.99 r_work: 0.3239 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP A 265 HIS 0.002 0.001 HIS A 392 PHE 0.013 0.001 PHE B 284 TYR 0.008 0.001 TYR B 464 ARG 0.006 0.001 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.04621 ( 578) hydrogen bonds : angle 3.87778 ( 1728) covalent geometry : bond 0.00338 ( 7316) covalent geometry : angle 0.54170 ( 9924) *********************** 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 : 0.727 Fit side-chains REVERT: A 366 ARG cc_start: 0.8314 (ttp-110) cc_final: 0.8026 (ttp-110) REVERT: B 366 ARG cc_start: 0.8510 (ttp-110) cc_final: 0.8242 (ttp-110) REVERT: B 463 LEU cc_start: 0.8119 (mm) cc_final: 0.7900 (mm) REVERT: B 480 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6777 (mp) outliers start: 22 outliers final: 5 residues processed: 109 average time/residue: 0.2066 time to fit residues: 29.6202 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 : 0.666 ------------------------------------------------------------------------------- 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 80 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 35 optimal weight: 0.0670 chunk 4 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 63 optimal weight: 0.0870 chunk 52 optimal weight: 1.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.143913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.116139 restraints weight = 7738.159| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.95 r_work: 0.3241 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7316 Z= 0.130 Angle : 0.508 6.504 9924 Z= 0.252 Chirality : 0.038 0.130 1196 Planarity : 0.005 0.054 1206 Dihedral : 12.331 79.018 1207 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.68 % Allowed : 19.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.27), residues: 946 helix: 2.20 (0.18), residues: 754 sheet: None (None), residues: 0 loop : -0.83 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 92 HIS 0.003 0.001 HIS B 392 PHE 0.009 0.001 PHE B 183 TYR 0.008 0.001 TYR A 464 ARG 0.006 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 578) hydrogen bonds : angle 3.78615 ( 1728) covalent geometry : bond 0.00303 ( 7316) covalent geometry : angle 0.50794 ( 9924) *********************** 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: 19 poor density : 95 time to evaluate : 0.758 Fit side-chains REVERT: B 480 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6758 (mp) outliers start: 19 outliers final: 8 residues processed: 112 average time/residue: 0.1947 time to fit residues: 29.4592 Evaluate side-chains 98 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 36 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** A 514 GLN ** B 177 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.139925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.112456 restraints weight = 7791.635| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.94 r_work: 0.3191 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1542 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= 0.164 Angle : 0.541 6.704 9924 Z= 0.269 Chirality : 0.039 0.135 1196 Planarity : 0.005 0.053 1206 Dihedral : 11.890 73.382 1207 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.96 % Allowed : 18.17 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.27), residues: 946 helix: 2.03 (0.18), residues: 758 sheet: None (None), residues: 0 loop : -0.68 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 265 HIS 0.003 0.001 HIS A 517 PHE 0.016 0.001 PHE A 284 TYR 0.007 0.001 TYR B 378 ARG 0.005 0.001 ARG B 366 Details of bonding type rmsd hydrogen bonds : bond 0.04780 ( 578) hydrogen bonds : angle 3.89331 ( 1728) covalent geometry : bond 0.00396 ( 7316) covalent geometry : angle 0.54090 ( 9924) *********************** 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 115 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.746 Fit side-chains REVERT: A 67 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7626 (ttp) REVERT: B 67 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.7620 (ttp) REVERT: B 463 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7869 (mm) outliers start: 21 outliers final: 10 residues processed: 113 average time/residue: 0.2057 time to fit residues: 30.9211 Evaluate side-chains 101 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 511 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 64 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 517 HIS ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.140292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.112779 restraints weight = 7657.878| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.93 r_work: 0.3195 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1672 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= 0.145 Angle : 0.522 7.425 9924 Z= 0.259 Chirality : 0.039 0.131 1196 Planarity : 0.004 0.052 1206 Dihedral : 11.669 70.942 1207 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.82 % Allowed : 18.31 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.27), residues: 946 helix: 2.12 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -0.65 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 92 HIS 0.002 0.001 HIS A 392 PHE 0.010 0.001 PHE B 183 TYR 0.006 0.001 TYR A 464 ARG 0.005 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 578) hydrogen bonds : angle 3.83249 ( 1728) covalent geometry : bond 0.00345 ( 7316) covalent geometry : angle 0.52185 ( 9924) *********************** 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 107 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.771 Fit