Starting phenix.real_space_refine on Tue Aug 4 20:31:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sms_55041/08_2026/9sms_55041.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sms_55041/08_2026/9sms_55041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sms_55041/08_2026/9sms_55041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sms_55041/08_2026/9sms_55041.map" model { file = "/net/cci-nas-00/data/ceres_data/9sms_55041/08_2026/9sms_55041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sms_55041/08_2026/9sms_55041.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 4121 2.51 5 N 1056 2.21 5 O 1192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6410 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 404 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain breaks: 1 Chain: "C" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3069 Classifications: {'peptide': 382} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 353} Chain: "D" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1889 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 16, 'TRANS': 220} Chain: "E" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 7, 'TRANS': 50} Chain: "S" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 1.30, per 1000 atoms: 0.20 Number of scatterers: 6410 At special positions: 0 Unit cell: (95.004, 99.372, 104.832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1192 8.00 N 1056 7.00 C 4121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 332.2 milliseconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1524 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 8 sheets defined 37.0% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 277 through 288 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 14 through 25 removed outlier: 3.750A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 104 Processing helix chain 'C' and resid 111 through 134 removed outlier: 3.529A pdb=" N GLU C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 148 removed outlier: 3.729A pdb=" N GLU C 148 " --> pdb=" O THR C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 153 removed outlier: 3.566A pdb=" N GLY C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 248 through 282 Processing helix chain 'C' and resid 354 through 381 Proline residue: C 371 - end of helix Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.651A pdb=" N SER D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 102 through 107' Processing helix chain 'D' and resid 119 through 139 removed outlier: 3.763A pdb=" N VAL D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 173 removed outlier: 3.851A pdb=" N LEU D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 194 Processing helix chain 'D' and resid 229 through 238 Processing helix chain 'D' and resid 254 through 272 removed outlier: 4.243A pdb=" N ASP D 272 " --> pdb=" O MET D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 299 removed outlier: 3.903A pdb=" N LEU D 291 " --> pdb=" O PRO D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 311 removed outlier: 3.595A pdb=" N ALA D 311 " --> pdb=" O GLN D 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 313 removed outlier: 4.145A pdb=" N LYS E 294 " --> pdb=" O ASN E 290 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 34 Processing helix chain 'S' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 299 through 300 removed outlier: 7.039A pdb=" N VAL D 82 " --> pdb=" O ASN E 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 36 through 42 removed outlier: 3.831A pdb=" N ARG C 36 " --> pdb=" O HIS C 59 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU C 40 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG C 55 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N SER C 42 " --> pdb=" O CYS C 53 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS C 53 " --> pdb=" O SER C 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 155 through 158 Processing sheet with id=AA4, first strand: chain 'C' and resid 194 through 195 Processing sheet with id=AA5, first strand: chain 'C' and resid 286 through 289 removed outlier: 4.924A pdb=" N VAL C 286 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU C 300 " --> pdb=" O VAL C 286 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 154 through 160 removed outlier: 5.845A pdb=" N TRP D 155 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL D 148 " --> pdb=" O TRP D 155 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU