Starting phenix.real_space_refine on Wed Mar 12 03:32:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wm5_37641/03_2025/8wm5_37641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wm5_37641/03_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_37641/03_2025/8wm5_37641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wm5_37641/03_2025/8wm5_37641.map" model { file = "/net/cci-nas-00/data/ceres_data/8wm5_37641/03_2025/8wm5_37641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wm5_37641/03_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-5624/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: 4.90, per 1000 atoms: 0.68 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: 1.90 Conformation dependent library (CDL) restraints added in 795.5 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: 0.55 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: 1.86 Time building geometry restraints manager: 2.21 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: 4.080 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.020 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.490 ------------------------------------------------------------------------------- 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= 0.436 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 *********************** 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 : 0.698 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: 0.2245 time to fit residues: 25.9747 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 : 0.704 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116662 restraints weight = 7641.465| |-----------------------------------------------------------------------------| r_work (start): 0.3364 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: 0.8055 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= 0.222 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 *********************** 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 : 0.766 Fit side-chains REVERT: A 366 ARG cc_start: 0.8315 (ttp-110) cc_final: 0.8027 (ttp-110) REVERT: B 366 ARG cc_start: 0.8511 (ttp-110) cc_final: 0.8243 (ttp-110) REVERT: B 463 LEU cc_start: 0.8108 (mm) cc_final: 0.7889 (mm) REVERT: B 480 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6759 (mp) outliers start: 22 outliers final: 5 residues processed: 109 average time/residue: 0.2146 time to fit residues: 30.9119 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 : 0.719 ------------------------------------------------------------------------------- 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: 0.9980 chunk 42 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 63 optimal weight: 0.0870 chunk 52 optimal weight: 1.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.140954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113228 restraints weight = 7783.553| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.95 r_work: 0.3202 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7316 Z= 0.240 Angle : 0.525 6.225 9924 Z= 0.262 Chirality : 0.039 0.138 1196 Planarity : 0.005 0.055 1206 Dihedral : 12.353 77.526 1207 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.82 % Allowed : 19.44 % Favored : 77.75 % 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: 2.32 (0.27), residues: 946 helix: 2.11 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -0.82 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 92 HIS 0.003 0.001 HIS B 392 PHE 0.011 0.001 PHE A 298 TYR 0.008 0.001 TYR A 464 ARG 0.007 0.001 ARG A 207 *********************** 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 120 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.637 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 118 average time/residue: 0.1958 time to fit residues: 30.8678 Evaluate side-chains 102 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 192 VAL 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 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: 3.9990 chunk 64 optimal weight: 0.0270 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 37 optimal weight: 0.0670 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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 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 = 0.3710 r_free = 0.3710 target = 0.144133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.116412 restraints weight = 7701.874| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.96 r_work: 0.3241 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7316 Z= 0.178 Angle : 0.502 6.932 9924 Z= 0.249 Chirality : 0.037 0.117 1196 Planarity : 0.004 0.053 1206 Dihedral : 11.753 74.416 1207 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.39 % Allowed : 19.01 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.40 (0.27), residues: 946 helix: 2.15 (0.18), residues: 758 sheet: None (None), residues: 0 loop : -0.75 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 92 HIS 0.002 0.001 HIS A 392 PHE 0.014 0.001 PHE B 284 TYR 0.008 0.001 TYR B 464 ARG 0.005 0.001 ARG A 207 *********************** 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: 17 poor density : 93 time to evaluate : 0.609 Fit side-chains REVERT: A 67 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7592 (ttp) REVERT: A 304 ARG cc_start: 0.7344 (ttt180) cc_final: 0.5813 (ttp80) REVERT: A 414 MET cc_start: 0.8809 (ttm) cc_final: 0.8521 (mtp) REVERT: B 67 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.7581 (ttp) REVERT: B 304 ARG cc_start: 0.7449 (ttt180) cc_final: 0.5876 (ttp80) REVERT: B 414 MET cc_start: 0.8791 (ttm) cc_final: 0.8522 (mtp) REVERT: B 463 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7892 (mm) outliers start: 17 outliers final: 10 residues processed: 108 average time/residue: 0.2052 time to fit residues: 29.5559 Evaluate side-chains 98 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 420 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 463 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 34 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.143193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.114874 restraints weight = 7642.040| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.99 r_work: 0.3191 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1651 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= 0.257 Angle : 0.532 7.107 9924 Z= 0.264 Chirality : 0.039 0.130 1196 Planarity : 0.004 0.054 1206 Dihedral : 11.691 71.744 1207 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.96 % Allowed : 19.15 % 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: 2.37 (0.27), residues: 946 helix: 2.11 (0.18), residues: 758 sheet: None (None), residues: 0 loop : -0.68 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 92 HIS 0.002 0.001 HIS A 392 PHE 0.010 0.001 PHE B 298 TYR 0.007 0.001 TYR B 378 ARG 0.003 0.000 ARG A 366 *********************** 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 111 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.620 Fit side-chains REVERT: A 67 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.7678 (ttp) REVERT: B 67 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7635 (ttp) REVERT: B 186 MET cc_start: 0.7940 (ttm) cc_final: 0.7731 (ttp) REVERT: B 463 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7931 (mm) outliers start: 21 outliers final: 10 residues processed: 108 average time/residue: 0.2280 time to fit residues: 32.5610 Evaluate side-chains 99 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 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 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: 0.0060 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B 431 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.142198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113829 restraints weight = 7740.335| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.00 r_work: 0.3180 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1800 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= 0.255 Angle : 0.536 7.603 9924 Z= 0.265 Chirality : 0.039 0.129 1196 Planarity : 0.005 0.053 1206 Dihedral : 11.498 71.017 1207 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.38 % Allowed : 18.31 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.40 (0.27), residues: 946 helix: 2.13 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -0.60 (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 517 PHE 0.010 0.001 PHE A 301 TYR 0.006 0.001 TYR A 378 ARG 0.007 0.001 ARG B 366 *********************** 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 111 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.665 Fit side-chains REVERT: A 67 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.7640 (ttp) REVERT: B 67 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7600 (ttp) REVERT: B 186 MET cc_start: 0.8124 (ttm) cc_final: 0.7882 (mtp) REVERT: B 463 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7929 (mm) outliers start: 24 outliers final: 13 residues processed: 107 average time/residue: 0.2243 time to fit residues: 31.3019 Evaluate side-chains 97 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** A 431 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111078 restraints weight = 7660.452| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.93 r_work: 0.3176 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1914 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= 0.266 Angle : 0.543 7.811 9924 Z= 0.268 Chirality : 0.040 0.141 1196 Planarity : 0.005 0.053 1206 Dihedral : 11.308 70.464 1207 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.10 % Allowed : 18.45 % 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: 2.14 (0.18), residues: 754 sheet: None (None), residues: 0 loop : -0.51 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 265 HIS 0.002 0.001 HIS A 392 PHE 0.010 0.001 PHE A 301 TYR 0.006 0.001 TYR B 378 ARG 0.007 0.001 ARG A 366 *********************** 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 : 0.755 Fit side-chains REVERT: A 67 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.7596 (ttp) REVERT: B 67 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7527 (ttp) REVERT: B 463 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7876 (mm) REVERT: B 511 THR cc_start: 0.7715 (OUTLIER) cc_final: 0.7504 (p) outliers start: 22 outliers final: 12 residues processed: 102 average time/residue: 0.2147 time to fit residues: 29.0605 Evaluate side-chains 93 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 0.0470 chunk 70 optimal weight: 0.8980 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 = 0.3664 r_free = 0.3664 target = 0.140308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.112700 restraints weight = 7686.673| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.96 r_work: 0.3191 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1955 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= 0.218 Angle : 0.533 8.542 9924 Z= 0.261 Chirality : 0.039 0.158 1196 Planarity : 0.004 0.053 1206 Dihedral : 11.147 70.511 1207 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.54 % Allowed : 18.59 % 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: 2.51 (0.27), residues: 946 helix: 2.20 (0.18), residues: 754 sheet: None (None), residues: 0 loop : -0.51 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 