side-chains REVERT: A 67 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7624 (ttp) REVERT: B 67 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7616 (ttp) REVERT: B 463 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7952 (mm) outliers start: 20 outliers final: 12 residues processed: 105 average time/residue: 0.1987 time to fit residues: 27.9650 Evaluate side-chains 93 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 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 55 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 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 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.140758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.113091 restraints weight = 7689.365| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.96 r_work: 0.3199 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1791 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 : 0.520 7.583 9924 Z= 0.257 Chirality : 0.038 0.124 1196 Planarity : 0.004 0.054 1206 Dihedral : 11.419 70.699 1207 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.38 % Allowed : 18.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.27), residues: 946 helix: 2.15 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -0.58 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 92 HIS 0.002 0.001 HIS A 392 PHE 0.009 0.001 PHE B 183 TYR 0.006 0.001 TYR A 464 ARG 0.007 0.001 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.04458 ( 578) hydrogen bonds : angle 3.79995 ( 1728) covalent geometry : bond 0.00324 ( 7316) covalent geometry : angle 0.52035 ( 9924) *********************** 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 103 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.768 Fit side-chains REVERT: A 67 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.7647 (ttp) REVERT: A 304 ARG cc_start: 0.7385 (ttt180) cc_final: 0.5846 (ttp80) REVERT: B 67 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.7568 (ttp) REVERT: B 304 ARG cc_start: 0.7444 (ttt180) cc_final: 0.5886 (ttp80) REVERT: B 463 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7932 (mm) outliers start: 24 outliers final: 13 residues processed: 99 average time/residue: 0.2323 time to fit residues: 30.3204 Evaluate side-chains 91 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 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 49 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111122 restraints weight = 7615.902| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.94 r_work: 0.3173 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7316 Z= 0.167 Angle : 0.547 7.806 9924 Z= 0.270 Chirality : 0.039 0.140 1196 Planarity : 0.005 0.053 1206 Dihedral : 11.324 70.039 1207 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.38 % Allowed : 17.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.27), residues: 946 helix: 2.07 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.52 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 92 HIS 0.003 0.001 HIS A 517 PHE 0.011 0.001 PHE B 301 TYR 0.007 0.001 TYR B 378 ARG 0.007 0.001 ARG B 366 Details of bonding type rmsd hydrogen bonds : bond 0.04812 ( 578) hydrogen bonds : angle 3.87290 ( 1728) covalent geometry : bond 0.00408 ( 7316) covalent geometry : angle 0.54712 ( 9924) *********************** 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 103 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.844 Fit side-chains REVERT: A 67 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.7668 (ttp) REVERT: B 67 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.7603 (ttp) REVERT: B 463 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7954 (mm) REVERT: B 511 THR cc_start: 0.7769 (OUTLIER) cc_final: 0.7537 (p) outliers start: 24 outliers final: 13 residues processed: 101 average time/residue: 0.2115 time to fit residues: 28.1337 Evaluate side-chains 93 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 427 VAL Chi-restraints excluded: chain A residue 445 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 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 33 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 HIS B 62 GLN B 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.112584 restraints weight = 7685.901| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.96 r_work: 0.3190 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1977 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= 0.141 Angle : 0.532 8.331 9924 Z= 0.261 Chirality : 0.039 0.156 1196 Planarity : 0.004 0.053 1206 Dihedral : 11.136 70.336 1207 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.54 % Allowed : 18.31 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.27), residues: 946 helix: 2.17 (0.18), residues: 754 sheet: None (None), residues: 0 loop : -0.57 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 92 HIS 0.003 0.001 HIS A 517 PHE 0.010 0.001 PHE B 183 TYR 0.005 0.001 TYR A 378 ARG 0.008 0.001 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.04513 ( 578) hydrogen bonds : angle 3.82355 ( 1728) covalent geometry : bond 0.00332 ( 7316) covalent geometry : angle 0.53226 ( 9924) *********************** 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 93 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.718 Fit side-chains REVERT: A 67 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.7651 (ttp) REVERT: A 304 ARG cc_start: 0.7375 (ttt180) cc_final: 0.5863 (ttp80) REVERT: B 67 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7572 (ttp) REVERT: B 304 ARG cc_start: 0.7473 (ttt180) cc_final: 0.5896 (ttp80) REVERT: B 463 