D 159 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE D 144 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL D 95 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL D 147 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE D 97 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LYS D 94 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE D 214 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE D 96 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL D 216 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N CYS D 98 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL D 211 " --> pdb=" O PHE D 242 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ASP D 244 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N THR D 213 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL D 246 " --> pdb=" O THR D 213 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU D 215 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE D 248 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR D 217 " --> pdb=" O ILE D 248 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 110 through 111 removed outlier: 3.709A pdb=" N LEU D 110 " --> pdb=" O THR D 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 12 through 16 269 hydrogen bonds defined for protein. 777 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.80 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2050 1.34 - 1.46: 1292 1.46 - 1.58: 3171 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6573 Sorted by residual: bond pdb=" CG GLN C 143 " pdb=" CD GLN C 143 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.51e+00 bond pdb=" CB MET D 127 " pdb=" CG MET D 127 " ideal model delta sigma weight residual 1.520 1.484 0.036 3.00e-02 1.11e+03 1.44e+00 bond pdb=" C TYR C 347 " pdb=" N PRO C 348 " ideal model delta sigma weight residual 1.334 1.357 -0.024 2.34e-02 1.83e+03 1.01e+00 bond pdb=" CB MET C 302 " pdb=" CG MET C 302 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.50e-01 bond pdb=" N PRO C 51 " pdb=" CA PRO C 51 " ideal model delta sigma weight residual 1.472 1.461 0.011 1.17e-02 7.31e+03 8.32e-01 ... (remaining 6568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 8482 1.47 - 2.94: 353 2.94 - 4.42: 65 4.42 - 5.89: 15 5.89 - 7.36: 3 Bond angle restraints: 8918 Sorted by residual: angle pdb=" C GLU S 34 " pdb=" N GLY S 35 " pdb=" CA GLY S 35 " ideal model delta sigma weight residual 122.63 117.95 4.68 1.38e+00 5.25e-01 1.15e+01 angle pdb=" N ASP C 248 " pdb=" CA ASP C 248 " pdb=" C ASP C 248 " ideal model delta sigma weight residual 110.80 104.00 6.80 2.13e+00 2.20e-01 1.02e+01 angle pdb=" C GLN C 150 " pdb=" N TYR C 151 " pdb=" CA TYR C 151 " ideal model delta sigma weight residual 121.54 126.94 -5.40 1.91e+00 2.74e-01 8.00e+00 angle pdb=" C GLN C 122 " pdb=" N GLN C 123 " pdb=" CA GLN C 123 " ideal model delta sigma weight residual 120.72 116.17 4.55 1.67e+00 3.59e-01 7.44e+00 angle pdb=" N GLY S 35 " pdb=" CA GLY S 35 " pdb=" C GLY S 35 " ideal model delta sigma weight residual 116.01 120.40 -4.39 1.64e+00 3.72e-01 7.17e+00 ... (remaining 8913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 3664 17.32 - 34.64: 233 34.64 - 51.96: 50 51.96 - 69.28: 30 69.28 - 86.60: 2 Dihedral angle restraints: 3979 sinusoidal: 1629 harmonic: 2350 Sorted by residual: dihedral pdb=" CD ARG D 85 " pdb=" NE ARG D 85 " pdb=" CZ ARG D 85 " pdb=" NH1 ARG D 85 " ideal model delta sinusoidal sigma weight residual 0.00 -26.10 26.10 1 1.00e+01 1.00e-02 9.79e+00 dihedral pdb=" CA GLU D 104 " pdb=" CB GLU D 104 " pdb=" CG GLU D 104 " pdb=" CD GLU D 104 " ideal model delta sinusoidal sigma weight residual -180.00 -121.06 -58.94 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LYS S 33 " pdb=" CA LYS S 33 " pdb=" CB LYS S 33 " pdb=" CG LYS S 33 " ideal model delta sinusoidal sigma weight residual -180.00 -123.33 -56.67 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 3976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 666 0.035 - 0.069: 211 0.069 - 0.104: 70 0.104 - 0.139: 31 0.139 - 0.173: 3 Chirality restraints: 981 Sorted by residual: chirality pdb=" CA ILE C 37 " pdb=" N ILE C 37 " pdb=" C ILE C 37 " pdb=" CB ILE C 37 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CA PRO D 221 " pdb=" N PRO D 221 " pdb=" C PRO D 221 " pdb=" CB PRO D 221 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CB ILE C 247 " pdb=" CA ILE C 247 " pdb=" CG1 ILE C 247 " pdb=" CG2 ILE C 247 