92 HIS 0.002 0.001 HIS A 517 PHE 0.011 0.001 PHE B 183 TYR 0.005 0.001 TYR B 464 ARG 0.008 0.001 ARG A 366 *********************** 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 : 0.679 Fit side-chains REVERT: A 67 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.7605 (ttp) REVERT: A 304 ARG cc_start: 0.7371 (ttt180) cc_final: 0.5855 (ttp80) REVERT: A 414 MET cc_start: 0.8837 (ttm) cc_final: 0.8539 (mtp) REVERT: B 67 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7630 (ttp) REVERT: B 463 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7927 (mm) REVERT: B 511 THR cc_start: 0.7785 (OUTLIER) cc_final: 0.7561 (p) outliers start: 18 outliers final: 10 residues processed: 94 average time/residue: 0.2330 time to fit residues: 28.7177 Evaluate side-chains 90 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 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: 0.0980 chunk 10 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 85 optimal weight: 0.0970 chunk 68 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.143694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.117016 restraints weight = 7668.091| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.89 r_work: 0.3227 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2008 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= 0.189 Angle : 0.526 9.155 9924 Z= 0.256 Chirality : 0.038 0.164 1196 Planarity : 0.004 0.052 1206 Dihedral : 10.847 71.683 1207 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.25 % Allowed : 18.59 % 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: 2.61 (0.27), residues: 946 helix: 2.26 (0.18), residues: 754 sheet: None (None), residues: 0 loop : -0.47 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 92 HIS 0.002 0.001 HIS A 392 PHE 0.011 0.001 PHE B 183 TYR 0.005 0.001 TYR B 464 ARG 0.009 0.001 ARG A 366 *********************** 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 95 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.634 Fit side-chains REVERT: A 67 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7560 (ttp) REVERT: A 304 ARG cc_start: 0.7401 (ttt180) cc_final: 0.5891 (ttp80) REVERT: A 414 MET cc_start: 0.8779 (ttm) cc_final: 0.8478 (mtp) REVERT: B 67 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.7620 (ttp) REVERT: B 304 ARG cc_start: 0.7412 (ttt180) cc_final: 0.5889 (ttp80) REVERT: B 414 MET cc_start: 0.8818 (ttm) cc_final: 0.8528 (mtp) REVERT: B 511 THR cc_start: 0.7739 (OUTLIER) cc_final: 0.7511 (p) outliers start: 16 outliers final: 11 residues processed: 93 average time/residue: 0.2104 time to fit residues: 25.9547 Evaluate side-chains 88 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 17 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 84 optimal weight: 0.0170 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.141762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114087 restraints weight = 7719.793| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.96 r_work: 0.3216 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2069 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= 0.211 Angle : 0.543 9.117 9924 Z= 0.262 Chirality : 0.039 0.172 1196 Planarity : 0.004 0.053 1206 Dihedral : 10.721 73.729 1207 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.97 % Allowed : 19.58 % 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: 2.57 (0.27), residues: 946 helix: 2.23 (0.18), residues: 754 sheet: None (None), residues: 0 loop : -0.47 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 92 HIS 0.002 0.001 HIS A 517 PHE 0.009 0.001 PHE B 183 TYR 0.005 0.001 TYR B 378 ARG 0.009 0.001 ARG B 366 ********************** 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: 14 poor density : 74 time to evaluate : 0.668 Fit side-chains REVERT: A 67 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.7616 (ttp) REVERT: A 304 ARG cc_start: 0.7458 (ttt180) cc_final: 0.5922 (ttp80) REVERT: A 414 MET cc_start: 0.8840 (ttm) cc_final: 0.8541 (mtp) REVERT: B 67 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.7668 (ttp) REVERT: B 304 ARG cc_start: 0.7452 (ttt180) cc_final: 0.5930 (ttp80) REVERT: B 511 THR cc_start: 0.7769 (OUTLIER) cc_final: 0.7542 (p) outliers start: 14 outliers final: 10 residues processed: 86 average time/residue: 0.2360 time to fit residues: 26.4200 Evaluate side-chains 86 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 B residue 67 MET 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 445 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: 0.8980 chunk 24 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 89 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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** B 517 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.142103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.114621 restraints weight = 7565.306| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.93 r_work: 0.3222 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2103 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= 0.218 Angle : 0.549 8.856 9924 Z= 0.265 Chirality : 0.039 0.235 1196 Planarity : 0.004 0.053 1206 Dihedral : 10.651 74.610 1207 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.97 % Allowed : 19.44 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.59 (0.27), residues: 946 helix: 2.24 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -0.45 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 92 HIS 0.002 0.001 HIS B 517 PHE 0.010 0.001 PHE A 183 TYR 0.005 0.001 TYR A 378 ARG 0.009 0.001 ARG A 366 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3676.81 seconds wall clock time: 63 minutes 58.18 seconds (3838.18 seconds total)