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7933 (mm) REVERT: B 511 THR cc_start: 0.7795 (OUTLIER) cc_final: 0.7571 (p) outliers start: 18 outliers final: 11 residues processed: 91 average time/residue: 0.2278 time to fit residues: 27.1329 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 : 0.780 ------------------------------------------------------------------------------- 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 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 42 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 85 optimal weight: 0.2980 chunk 68 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.139799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.112130 restraints weight = 7688.759| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.95 r_work: 0.3191 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2035 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= 0.147 Angle : 0.538 8.493 9924 Z= 0.265 Chirality : 0.039 0.162 1196 Planarity : 0.004 0.053 1206 Dihedral : 10.948 71.334 1207 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.54 % Allowed : 18.73 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.27), residues: 946 helix: 2.14 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.65 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 265 HIS 0.002 0.001 HIS A 392 PHE 0.009 0.001 PHE B 183 TYR 0.005 0.001 TYR A 386 ARG 0.009 0.001 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.04583 ( 578) hydrogen bonds : angle 3.82612 ( 1728) covalent geometry : bond 0.00350 ( 7316) covalent geometry : angle 0.53834 ( 9924) *********************** 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 96 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.757 Fit side-chains REVERT: A 67 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.7662 (ttp) REVERT: A 304 ARG cc_start: 0.7383 (ttt180) cc_final: 0.5851 (ttp80) REVERT: B 67 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7560 (ttp) REVERT: B 186 MET cc_start: 0.7737 (ttm) cc_final: 0.7536 (ttp) REVERT: B 304 ARG cc_start: 0.7418 (ttt180) cc_final: 0.5905 (ttp80) REVERT: B 463 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7934 (mm) REVERT: B 511 THR cc_start: 0.7795 (OUTLIER) cc_final: 0.7570 (p) outliers start: 18 outliers final: 12 residues processed: 93 average time/residue: 0.2246 time to fit residues: 27.4957 Evaluate side-chains 90 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 84 optimal weight: 0.0770 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 517 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.140397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.112682 restraints weight = 7735.491| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.95 r_work: 0.3195 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7316 Z= 0.143 Angle : 0.542 8.758 9924 Z= 0.265 Chirality : 0.039 0.173 1196 Planarity : 0.004 0.053 1206 Dihedral : 10.794 72.953 1207 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.39 % Allowed : 18.87 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.27), residues: 946 helix: 2.16 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.62 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 265 HIS 0.003 0.001 HIS B 517 PHE 0.009 0.001 PHE B 183 TYR 0.005 0.001 TYR A 378 ARG 0.010 0.001 ARG B 366 Details of bonding type rmsd hydrogen bonds : bond 0.04552 ( 578) hydrogen bonds : angle 3.81256 ( 1728) covalent geometry : bond 0.00340 ( 7316) covalent geometry : angle 0.54170 ( 9924) ********************** 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 88 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.733 Fit side-chains REVERT: A 67 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7643 (ttp) REVERT: A 304 ARG cc_start: 0.7388 (ttt180) cc_final: 0.5885 (ttp80) REVERT: B 67 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7558 (ttp) REVERT: B 186 MET cc_start: 0.7722 (ttm) cc_final: 0.7505 (ttp) REVERT: B 304 ARG cc_start: 0.7390 (ttt180) cc_final: 0.5886 (ttp80) REVERT: B 463 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7876 (mm) REVERT: B 511 THR cc_start: 0.7780 (OUTLIER) cc_final: 0.7549 (p) outliers start: 17 outliers final: 12 residues processed: 86 average time/residue: 0.2387 time to fit residues: 26.7042 Evaluate side-chains 87 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 77 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 82 optimal weight: 0.0070 chunk 43 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN B 517 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.113802 restraints weight = 7568.674| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.94 r_work: 0.3210 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2111 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= 0.135 Angle : 0.533 9.090 9924 Z= 0.261 Chirality : 0.038 0.172 1196 Planarity : 0.004 0.052 1206 Dihedral : 10.689 74.039 1207 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.39 % Allowed : 19.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.27), residues: 946 helix: 2.20 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.56 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 92 HIS 0.002 0.001 HIS A 392 PHE 0.010 0.001 PHE A 183 TYR 0.005 0.001 TYR A 378 ARG 0.009 0.001 ARG B 366 Details of bonding type rmsd hydrogen bonds : bond 0.04441 ( 578) hydrogen bonds : angle 3.77893 ( 1728) covalent geometry : bond 0.00312 ( 7316) covalent geometry : angle 0.53250 ( 9924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3550.57 seconds wall clock time: 62 minutes 15.58 seconds (3735.58 seconds total)