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 978 not shown) Planarity restraints: 1153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 219 " 0.079 5.00e-02 4.00e+02 1.20e-01 2.30e+01 pdb=" N PRO D 220 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO D 220 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO D 220 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 85 " -0.368 9.50e-02 1.11e+02 1.66e-01 2.11e+01 pdb=" NE ARG D 85 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG D 85 " -0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG D 85 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG D 85 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 133 " -0.283 9.50e-02 1.11e+02 1.28e-01 1.29e+01 pdb=" NE ARG D 133 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG D 133 " -0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG D 133 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG D 133 " -0.000 2.00e-02 2.50e+03 ... (remaining 1150 not shown) Histogram of nonbonded interaction distances: 2.60 - 3.06: 4420 3.06 - 3.52: 6666 3.52 - 3.98: 10509 3.98 - 4.44: 12941 4.44 - 4.90: 18918 Nonbonded interactions: 53454 Sorted by model distance: nonbonded pdb=" N ASP C 95 " pdb=" OD1 ASP C 95 " model vdw 2.599 3.120 nonbonded pdb=" N GLY C 293 " pdb=" N PHE C 294 " model vdw 2.610 2.560 nonbonded pdb=" N TYR C 347 " pdb=" O TYR C 347 " model vdw 2.618 2.496 nonbonded pdb=" O THR C 334 " pdb=" N GLY C 337 " model vdw 2.631 3.120 nonbonded pdb=" N GLN C 338 " pdb=" O GLN C 338 " model vdw 2.635 2.496 ... (remaining 53449 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.420 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.610 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 0.003 0.044 6573 Z= 0.162 Angle : 0.707 7.361 8918 Z= 0.403 Chirality : 0.042 0.173 981 Planarity : 0.011 0.166 1153 Dihedral : 13.195 86.599 2455 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.28), residues: 788 helix: 0.71 (0.31), residues: 267 sheet: -1.29 (0.43), residues: 129 loop : -1.92 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.005 ARG D 85 TYR 0.025 0.002 TYR C 268 PHE 0.015 0.002 PHE C 73 TRP 0.024 0.003 TRP C 69 HIS 0.006 0.001 HIS C 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 6573) covalent geometry : angle 0.70653 / 0.40 ( 8918) hydrogen bonds : bond 0.12622 / 8.60 ( 269) hydrogen bonds : angle 6.81482 / 4.73 ( 777) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 HIS cc_start: 0.5545 (p90) cc_final: 0.3488 (p90) REVERT: C 330 VAL cc_start: 0.7312 (m) cc_final: 0.6855 (m) REVERT: D 155 TRP cc_start: 0.8129 (t-100) cc_final: 0.7570 (t60) REVERT: D 162 ASP cc_start: 0.8707 (m-30) cc_final: 0.8475 (p0) REVERT: D 167 CYS cc_start: 0.9091 (m) cc_final: 0.8672 (m) REVERT: D 204 THR cc_start: 0.9267 (m) cc_final: 0.8917 (p) REVERT: D 232 MET cc_start: 0.7626 (mtp) cc_final: 0.7193 (mpp) REVERT: D 295 MET cc_start: 0.8475 (tpt) cc_final: 0.8229 (tpt) REVERT: S 1 MET cc_start: 0.7036 (ptt) cc_final: 0.6729 (ptp) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.0901 time to fit residues: 21.5368 Evaluate side-chains 107 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN C 214 GLN C 281 HIS C 311 HIS C 332 HIS C 342 GLN C 356 ASN D 182 ASN D 203 GLN D 225 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.083747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.060412 restraints weight = 21536.985| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.87 r_work: 0.3056 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6573 Z= 0.177 Angle : 0.670 9.687 8918 Z= 0.335 Chirality : 0.043 0.194 981 Planarity : 0.005 0.060 1153 Dihedral : 4.173 14.055 854 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.77 % Allowed : 13.97 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.29), residues: 788 helix: 1.87 (0.31), residues: 266 sheet: -0.67 (0.47), residues: 121 loop : -1.08 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 133 TYR 0.024 0.002 TYR E 303 PHE 0.024 0.002 PHE E 277 TRP 0.016 0.002 TRP D 261 HIS 0.004 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 6573) covalent geometry : angle 0.67009 / 0.34 ( 8918) hydrogen bonds : bond 0.04551 / 3.07 ( 269) hydrogen bonds : angle 5.63478 / 3.93 ( 777) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 LYS cc_start: 0.7825 (mtmt) cc_final: 0.7622 (tttt) REVERT: C 345 LYS cc_start: 0.8513 (ttmm) cc_final: 0.8233 (mtpp) REVERT: D 127 MET cc_start: 0.8713 (ppp) cc_final: 0.8136 (ptm) REVERT: D 162 ASP cc_start: 0.8807 (m-30) cc_final: 0.8374 (p0) REVERT: D 167 CYS cc_start: 0.9067 (m) cc_final: 0.8864 (m) REVERT: D 203 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: D 232 MET cc_start: 0.7851 (mtp) cc_final: 0.7564 (mtp) REVERT: D 261 TRP cc_start: 0.7784 (p-90) cc_final: 0.7533 (p-90) REVERT: E 303 TYR cc_start: 0.8939 (t80) cc_final: 0.8577 (t80) REVERT: S 40 GLN cc_start: 0.7566 (mm-40) cc_final: 0.7343 (tp40) outliers start: 20 outliers final: 10 residues processed: 129 average time/residue: 0.0758 time to fit residues: 12.8872 Evaluate side-chains 106 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 13 ILE Chi-restraints excluded: chain S residue 50 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 8 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 HIS D 125 GLN D 191 GLN D 203 GLN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.080429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.055357 restraints weight = 21771.662| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.74 r_work: 0.2946 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 6573 Z= 0.246 Angle : 0.670 6.315 8918 Z= 0.337 Chirality : 0.043 0.161 981 Planarity : 0.005 0.044 1153 Dihedral : 4.380 17.658 854 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.35 % Allowed : 14.94 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.30), residues: 788 helix: 1.94 (0.31), residues: 266 sheet: -0.82 (0.45), residues: 136 loop : -0.71 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG C 133 TYR 0.019 0.002 TYR E 303 PHE 0.014 0.002 PHE C 173 TRP 0.014 0.002 TRP C 105 HIS 0.003 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.25 ( 6573) covalent geometry : angle 0.67038 / 0.34 ( 8918) hydrogen bonds : bond 0.04374 / 2.95 ( 269) hydrogen bonds : angle 5.32795 / 3.71 ( 777) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 LYS cc_start: 0.8513 (mtmt) cc_final: 0.8218 (tttt) REVERT: C 317 PHE cc_start: 0.8073 (m-80) cc_final: 0.7754 (t80) REVERT: D 105 MET cc_start: 0.8505 (ttm) cc_final: 0.8297 (tpp) REVERT: D 127 MET cc_start: 0.8698 (ppp) cc_final: 0.8330 (ppp) REVERT: D 162 ASP cc_start: 0.8919 (m-30) cc_final: 0.8330 (p0) REVERT: D 232 MET cc_start: 0.7821 (mtp) cc_final: 0.7541 (mtp) REVERT: S 11 LYS cc_start: 0.9048 (tptt) cc_final: 0.8825 (tptp) REVERT: S 59 TYR cc_start: 0.7354 (m-80) cc_final: 0.7118 (m-80) outliers start: 17 outliers final: 10 residues processed: 113 average time/residue: 0.0834 time to fit residues: 12.4430 Evaluate side-chains 105 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain S residue 13 ILE Chi-restraints excluded: chain S residue 50 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN ** D 223 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 = 0.3740 r_free = 0.3740 target = 0.079753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.054371 restraints weight = 21914.014| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.76 r_work: 0.2914 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6573 Z= 0.221 Angle : 0.629 7.113 8918 Z= 0.311 Chirality : 0.043 0.168 981 Planarity : 0.004 0.032 1153 Dihedral : 4.417 17.218 854 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.21 % Allowed : 15.35 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.30), residues: 788 helix: 1.90 (0.31), residues: 267 sheet: -0.64 (0.47), residues: 141 loop : -0.60 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 133 TYR 0.020 0.002 TYR D 209 PHE 0.012 0.002 PHE A 287 TRP 0.028 0.003 TRP D 261 HIS 0.005 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 ( 6573) covalent geometry : angle 0.62910 / 0.31 ( 8918) hydrogen bonds : bond 0.04124 / 2.78 ( 269) hydrogen bonds : angle 5.15458 / 3.60 ( 777) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 LYS cc_start: 0.8686 (mtmt) cc_final: 0.8464 (tttt) REVERT: C 317 PHE cc_start: 0.8106 (m-80) cc_final: 0.7798 (t80) REVERT: D 162 ASP cc_start: 0.8955 (m-30) cc_final: 0.8361 (p0) REVERT: D 232 MET cc_start: 0.7743 (mtp) cc_final: 0.7441 (mtp) REVERT: S 11 LYS cc_start: 0.9020 (tptt) cc_final: 0.8780 (tptp) outliers start: 16 outliers final: 12 residues processed: 114 average time/residue: 0.0808 time to fit residues: 11.9598 Evaluate side-chains 99 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain S residue 4 PHE Chi-restraints excluded: chain S residue 13 ILE Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 56 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 GLN ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.080274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.054631 restraints weight = 22064.946| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.81 r_work: 0.2926 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6573 Z= 0.153 Angle : 0.611 7.617 8918 Z= 0.302 Chirality : 0.042 0.198 981 Planarity : 0.004 0.048 1153 Dihedral : 4.405 21.108 854 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.49 % Allowed : 16.18 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.30), residues: 788 helix: 2.02 (0.31), residues: 268 sheet: -0.63 (0.48), residues: 139 loop : -0.66 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 54 TYR 0.019 0.002 TYR S 59 PHE 0.010 0.001 PHE E 277 TRP 0.021 0.002 TRP D 261 HIS 0.003 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 6573) covalent geometry : angle 0.61122 / 0.30 ( 8918) hydrogen bonds : bond 0.03883 / 2.59 ( 269) hydrogen bonds : angle 5.02633 / 3.53 ( 777) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8265 (pm20) REVERT: C 317 PHE cc_start: 0.8017 (m-80) cc_final: 0.7777 (t80) REVERT: D 85 ARG cc_start: 0.7402 (mtp85) cc_final: 0.6869 (mmt-90) REVERT: D 162 ASP cc_start: 0.8902 (m-30) cc_final: 0.8441 (p0) REVERT: D 232 MET cc_start: 0.7762 (mtp) cc_final: 0.7526 (mtp) REVERT: S 34 GLU cc_start: 0.8375 (pp20) cc_final: 0.8012 (pm20) outliers start: 18 outliers final: 13 residues processed: 111 average time/residue: 0.0671 time to fit residues: 9.9687 Evaluate side-chains 102 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain S residue 13 ILE Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 56 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 0.0270 chunk 76 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 GLN ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN D 249 HIS ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.079373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.053808 restraints weight = 21998.033| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.73 r_work: 0.2898 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6573 Z= 0.196 Angle : 0.654 8.223 8918 Z= 0.324 Chirality : 0.043 0.192 981 Planarity : 0.004 0.034 1153 Dihedral : 4.392 20.298 854 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.18 % Allowed : 17.15 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.30), residues: 788 helix: 1.93 (0.31), residues: 268 sheet: -0.65 (0.47), residues: 139 loop : -0.59 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 54 TYR 0.023 0.002 TYR E 303 PHE 0.011 0.001 PHE C 173 TRP 0.024 0.002 TRP D 261 HIS 0.003 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 ( 6573) covalent geometry : angle 0.65384 / 0.32 ( 8918) hydrogen bonds : bond 0.03932 / 2.61 ( 269) hydrogen bonds : angle 5.02835 / 3.55 ( 777) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8217 (mp10) REVERT: C 139 MET cc_start: 0.8801 (mmm) cc_final: 0.8533 (mmm) REVERT: C 317 PHE cc_start: 0.8122 (m-80) cc_final: 0.7858 (t80) REVERT: D 85 ARG cc_start: 0.7461 (mtp85) cc_final: 0.6963 (mmt-90) REVERT: D 155 TRP cc_start: 0.8410 (t-100) cc_final: 0.8128 (t-100) REVERT: D 162 ASP cc_start: 0.8921 (m-30) cc_final: 0.8474 (p0) REVERT: D 192 GLN cc_start: 0.9137 (mt0) cc_final: 0.8889 (pt0) REVERT: D 232 MET cc_start: 0.7715 (mtp) cc_final: 0.7345 (mtp) REVERT: S 11 LYS cc_start: 0.8870 (tptt) cc_final: 0.8631 (tptp) outliers start: 23 outliers final: 14 residues processed: 109 average time/residue: 0.0645 time to fit residues: 9.4620 Evaluate side-chains 102 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain S residue 13 ILE Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 56 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 GLN ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.079945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.054534 restraints weight = 21773.170| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.63 r_work: 0.2925 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6573 Z= 0.147 Angle : 0.628 7.814 8918 Z= 0.312 Chirality : 0.042 0.186 981 Planarity : 0.004 0.034 1153 Dihedral : 4.333 20.005 854 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.77 % Allowed : 17.01 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.30), residues: 788 helix: 1.93 (0.31), residues: 274 sheet: -0.58 (0.48), residues: 139 loop : -0.71 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 131 TYR 0.020 0.002 TYR S 59 PHE 0.010 0.001 PHE C 173 TRP 0.026 0.002 TRP D 261 HIS 0.003 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 6573) covalent geometry : angle 0.62817 / 0.31 ( 8918) hydrogen bonds : bond 0.03899 / 2.58 ( 269) hydrogen bonds : angle 4.93115 / 3.47 ( 777) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 139 MET cc_start: 0.8890 (mmm) cc_final: 0.8575 (mmm) REVERT: C 317 PHE cc_start: 0.7999 (m-80) cc_final: 0.7799 (t80) REVERT: D 85 ARG cc_start: 0.7554 (mtp85) cc_final: 0.7017 (mmt-90) REVERT: D 155 TRP cc_start: 0.8335 (t-100) cc_final: 0.8108 (t-100) REVERT: D 162 ASP cc_start: 0.8847 (m-30) cc_final: 0.8446 (p0) REVERT: D 232 MET cc_start: 0.7651 (mtp) cc_final: 0.7339 (mtp) REVERT: E 291 GLN cc_start: 0.8719 (tp-100) cc_final: 0.8396 (tp-100) REVERT: S 3 ILE cc_start: 0.8029 (tt) cc_final: 0.7651 (mm) outliers start: 20 outliers final: 11 residues processed: 108 average time/residue: 0.0593 time to fit residues: 8.7253 Evaluate side-chains 104 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain S residue 13 ILE Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 67 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 6 optimal weight: 0.0870 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 2 GLN ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.080647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.055604 restraints weight = 21970.252| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.72 r_work: 0.3006 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.6281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6573 Z= 0.143 Angle : 0.640 8.323 8918 Z= 0.319 Chirality : 0.042 0.158 981 Planarity : 0.004 0.035 1153 Dihedral : 4.298 19.124 854 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.52 % Allowed : 17.98 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.30), residues: 788 helix: 1.88 (0.31), residues: 274 sheet: -0.62 (0.47), residues: 140 loop : -0.76 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 133 TYR 0.017 0.001 TYR E 303 PHE 0.010 0.001 PHE C 306 TRP 0.030 0.002 TRP D 261 HIS 0.004 0.001 HIS D 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 6573) covalent geometry : angle 0.63954 / 0.32 ( 8918) hydrogen bonds : bond 0.03741 / 2.46 ( 269) hydrogen bonds : angle 4.87564 / 3.45 ( 777) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLN cc_start: 0.8867 (pm20) cc_final: 0.8309 (mp10) REVERT: C 317 PHE cc_start: 0.8125 (m-80) cc_final: 0.7894 (t80) REVERT: D 85 ARG cc_start: 0.7662 (mtp85) cc_final: 0.7075 (mtt-85) REVERT: D 105 MET cc_start: 0.8661 (tpp) cc_final: 0.8326 (tpp) REVERT: D 162 ASP cc_start: 0.8884 (m-30) cc_final: 0.8455 (p0) REVERT: D 192 GLN cc_start: 0.9114 (mt0) cc_final: 0.8871 (pt0) REVERT: D 232 MET cc_start: 0.7615 (mtp) cc_final: 0.7368 (mtp) REVERT: E 291 GLN cc_start: 0.8769 (tp-100) cc_final: 0.8446 (tp-100) REVERT: S 31 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7604 (tt0) outliers start: 11 outliers final: 9 residues processed: 104 average time/residue: 0.0657 time to fit residues: 9.0912 Evaluate side-chains 100 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain S residue 13 ILE Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 56 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 0.4980 chunk 24 optimal weight: 0.0870 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 GLN ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 40 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 = 0.3819 r_free = 0.3819 target = 0.081184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.056168 restraints weight = 22288.074| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.76 r_work: 0.3024 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.6409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6573 Z= 0.130 Angle : 0.648 9.909 8918 Z= 0.319 Chirality : 0.042 0.138 981 Planarity : 0.004 0.035 1153 Dihedral : 4.262 18.437 854 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.66 % Allowed : 18.12 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.30), residues: 788 helix: 1.94 (0.31), residues: 274 sheet: -0.56 (0.46), residues: 142 loop : -0.72 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 133 TYR 0.016 0.001 TYR E 303 PHE 0.016 0.001 PHE C 306 TRP 0.031 0.002 TRP D 155 HIS 0.004 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 6573) covalent geometry : angle 0.64795 / 0.32 ( 8918) hydrogen bonds : bond 0.03707 / 2.47 ( 269) hydrogen bonds : angle 4.76314 / 3.38 ( 777) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLN cc_start: 0.8813 (pm20) cc_final: 0.8107 (mp10) REVERT: D 85 ARG cc_start: 0.7741 (mtp85) cc_final: 0.7074 (mmt-90) REVERT: D 162 ASP cc_start: 0.8865 (m-30) cc_final: 0.8512 (p0) REVERT: D 192 GLN cc_start: 0.9139 (mt0) cc_final: 0.8907 (pt0) REVERT: D 232 MET cc_start: 0.7663 (mtp) cc_final: 0.7402 (mtp) REVERT: E 291 GLN cc_start: 0.8763 (tp-100) cc_final: 0.8450 (tp-100) REVERT: S 1 MET cc_start: 0.7430 (ttp) cc_final: 0.7215 (ttm) REVERT: S 31 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7562 (tt0) outliers start: 12 outliers final: 10 residues processed: 97 average time/residue: 0.0774 time to fit residues: 9.9197 Evaluate side-chains 100 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain S residue 13 ILE Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 56 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 10.0000 chunk 26 optimal weight: 0.2980 chunk 3 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 13 optimal weight: 0.0010 chunk 54 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 40 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 = 0.3760 r_free = 0.3760 target = 0.080428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.055576 restraints weight = 21745.813| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.68 r_work: 0.2944 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.6544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6573 Z= 0.139 Angle : 0.654 9.386 8918 Z= 0.324 Chirality : 0.042 0.140 981 Planarity : 0.005 0.099 1153 Dihedral : 4.275 18.480 854 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.38 % Allowed : 18.53 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.30), residues: 788 helix: 1.88 (0.31), residues: 274 sheet: -0.55 (0.46), residues: 142 loop : -0.74 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 164 TYR 0.018 0.002 TYR C 263 PHE 0.023 0.001 PHE C 317 TRP 0.054 0.003 TRP D 155 HIS 0.003 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 6573) covalent geometry : angle 0.65430 / 0.32 ( 8918) hydrogen bonds : bond 0.03743 / 2.44 ( 269) hydrogen bonds : angle 4.75445 / 3.38 ( 777) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLN cc_start: 0.8800 (pm20) cc_final: 0.8263 (mp10) REVERT: C 139 MET cc_start: 0.8708 (mmm) cc_final: 0.8477 (mmm) REVERT: D 85 ARG cc_start: 0.7722 (mtp85) cc_final: 0.7157 (mtt-85) REVERT: D 97 ILE cc_start: 0.9017 (mt) cc_final: 0.8722 (tp) REVERT: D 162 ASP cc_start: 0.8813 (m-30) cc_final: 0.8476 (p0) REVERT: D 232 MET cc_start: 0.7628 (mtp) cc_final: 0.7387 (mtp) REVERT: D 268 MET cc_start: 0.9638 (mmm) cc_final: 0.9393 (mmm) REVERT: E 291 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8411 (tp-100) REVERT: S 1 MET cc_start: 0.7284 (ttp) cc_final: 0.7058 (ttm) REVERT: S 31 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7515 (tt0) outliers start: 10 outliers final: 8 residues processed: 97 average time/residue: 0.0708 time to fit residues: 9.1664 Evaluate side-chains 95 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 56 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 43 optimal weight: 0.0050 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 chunk 4 optimal weight: 3.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 GLN ** S 40 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 = 0.3765 r_free = 0.3765 target = 0.080667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.055599 restraints weight = 21920.392| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.77 r_work: 0.2946 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.6699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6573 Z= 0.140 Angle : 0.670 11.982 8918 Z= 0.331 Chirality : 0.042 0.192 981 Planarity : 0.005 0.055 1153 Dihedral : 4.273 18.633 854 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.83 % Allowed : 18.95 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.30), residues: 788 helix: 1.75 (0.31), residues: 274 sheet: -0.62 (0.46), residues: 141 loop : -0.74 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 164 TYR 0.017 0.002 TYR C 349 PHE 0.016 0.001 PHE C 317 TRP 0.019 0.002 TRP D 155 HIS 0.003 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 6573) covalent geometry : angle 0.66967 / 0.33 ( 8918) hydrogen bonds : bond 0.03840 / 2.47 ( 269) hydrogen bonds : angle 4.74709 / 3.36 ( 777) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1558.25 seconds wall clock time: 27 minutes 27.34 seconds (1647.34 seconds total)